The Hidden Inactive Ingredient: Biological Products in Recombinant Pharmaceuticals – P&T Community

INTRODUCTION

Pharmaceutical products have long been prepared with various inactive ingredients to enhance pharmacokinetics, stability, and pharmaceutical elegance. In an age where the use of recombinant technologies is rapidly increasing and consumers are more aware of inactive ingredients in food and cosmetic products, there remains a paucity of centralized information to help medical professionals counsel their patients about recombinant technologies. Although patient-specific factors such as race, age, and weight are considered when prescribing and dispensing medications, oftentimes religion and dietary habits are left out of the conversation. The increasing array of biopharmaceuticals on the market and in production creates an opportunity for healthcare providers and patients to enhance their knowledge of these issues. The purpose of this review is to create a centralized resource for healthcare providers that describes some common dietary restrictions of select faith and ethnic groups and to identify FDA-approved medications of biologic origin.

A biopharmaceutical is any active agent biological in nature and manufactured using living organisms.1 Since the 1980s, scientists have been harnessing the power of single-cell organisms to create unique proteins that can be used to treat a wide range of disease states ranging from diabetes to hematologic disorders. The recombinant process enhances scientists ability to modify and manipulate protein structure and function to produce a targeted agent for therapeutic purposes. Now, almost 40 years later, recombinant technologies are on the rise using a wider range of bacterial, fungal, and animal cell lines.1,2

Original biopharmaceuticals were replacement proteins such as insulin, hormones, and antibodies. Advancements in the field have widened the scope of indications to hematologic and oncologic disorders. Recombinant products for use in oncology have been expanding over the past two decades, with a focus on monoclonal antibody production. The area of targeted drug delivery within oncology is a rapidly growing field, with promise for new agents or enhancements to existing agents that can improve antitumor cytotoxicity while reducing adverse effects. As this technology continues to advance, scientists are experimenting with alternative ways to produce biopharmaceuticals by way of transgenic organisms and animal cloning.3

The process of creating a recombinant product involves transferring the specific genes responsible for creating the protein into a bacteria, yeast, or animal cell. Historically, Escherichia coli was the prominent cell line that was used, and even today is the cell line used to manufacturer medications such as insulin and filgrastim. Over time, scientists explored the use of yeast cells, namely Saccharomyces cerevisiae, and other mammalian cells such as Chinese hamster ovary (CHO) cells.

The use of mammalian cell lines has increased in recent years because of the cell systems ability to produce glycosylated proteins.2 Glycosylation is one of the most complex post-translational modifications that occurs to a protein but it offers certain pharmaceutical advantages, such as increased plasma half-life.4 Many antibodies that were formed as a result of recombinant technology combine fragments from two different species. Often, these are combined with human fragments to form chimeric antibodies. Most commonly, murine antibody fragments have been fused with human fragments to produce an antibody that is more human-like. This differs from a humanized antibody, which may contain elements of nonhuman origin but maintains essentially the same amino acid sequence that can be found in the human antibody.5 Irrespective of drug development, a pharmaceutical manufacturers choice of cell line is balanced by the complexity of protein folding and post-translational modifications with a cell line that is easy to maintain and simple to culture.

The nomenclature of recombinant products is regulated by the World Health Organization (WHO)s International Nonproprietary Names (INN). Names awarded an INN are selected by WHO on the advice of experts from the organizations Expert Advisory Panel on the International Pharmacopoeia and Pharmaceutical Preparations.

The product names can assist health practitioners in understanding how the products are manufactured based on the pre-stems and stems of the names.6 It is beyond the scope of our review to discuss all the nomenclature, but monoclonal antibody medications are a good example of this practice. Previously, two infixes denoted the target of the drug as well as the source. In 2015, the INN together with the United States Adopted Name (USAN) Council agreed that to simplify drug naming, the source infix would be dropped.5 The name now consists of a prefix, a target infix, and the suffix -mab (Table 1).

Often the most convenient source of information on how a drug is manufactured is the package insert. However, information about the recombinant process and the cell line from which the pharmaceutical product is made frequently isnt relayed to the patient during counseling. To compile a compendium of medications from animal origin, we undertook an extensive review of all Food and Drug Administration (FDA)-approved medications using a data set of 15,797 entries based on the National Drug Code (NDC) from the FDA website, on December 2, 2016.7 Duplicate entries based on nonproprietary names were deleted. We also initially excluded entries whose marketing category included cosmetic, over-the-counter (OTC) drug monograph, unapproved homeopathic, or unapproved medical gas, and entries whose product type was a standardized or non-standardized allergenic extract. The remaining 666 records we reviewed manually, and we also reviewed package inserts for possible inclusion. Table 2 is organized by the type of cell line used in the manufacturing process, listed alphabetically by generic name.

Additional ingredients involved in the preparation of pharmaceutical products also may be derived from animal products. Gelatin is a substance of bovine or porcine origin that is commonly used for commercially made capsules.8 A WHO memo from 2001 addresses a ruling that allows Muslims to accept gelatin because it has been transformed from its original source,8,9 although not all Muslims accept the ruling. Specialized compounding centers may offer vegetable-based capsules for those who refuse gelatin-based products.

Lactose is a common sugar that is found as a filler in many capsules and tablets and is derived from cows milk. In addition, lactulose can be synthetically produced in large quantities in the laboratory. Lanolin is a fat extracted from sheeps wool that is used as an ingredient and base in many ointments and topical medications. It is important to consider all ingredients within a pharmaceutical preparation, including all the inactive ingredients.8

It is well known within the medical community that Jehovahs Witnesses patients abstain from blood products. This issue often comes to a head when a patient is critically ill and in need of a transfusion. Many hospitals have developed policies and standard procedures for approaching these situations to respect the autonomy of the patient while continuing to offer appropriate and excellent medical care. Although this restriction is widely known, providers might not be so familiar with other, less common restrictions.

Even within a faith or ethnic group there can be differences about dietary restrictions, but having a general sense of what these restrictions are will enable providers to provide a patient-centered care approach. A lack of communication might lead to distrust and decreased patient satisfaction if a patient subsequently learned how a particular medication is processed and handled.

The decision to adhere to strict dietary restrictions is an individual choice. Through conversations with the patient, a provider can identify the personal dietary beliefs that might affect their therapy selection. Certain religious organizations have thus made formal statements to relieve their followers of strict dietary considerations as they relate to medicine and health. For example, Muslims are permitted to ingest gelatin capsules because the product is believed to be transformed in property and in character. Shariah law also allows for the use of insulin products in case of necessity.9 Table 3 lists common religious and faith-based groups that follow specific dietary restrictions.8,1215 It is important to note that within these general classifications, there are also various practices arising from individual beliefs.

There is no consensus on how to deal with patient refusal based on faith or ethnic beliefs. Because adherence to diet that is based on religion is personal to the patient, it requires a personal response from the provider. Oftentimes, a patients refusal to use a specific product can be met with misunderstanding and frustration by the provider. Sometimes a conversation about the risks and benefits can persuade the patient to adhere to a medication while at other times, frank refusal can lead to patient morbidity and mortality. In certain situations, it would be appropriate to routinely solicit information regarding religious or personal prohibitions in order to identify potential conflicts with the treatment plan. Maintaining open communication with the patient can prevent such conflicts. In the authors experience, patients also may be misinformed about specific pharmaceuticals as a result of their own Internet searches; this can make them hesitant to trust the healthcare team, who can provide them with well-researched information. When confronted with these situations, the goal of healthcare professionals should be to provide their patients with treatment options and sound medical advice while simultaneously respecting patients autonomy when they make their decisions.

Consider the following example of an individual who abstains from pork products. Patients receiving dialysis must have their hemodialysis catheter flushed and locked with an anticoagulant solution to maintain the catheters patency. Normally, heparin locks are the anticoagulant of choice for this indication, but patients who strictly adhere to pork restrictions may refuse these. Heparin in central venous lines is more effective than normal saline at reducing the amount of line occlusions.10 Sodium citrate might be another option but it will present additional challenges because of procurement and availability.11 Additional options and their risks and benefits can be discussed with the patient to ensure a solution is found that meets everyones needs.

As technological advances enhance the ability of researchers and healthcare professionals to provide medications that target specific receptors, the challenge will be to provide consistent and relevant information to the patient. Providers may encounter the need to discuss a patients personal beliefs and opinions of medication-manufacturing processes while they are administering health care. A regularly updated, centralized resource that is easily accessible to providers at the point of treatment is necessary to help inform patients about their healthcare decisions. Although patients decisions and beliefs can be misunderstood by and prove frustrating for providers, this knowledge will help to prepare and facilitate a productive discussion regarding patients desired outcomes.

Disclosure: The authors declare no conflicts or financial interest in any product or service mentioned in the manuscript, including grants, equipment, medications, employment, gifts, and honoraria.

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The Hidden Inactive Ingredient: Biological Products in Recombinant Pharmaceuticals - P&T Community

Fava Is All About Balance – East Bay Express

Some chefs dream of white tablecloth, three-Michelin-star glory. But Sylvie Osborne-Calierno and Jeremy Scheiblauer, a duo of chefs and best friends, had other plans in mind.

"We always knew we wanted a tiny little spot," Osborne-Calierno said. So when they heard that the 42-year-old Juice Bar Collective on Vine Street was closing, they jumped at the chance to carve out their own tiny slice of North Berkeley.

It's not that Osborne-Calierno and Scheiblauer lacked the pedigrees to open a larger restaurant. The friends met cooking at Chez Panisse 12 years ago, and both went on to open other restaurants Osborne-Calierno with Toto, a brunch restaurant in Barcelona, Spain, and Scheiblauer with Heyday, a lunch spot in San Francisco's Financial district. Both ultimately returned to Chez Panisse, where they were working until Fava's opening.

Alice Waters' guiding principles are evident in the food that comes out of Fava's kitchen: the insistence upon fresh, top-quality ingredients, simply prepared without relying on fancy equipment. But Fava drops the French cooking techniques, the four-course format, and the triple-digit price tag in favor of a shoebox-sized, counter-service only restaurant, equipped with compostable plates and a few outdoor folding tables and chairs.

With such a small space, the duo had to pare down Fava's menu to just the essentials: a few salads, sandwiches, and a daily soup, plus fresh juices and sesame-chocolate chip cookies.

"It really gives you constraints that sometimes maybe feel a little tight," Osborne-Calierno said. "But at the same time, it really forces you to really hone down and get to the real soul of what you're trying to do."

Fava's style isn't easy to distill into a few words or labels, but the menu, which happens to be entirely housemade and organic, is clearly Mediterranean and Middle Eastern influenced. Latin American influences also make their way onto the menu, albeit more subtly. "We don't really feel pegged to any one culture," Osborne-Calierno said. "We just make things that taste good."

The lamb flatbread is one of the restaurant's best sellers, and for good reason. The bread itself, which lies somewhere between naan and pita, is made in-house every day with whole wheat flour. The last bit of cooking gets done on a plancha, giving it the same effect as freshly made bread. The bread was delightfully airy, chewy, and elastic, with a touch of crispness around the edges and a nutty, toasty flavor. On top of the flatbread was a smear of harissa, which lent bright color and a punch of cumin. Layered on top of that were tender, juicy slices of lamb shoulder braised in a tomatoey broth "grandma-style," Osborne-Calierno calls it, as opposed to French cooking techniques that incorporate mirepoix and wine. Dollops of creamy, rich yogurt topped the lamb, followed by crunchy red cabbage tossed with a touch of vinegar. The crowning glory was a copious handful of mint, dill, and cilantro.

At first, I was taken aback by how many herbs were on top of the flatbread, and since you're eating it open-faced, you're likely to end up with an entire sprig of mint sticking out of your mouth at some point. But the whole thing was surprisingly well-balanced, and it struck me how the herbs and vegetables shone just as brightly as the lamb. The herbs also kept the sandwich light and refreshing, which was a minor miracle considering that lamb is such a fatty, richly flavored protein. "We don't believe in there being too [many] herbs," Osborne-Calierno laughed. "We like to treat herbs like they're a lettuce, like they're a vegetable."

Fava's menu is primarily vegetable-focused every other item on the menu when I visited was vegetarian. I particularly enjoyed the escarole salad. The slight bitterness of the crisp, lightly dressed leaves was perfectly balanced by slices of juicy melon, while housemade chile almonds added a little earthiness and spiciness. Bulgur wheat served double duty, not only by making the salad more filling, but also by brightening it up with plenty of lemon juice. The most striking part was the leaves of purple basil on top, which added an unexpected pop of color and flavor.

"I like the purple basil ... it kinda looks crazy," said Osborne-Calierno. "[We] kinda try to be a little crazy, spice up North Berkeley a little bit."

Also on offer was a hummus bowl with roasted eggplant, topped with cherry tomatoes, French feta, red cabbage, and purslane. The hummus was exceptionally smooth with plenty of tahini flavor, while the golden tomatoes were firm and perfectly ripe. I appreciated the use of French feta here, which provided a punch of salt with a creamier, milder flavor than its Greek and Bulgarian counterparts. Like all the other dishes I tried, it was also a beautiful dish to look at, with the green purslane and purple cabbage dominating the dish with little golden tomatoes shining like gems amid a background of hummus.

For maximum Instagrammability, try one of the brightly colored yet not-too-sweet housemade juices to enhance the look of your meal. I particularly loved the mango lassi, which was creamy and tangy with plenty of real mango flavor. The hibiscus lemonade and green juice, on the other hand, were refreshing and tart.

A rotating selection of soups and sides rounds out the menu. I wasn't a big fan of the side of roasted sweet potatoes. Though they were perfectly roasted and caramelized, they needed a little salt for balance.

The soups, though, are worth ordering. On one of my visits, it was a warm tomato soup with firm chickpeas and a dollop of zesty, creamy lime yogurt; on another, it was a red lentil soup topped with a drizzle of lemon oil for an unexpected citrusy kick.

Don't leave Fava without one (or more) of the sesame chocolate chip cookies. The sesame provided a nutty flavor and subtle richness to the cookie, while giving it a chewier-than-usual texture. Best of all, the cookies used dark chocolate wafers rather than chocolate chips, which provided luscious pools of fruity, bitter dark chocolate.

No, it's not health food. But like everything else at Fava, it's all about balance. Asked whether Fava will open for dinner one day, the duo said they'd like to stick to lunch hours and possibly breakfast one day so they can balance cooking with having an actual life outside of the kitchen, which is a rarity in the restaurant industry.

Osborne-Calierno is the mother of 5-year-old twins. When Scheiblauer isn't cooking in the kitchen, he's busy playing synths in his post-punk, new wave band called Vandal Moon. Sure, the duo is ushering a youthful, casual vibe with plenty of fresh flavors into North Berkeley but unlike generations before them, they won't sacrifice having a balanced lifestyle.

"I don't think moms should have to choose between 'I'm either a mom or I'm a chef,'" Osborne-Calierno said. "We are all these things at once, and that's really important."

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Fava Is All About Balance - East Bay Express

Amazon fish wears nature’s ‘bullet-proof vest’ to thwart piranhas – Reuters

WASHINGTON (Reuters) - One of the worlds largest freshwater fish is protected by the natural equivalent of a bullet-proof vest, helping it thrive in the dangerous waters of the Amazon River basin with flexible armor-like scales able to withstand ferocious piranha attacks.

FILE PHOTO: Diver Alex Reeson checks on the Arapaima or Pirarucu fishes in the tropical section of Europe's biggest freshwater aquarium Aquatis, due to open October 21, in Lausanne, Switzerland October 17, 2017. REUTERS/Denis Balibouse/File Photo

Researchers from the University of California, San Diego and University of California, Berkeley on Wednesday described the unique structure and impressive properties of the dermal armor of the fish, called Arapaima gigas. They said their findings can help guide development of better body armor for people as well as applications in aerospace design.

The fish, also known as pirarucu, gets up to 10 feet (3 meters) long and weighs up to 440 pounds (200 kg). Arapaima, a fish that can breathe air and survive up to a day outside of the water, inhabits rivers in Brazil, Guyana and Peru infested with piranhas, known for razor-sharp teeth, incredible bite strength and deadly feeding frenzies.

There long has been an evolutionary arms race in which predators develop ways to kill - like sharp teeth - and other animals develop ways to stay alive like the dermal armor seen in various fish, dinosaurs and mammals over time. Arapaimas scales, the researchers said, possess all the best attributes of a bullet-proof vest, but the elements are better integrated into one solid piece combining imperviousness and flexibility.

Such lightweight and tough materials like fish scales are the sexy topics that materials scientists are pursuing, said Wen Yang, a UCSD materials scientist who helped lead the study published in the journal Matter.

It is true that the natural armor is similar to artificial body armor because of the similar scale overlapping system. However, the natural armor such as these fish scales is tough and much lighter, without impeding body flexibility and locomotion, Yang added. Remember that the fish scales were developed through hundreds of millions of years. They are very advanced.

The researchers conducted laboratory tests of the scales.

The scales, they found, have a hardmineralized outer layer to resist penetration that is bound to a tough-but-flexible inner layer by collagen themain structural protein in skin and other connective tissues in the body.

This structure means the scales can become deformed when bitten by a piranha but are not torn, broken or pierced, protecting the fish from injury.

We were able to see how the collagen fibers deform without a catastrophic failure including the mechanisms of twisting, folding, sliding, stretching, delamination, Yang said.

The study was backed by the U.S. Air Force Office of Scientific Research.

Reporting by Will Dunham; Editing by Sandra Maler

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Amazon fish wears nature's 'bullet-proof vest' to thwart piranhas - Reuters

9 must-have Instant Pot accessories for healthy eating – CNET

Making bread in an Instant Pot is easy.

The Instant Pot is one of our must-have kitchen devices and with the right Instant Pot accessories the miracle machine can be a great tool for health and wellness, too. As it's a combination pressure cooker, slow cooker, steamer, rice cooker, warmer and more, you can make thousands of satiating mealsin your programmableInstant Pot (plus using fewer dirty dishes). From flavorful meat stews and fall-off-the-bone short ribs to summer shrimp boils and nutrient-packed soups, most healthy Instant Pot recipes are done in minutes and require minimal prep.

Read more on CNET:What's the best Instant Pot to buy? Instant Pot Duo vs. Lux vs. Ultra

One reason an Instant Pot is perfect for preparing dishes forhealthy eatingis how fast it cooks tender meats, perfect beans, creamy Greek yogurt, eggs and other proteins, integral to a balanced diet. With the help of a few smart, healthy Instant Pot accessories like cups for cooking eggs, steamed vegetable baskets and a few cookbooks with healthy Instant Pot recipes in mind, you can stay committed to your Whole30 or keto planor maintain a more balanced diet with loads of protein and nutrient-packed vegetables.

Now playing: Watch this: 8 essential Instant Pot tips

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Below are nine of the best Instant Pot accessories to have around for eating healthy all week (and year) long.

Disclosure:These products and services are independently chosen by our editors. CNET may get a share of the revenue if you buy anything featured on our site.

This Instant Pot steamer basket will make cooking veggies or boiling eggs even easier, and any dietician will tell you steaming adds the least amount of fat to foods while best maintaining their nutritional integrity. This steamer basket Instant Pot accessory is available in three different sizes (3-quart, 6-quart and 8-quart) so there's a size that will fit perfectly for any Instant Pot model. The stainless steel steamer basket also comes with a silicone handle, to keep it from getting too hot and burning your hands!

Serving a similar function as the basket above, this BPA-free silicone version has the added bonus of folding up flat for easy storage so is a great choice for smaller spaces. It also cleans up more easily than metal since it's naturally nonstick. It can be used with 6-quart and 8-quart Instant Pots.

The Instant Pot does come with a metal rack, but this BPA-free silicone version is far easier to clean since it's nonstick. It elevates your food from the liquid in the pot, while the vented bottom promotes better airflow for even cooking and also allows any rendered fat to drain. Use with 6-quartand 8-quart Instant Pots. When not in use, it works as a heat-safe trivet too.

This healthy Instant Pot cookbook contains easy recipes for dishes you'll love, all of which were developed specifically for a low-carb, high-protein keto diet. An Instant Pot is one of the best tools for a high-protein, low-carb lifestyle, cooking savory dishes like fall-off-the-bone red meats, quick chicken and fish and fresh vegetables in a fraction of the time it takes in an oven.

Read more:15 healthy Instant Pot recipes for breakfast, lunch and dinner

Make perfect soft- or hard-boiled eggs in your multicooker with this handy Instant Pot egg steamer rack. It holds nine eggs, making this steam tool ideal for healthy meal prep. Chop up some hard-boiled eggs for your salad or add a soft-boiled egg on top of avocado toast for an easy, healthy weekday breakfast.

If you love Starbucks'sous vide egg bites, you need these silicone Instant Pot egg molds that let you make your own at home. Packed with protein, they're a meal prepper's dream. Customize them with any additions you want, make a double batch on Sunday and grab them for healthy breakfasts and lunch all week long. This silicone mold set for two comes with lids, spoons and a steamer rack, but if you only want one, you can buy asingle egg bite mold with lid by itself.

Read more:Why you should own an Instant Pot: 5 reasons, plus recipes and tips

Whip up some light, healthy meals in your Instant Pot with this great healthy multicooker cookbook, which includes 75 simple recipes all suited for the miracle machine. Each healthy Instant Pot recipe includes a gluten-free option and they are all free of refined sugars. The sweet and savory dishes range from an Instant Pot eggplant parmesan bake to flourless banana oat bread to one-pot chocolate cake and frosting -- yum.

Read more:10 foods you should not cook in your Instant Pot

As if the Instant Pot wasn't convenient enough, these stackable stainless steel Instant Pot inserts are for cooking multiple things at once, like a protein and sides. Each stainless steel inner pot can also serve as layer pans for cooking lasagna or cheesecake on cheat day, but we recommend them as one of the best Instant Pot accessories for anyone looking to save time and make more than one dish at a time in an Instant Pot. Try multiple proteins to keep meal prep interesting, easy and fast!

Read more:13 Instant Pot recipes we keep coming back to

Read more:The hunt for the best air fryer

You can make your own yogurt easily at home with this nifty Instant Pot yogurt maker accessory. We love that it's easy to use and easy to clean. This is a perfect tool for anyone making yogurt or smoothies to power up in the morning. Try creating different flavors and varieties such as Greek yogurt. Incorporate unique add-ins to shake up your healthy breakfast routine.

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9 must-have Instant Pot accessories for healthy eating - CNET

Researchers Find Fish Wearing Natural ‘Bullet-Proof Vest’ to Thwart Piranhas in Amazon – News18

One of the worlds largest freshwater fish is protected by the natural equivalent of a bullet-proof vest, helping it thrive in the dangerous waters of the Amazon River basin with flexible armor-like scales able to withstand ferocious piranha attacks.

Researchers from the University of California, San Diego and University of California, Berkeley on Wednesday described the unique structure and impressive properties of the dermal armor of the fish, called Arapaima gigas. They said their findings can help guide development of better body armor for people as well as applications in aerospace design.

The fish, also known as pirarucu, gets up to 10 feet (3 meters) long and weighs up to 440 pounds (200 kg). Arapaima, a fish that can breathe air and survive up to a day outside of the water, inhabits rivers in Brazil, Guyana and Peru infested with piranhas, known for razor-sharp teeth, incredible bite strength and deadly feeding frenzies.

There long has been an evolutionary arms race in which predators develop ways to kill - like sharp teeth - and other animals develop ways to stay alive like the dermal armor seen in various fish, dinosaurs and mammals over time. Arapaimas scales, the researchers said, possess all the best attributes of a bullet-proof vest, but the elements are better integrated into one solid piece combining imperviousness and flexibility.

Such lightweight and tough materials like fish scales are the sexy topics that materials scientists are pursuing, said Wen Yang, a UCSD materials scientist who helped lead the study published in the journal Matter.

It is true that the natural armor is similar to artificial body armor because of the similar scale overlapping system. However, the natural armor such as these fish scales is tough and much lighter, without impeding body flexibility and locomotion, Yang added. Remember that the fish scales were developed through hundreds of millions of years. They are very advanced.

The researchers conducted laboratory tests of the scales.

The scales, they found, have a hard mineralized outer layer to resist penetration that is bound to a tough-but-flexible inner layer by collagen the main structural protein in skin and other connective tissues in the body.

This structure means the scales can become deformed when bitten by a piranha but are not torn, broken or pierced, protecting the fish from injury.

We were able to see how the collagen fibers deform without a catastrophic failure including the mechanisms of twisting, folding, sliding, stretching, delamination, Yang said.

The study was backed by the U.S. Air Force Office of Scientific Research.

Get the best of News18 delivered to your inbox - subscribe to News18 Daybreak. Follow News18.com on Twitter, Instagram, Facebook, Telegram, TikTok and on YouTube, and stay in the know with what's happening in the world around you in real time.

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Researchers Find Fish Wearing Natural 'Bullet-Proof Vest' to Thwart Piranhas in Amazon - News18

Structural Biochemistry/Proteins/Protein Folding …

Protein folding is a process in which a polypeptide folds into a specific, stable, functional, three-dimensional structure. It is the process by which a protein structure assumes its functional shape or conformation

Proteins are formed from long chains of amino acids; they exist in an array of different structures which often dictate their functions. Proteins follow energetically favorable pathways to form stable, orderly, structures; this is known as the proteins native structure. Most proteins can only perform their various functions when they are folded. The proteins folding pathway, or mechanism, is the typical sequence of structural changes the protein undergoes in order to reach its native structure. Protein folding takes place in a highly crowded, complex, molecular environment within the cell, and often requires the assistance of molecular chaperones, in order to avoid aggregation or misfolding. Proteins are comprised of amino acids with various types of side chains, which may be hydrophobic, hydrophilic, or electrically charged. The characteristics of these side chains affect what shape the protein will form because they will interact differently intramolecularly and with the surrounding environment, favoring certain conformations and structures over others. Scientists believe that the instructions for folding a protein are encoded in the sequence. Researchers and scientists can easily determine the sequence of a protein, but have not cracked the code that governs folding (Structures of Life 8).

Early scientists who studied proteomics and its structure speculated that proteins had templates that resulted in their native conformations. This theory resulted in a search for how proteins fold to attain their complex structure. It is now well known that under physiological conditions, proteins normally spontaneously fold into their native conformations. As a result, a protein's primary structure is valuable since it determines the three-dimensional structure of a protein. Normally, most biological structures do not have the need for external templates to help with their formation and are thus called self-assembling.

Protein renaturation known since the 1930s. However, it was not until 1957 when Christian Anfinsen performed an experiment on bovine pancreatic RNase A that protein renaturation was quantified. RNase A is a single chain protein consisting of 124 residues. In 8M urea solution of 2-mercaptoethanol, the RNase A is completely unfolded and has its four disulfide bonds cleaved through reduction. Through dialysis of urea and introducing the solution to O2 at pH 8, the enzymatically active protein is physically incapable of being recognized from RNase A. As a result, this experiment demonstrated that the protein spontaneously renatured.

One criteria for the renaturation of RNase A is for its four disulfide bonds to reform. The likelihood of one of the eight Cys residues from RNase A reforming a disulfide bond with its native residue compared to the other seven Cys residues is 1/7. Furthermore, the next one of remaining six Cys residues randomly forming the next disulfide bond is 1/5 and etc. As a result, the probability of RNase A reforming four native disulfide links at random is (1/7 * 1/5 * 1/3 * 1/1 = 1/105). The result of this probability demonstrates that forming the disulfide bonds from RNase A is not a random activity.

When RNase A is reoxidized utilizing 8M urea, allowing the disulfide bonds to reform when the polypeptide chain is a random coil, then RNase A will only be around 1 percent enzymatically active after urea is removed. However, by using 2-mercaptoethanol, the protein can be made fully active once again when disulfide bond interchange reactions occur and the protein is back to its native state. The native state of the RNase A is thermodynamically stable under physiological conditions, especially since a more stable protein that is more stable than that of the native state requires a larger activation barrier, and is kinetically inaccessible.

By using the enzyme protein disulfide isomerase (PDI), the time it takes for randomized RNase A is minimized to about 2 minutes. This enzyme helps facilitate the disulfide interchange reactions. In order for PDI to be active, its two active site Cys residues needs to be in the -SH form. Furthermore, PDI helps with random cleavage and the reformation of the disulfide bonds of the protein as it attain thermodynamically favorable conformations.

Proteins in a "scrambled" state go through PDI to renature, and their native state does not utilize PDI because native proteins are in their stable conformations. However, proteins that are posttranslationally modified need the disulfide bonds to stabilize their rather unstable native form. One example of this is insulin, a polypeptide hormone. This 51 residue polypeptide has two disulfide bonds that is inactivated by PDI. The following link is an image showing insulin with its two disulfide bonds. Through observation of this phenomenon, scientists were able to find that insulin is made from proinsulin, an 84-residue single chain. This link provides more information on the structure of proinsulin and its progression on becoming insulin. The disulfide bonds of proinsulin need to be intact before conversion of becoming insulin through proteolytic excision of its C chain which is an internal 33-residue segment. However, according to two findings, the C chain is not what dictates the folding of the A and B chains, but instead holds them together to allow formation of the disulfide bonds. For one, with the right renaturing conditions in place, scrambled insulin can become its native form with a 30% yield. This yield can be increased if the A and B chains are cross-linked. Secondly, through analysis of sequences of proinsulin from many species, mutations are permitted at the C chain eight times more than if it were for A and B chains.

There are various interactions that help stabilize structures of native proteins. Specifically, it is important to examine how the interactions that form protein structures are organized. In addition, there are only a small amount of possible polypeptide sequences that allow for a stable conformation. Therefore, it is evident that specific sequences are used through evolution in biological systems.

On average, about sixty percent of proteins contain a high amount of alpha helices, and beta pleated sheets. Through hydrophobic interactions, the protein is able to achieve compact nonpolar cores, but they lack the ability to specify which polypeptides to restrict in particular conformations. As seen in polypeptide segments in the coil form, the amount of hydrogen boding is not lesser than that of alpha helices and beta pleated sheets. This observation demonstrates that the different kinds of conformations of polypeptides are not limited by hydrogen bonding requirements. Ken Dill has suggested that helices and sheets occur as a result of the steric hindrance in condensed polymers. Through experimentation and simulation of conformations with simple flexible chains, it can be determined that the proportion of beta pleated sheets and alpha helices increase as the level of complication of chains is increased. Therefore, it can be concluded that helices and sheets are important in the complex structure of a protein, as they are compact in protein folding. The coupling of different forces such as hydrogen bonding, ion pairing, and van der Waals interactions further aids in the formation of alpha helices and beta sheets.

By investigating protein modification, the role of different classes of amino acid residues in protein folding can be determined. For example, in a particular study the free primary amino groups of RNase A were derivatized with poly-DL-alanine which consist of 8 residue chains. The poly-Ala chains are large in size and are water-soluble, thus allowing the RNase's 11 free amino groups to be joined without interference of the native structure of the protein or its ability to refold. As a result, it can be concluded that the protein's internal residues facilitates its native conformation because the RNase A free amino groups are localized on the exterior. Furthermore, studies have shown that mutations that occur on the surface of residues are common, and less likely to change the protein conformation compared to changes of internal residues that occur. This finding suggests that protein folding is mainly due to the hydrophobic forces.

George Rose demonstrated that protein domains consisted of subdomains, and furthermore have sub-subdomains, and etc. As a result, it is evident that large proteins have domains that are continuous, compact, and physically separable. When a polypeptide segment within a native protein is visualized as a string with many tangles, a plane can be seen when the string is cut into two segments. This process can be repeated when n/2 residues of an n-residue domain is highlighted with a blue and red color. As this process is repeated it can be seen that at all stages, the red and blue areas of the protein do not interpenetrate with one another. The following link shows an X-ray structure of HiPIP (high potential iron protein) and its first n/2 residues on the n-residue protein colored red and blue. Furthermore, the subsequent structures shown in the second and third row show this process of n/2 residue splitting reiterated as shown where the left side of the protein has its first and last halves with red and blue while the rest of the chain colored in gray. Through this example, it is clearly seen that protein structures are organized in a hierarchical way, meaning that the polypeptide chains are seen as sub-domains that are themselves compact structures and interact with adjacent structures. These interactions forms a larger well organized structure largely due to hydrogen bonding interactions and has an important role in understanding how polypeptides fold to form their native structure.

Since the side chains inside globular proteins fit together with much complementary its packing density can be almost like that of organic crystals. As a result, in order to confirm whether or not this phenomenon of high packing density was an important factor in contributing to protein structure, Eaton Lattman along with George Rose attempted to verify if there was an interaction between side chains that was preferred in a globular protein. They analyzed a total of 67 well studied structures of globular proteins, and concluded that there were no preferred interactions. This experiment demonstrated that packing is not what directs the native fold, but instead the native fold is necessary for packing of a globular protein. This notion can be further supported as members of a protein family result in the same fold despite their lack of sequence similarity and distant relationships.

In addition, structural experimental data have shown that there are a variety of ways that a protein's internal residues can become compact together in an efficient manner. In an extensive study done by Brian Matthews based on T4 lysozyme, which is produced by bacteriophage T4, it was found that changes in the residues of the T4 lysozyme only affected local shifts and did not result in any global structure change. The following link gives an X-ray view of T4 lysozyme and a brief biochemical description of the structure. Matthews took over 300 different mutants of the 164 residue T4 lysozyme, and compared them with one another. Also, it was observed that the T4 lysozyme could withstand insertions of about 4 residues while still not having any major structural changes to the overall protein structure nor enzyme activity. Furthermore, by using assay techniques it was demonstrated that only 173 of the mutants in T4 of the 2015 single residue substitutions done had significant amounts of enzymatic activity diminished. Through these experiments, it is evident that protein structures are extremely withstanding.

Levinthal's paradox is a thought experiment, also constituting a self-reference in the theory of protein folding. In 1969, Cyrus Levinthal noted that, because of the very large number of degrees of freedom in an unfolded polypeptide chain, the molecule has an astronomical number of possible conformations. An estimate of 3300 or 10143 was made in one of his papers.

The Levinthal paradox observes that if a protein were folded by sequentially sampling of all possible conformations, it would take an large amount of time to do so, even if the conformations were sampled at a rapid rate . Based upon the observation that proteins fold much faster than this, Levinthal then proposed that a random conformational search does not occur, and the protein must, therefore, fold through a series of meta-stable intermediate states.

In 1969 Cyrus Levinthal calculated that if a protein were to randomly sample every possible conformation as it folded from the unfolded state to the native state it would take an astronomical amount of time, even if the protein reached 100 billion conformations in one second. Observing that proteins fold in a relatively short amount of time, Levinthal proposed that proteins fold in a fixed and directed process. We now know that while protein folding is not a random process there does not seem to be a single fixed protein folding pathway.This observation came to be known as the Levinthal paradox. This paradox clearly reveals that proteins do not fold by trying every possible conformation. Instead, they must follow at least a partly defined folding pathway made up of intermediates between the fully denatured proteins and its native structure.

The way out of the Levinthal Paradox is to recognize cumulative selection. According to Richard Dawkins, he asked how long it would take a monkey poking randomly at a typewriter to reproduce "Methinks it is like a weasel", Hamlet's remark to Polonius. A large number of keystrokes, of the order of 1040 would be required. Yet if we suppose that each correct character was preserved, allowing the monkey to retype only the wrong ones, only a few thousand keystrokes, on average, would be needed. The crucial difference between these scenarios is that the first utilizes a completely random search whereas in the second case, partly correct intermediates are retained. This also reveals that the essence of protein folding is the tendency to retain partly correct intermediates, although the protein-folding problem is much more difficult than the one presented to Shakespeare example above.

In order to correctly understand the protein-folding problem, we must consider certain characteristics of protein. Since proteins are only marginally stable, the free-energy difference between the folded and the unfolded states of a typical 1000-residue protein is 42 kJ mol1 and thus each residue contributes on average only 0.42 kJ mol1 of energy to maintain the folded state. This amount is less than the amount of thermal energy, which is 2.5 kJ mol1 at room temperature. This meagre stabilization energy means that correct intermediates, especially those formed early in folding, can be lost. The interactions that lead to cooperative folding, nonetheless, can stabilize intermediates as structure builds up. Thus, local regions that have significant structural preference, though not necessarily stable on their own, will tend to adopt their favored structures and, as they form, can interact with one other, resulting in increased stabilization. Nucleation-condensation model refers to this conceptual framework in solving the protein-folding challenge.

Proteins folding forms energetically favorable structures stabilized by hydrophobic interactions clumping, hydrogen bonding and Van der Waals forces between amino acids. Protein folding first forms secondary structures, such as alpha helices, beta sheets, and loops. Different amino acids have different tendencies for whether they are going to form Alpha Helices, Beta sheets, or Beta Turns based upon polarity of the amino acid and rotational barriers. For example, the amino acids, valine, threonine, isoleucine, tend to destabilize the alpha helices due to steric hindrance. Thus, they prefer conformational shifts towards Beta sheets rather than alpha helices. The relative frequencies of the amino acids in secondary structures are grouped according to their preferences for alpha helices, beta sheets or turns (Table 1). Table 1: Relative frequencies of amino acid residues in secondary structuresThese structures in turn, fold to form tertiary structures, stabilized by the formation of intramolecular hydrogen bonds. Covalent bonding may also occur during the folding to a tertiary structure, through the formation of disulfide bridges or metal clusters. According to Robert Pains Mechanisms of Protein Folding, molecules also often pass through an intermediate molten globule state formed from a hydrophobic collapse (in which all hydrophobic side-chains suddenly slide inside the protein or clump together) before reaching their native confirmation. However, this means all the main chain NH and CO groups are buried in a non-polar environment, but they prefer an aqueous one, so secondary structures must fit together very well, so that the stabilization through hydrogen bonding and Van der Waals forces interactions overrides their hydrophilic tendencies. The strengths of hydrogen bonds in a protein vary depending on their position in the structure; H-bonds formed in the hydrophobic core contribute more to the stability of the native state than H-bonds exposed to the aqueous environment.

Water-soluble proteins fold into compact structures with non-polar, hydrophobic cores. The inside of protein contains non-polar residues in center (i.e. - leucine, valine, methionine and phenylalanine), while the outside contains primarily polar, charged residues (i.e. - aspatate, glutamate, lysine and arginine). This way the polar, charged molecules can interact with the surrounding water molecules while the hydrophobic molecules are protected from the aqueous surroundings. Minimizing the number of hydrophobic side chains on the outer part of the structure makes the protein structure thermodynamically more favorable because the hydrophobic molecules prefer to be clumped together, when surrounded by an aqueous environment (i.e. hydrophobic effect). Proteins that span biological membranes (i.e. - porin) have an inside out distribution, with respect to the water-soluble native structure, they have hydrophobic residue covered outer surfaces, with water filled centers lined with charged and polar amino acids.

In Folding Scene Investigation: Membrane Proteins, a paper written by Paula J Booth and Paul Curnow, the authors attempt to answer how the folding mechanisms of integral membrane proteins with helical structures work.Studying the folding of membrane proteins has always been difficult as these proteins are generally large and made of more than one subunit. The proteins posses a high degree of conformational flexibilitywhich is necessary for them to perform their function in the cell. Also, these proteins have both hydrophobic surfaces, facing the membrane, and hydrophilic surfaces, facing the aqueous regions on either side of the membrane. The proteins are move laterally and share the elastic properties of the lipid bilayer in which they are embedded. In order to study these proteins, Booth and Curnow believe that one must manipulate the lipid bilayer and combine kinetic and thermodynamic methods of investigation.

Reversible Folding and Linear Free EnergyThe free energy of protein folding is measured by reversible chemical denaturation. The reversible folding of a protein depends on this free energy. For the helix proteins that were being studied, it was proven that a reversible, two-state process is followed. bR (a helical membrane protein called bacteriorhodopsin) reversibly unfolds if SDS (a denaturant which is an anionic detergent) is added to mixed lipid, detergent micells. The two-state reaction involves a partly unfolded SDS state and a folded bR state. By comparing the logs of the unfolding and folding rate, and the SDS mole fraction, a linear plot was generated proving a linear relationship. This plot proved that bR had a very high stability outside of its membraneproving that it was unexpectedly stable. Furthermore, bR was so stable outside of the membrane that it would not unfold during a reasonable period of time without addition of denaturant.

Comparison with Water-Soluble ProteinsBooth and Curnow studied the 3 membrane proteins about which the most information is held: bR, DGK (Escherichia coli diacylglycerol kinase) and KcsA (Sterptococcus lividans potassium channel). These three membrane proteins were compared to water-soluble proteins (which fold by 2 or 3 state kinetics). The overall free energy change of unfolding in the absence of denaturant was the same for water-soluble proteins and membrane proteins of similar size. This proves that it is the balance of weak forces rather than the types of forces that stabilize the protein that determines its stability. It was proven that H-bonds in the membrane proteins were of similar strength to those of the water-soluble proteins, rather than being stronger in membrane proteins as was expected.

Mechanical Strength and Unfolding Under Applied ForceDynamic force microscopy can be used to measure the mechanical response of a particular region of a protein under applied force. The unfolding force in this case depends on the activation barrier. This unfolding has nothing to do with the thermodynamic stability of a protein. For unfolding under applied force, the membrane proteins (especially bR) seem to follow the rules of Hammond behavior. The energy difference between two consecutive states of this reaction is reduced and the states become similar in structure.

Influence of Surrounding MembraneMembrane proteins are influenced greatly by the membranes they are surrounded by. If the lipids incorporate in detergent micells-increasing the stability of the lipid structureboth the protein and its folding are stabilized. Different combinations of different lipids can result in different stabilities or folding of membrane proteins. The size of the membrane can also affect the membrane protein.Different types of lipids cause different membrane properties. A type of lipids called PE lipids have higher spontaneous curvatures than a second type of lipid called a PC lipid. By adding PE lipids to PC lipids the monolayer curvature of the bilayer increases. Increasing the curvature of the lipid bilayer increases the stability of the protein folding.

In mitochondria, the proteins that are made from the ribosomes are directly take in from the cytosol. Mitochondrial proteins are first completely synthesized in the cytosol as mitochondrial precursor proteins, then taken up into the membrane. The Mitochondrial proteins contain specific signal sequence at their N terminus. These signal sequences are often removed after entering the membrane but proteins entering membranes that has outer, inner, inter membrane have internal sequences that play a major movement in the translocation within the inner membrane.

Protein translocation plays a major role in translocating proteins across the mitochondrial membranes. Four major multi-subunit protein complexes are found in the outer and the inner membrane. TOM complexes are found in the outer membrane, and two types of TIM complexes are found integrated within the inner membrane: TIM23 and TIM22. The complexes act as receptors for the mitochondrial precursor proteins.

TOM: imports all nucleus encoded proteins. It primarily starts the transport of the signal sequence into the inter membrane space and inserts the transmembrane proteins into outer membrane space. A Beta barrel complex called the SAM complex is then in charge of properly folding the protein in the outer membrane. TIM23 found in the inner membrane moderates the insertion of soluble proteins into the matrix, and facilitates the insertion of transmembrane proteins into the inner membrane. TIM23, another inner membrane complex facilitates the insertion inner membrane proteins comprised of transporters that move ADP, ATP, and phosphate across the mitochondrial membranes. OXA, yet another inner membrane complex, helps insert inner membrane proteins that were synthesized from the mitochondria itself and the insertion of inner membrane proteins that were first transported into the matrix space.File:Translocation.jpg

The place where the protein chain begins to fold is a topic that is greatly studied. As the nascent chain goes through the exit tunnel of the ribosome and into the cellular environment, when does the chain begin to fold? The idea of cotranslational folding in the ribosomal tunnel will be discussed. The nascent chain of the protein is bound to the peptidyl transferase centre (PTC) at its C terminus and will emerge in a vectorial manner. The tunnel is very narrow and enforces a certain rigidity on the nascent chain, with the addition of each amino acid the conformational space of the protein increases. Co translational folding can be a big help in reducing the possible conformational space by helping the protein to acquire a significant level of native state while still in the ribosomal tunnel. The length of the protein can also give a good estimate of its three dimensional structure. Smaller chains tend to favor beta sheets while longer chains (like those reaching 119 out of 153 residues) tend to favor the alpha helix.

The ribosomal tunnel is more than 80 in length and its width is around 10-20 . Inside the tunnel are auxiliary molecules like the L23, L22, and L4 proteins that interact with the nascent chain help with the folding. The tunnel also has hydrophilic character and helps the nascent chain to travel through it without being hindered. Although rigid, the tunnel is not passive conduit but whether or not it has the ability to promote protein folding is unknown. A recent experiment involving cryoEM has shown that there are folding zones in the tunnel. At the exit port (some 80 from the PTC), the nascent chain has assumed a preferred low order conformation. This enforces the suggestion that the chain can have degrees of folding at certain regions. Although some low order folding can occur, the adoption of the native state occurs outside the tunnel, but not necessarily when the nascent chain has been released. The bound nascent chain (RNC) adopts partially folded structure and in a crowded cellular environment, this can cause the chain to self-associate. This self-association, however, is relieved with the staggered ribosomes lined along the exit tunnel that maximizes the distances between the RNC.

Generation of RNC for studies:

One technique of generating RNC and taking snapshots as it emerges from the tunnel is to arrest translation. A truncated DNA without a termination sequence is used. This allows for the nascent chain to remain bound until desired. To determining the residues of the chain, they can be labeled by carbon-13 or nitrogen-15 and later detected by NMR spectroscopy. Another technique is the PURE method and it contains the minimal components required for translation. This method has been used to study the interaction of the chains and auxiliary molecules like the TF chaperone. This method is coupled with quartz-crystal microbalance technique to analyze the synthesis by mass. An in vivo technique in generating RNC chain can be done by stimulating it in a high cell density. This is initially done in an unlabeled environment, the cells are then transferred to a labeled medium. The RNC is generated by SecM. The RNC is purified by affinity chromatography and detected by SDS-PAGE or immunoblotting.

By generating the RNCs, many experiments can be done to study more about the emerging nascent chain. As mentioned above, the chain emerges from the exit tunnel in a vectorial manner. This enables the chain to sample the native folding and increases the probability of folding to the native state. Along with this vectorial folding, chaperones also help in favorable folding rates and correct folding.

Protein Entering the Mammalian ER:The endoplasmic reticulum (ER) is a main checkpoint for protein maturation to ensure that only correctly folded proteins are secreted and delivered to the site of action. The protein entrance to the ER begins with recognition of a N terminus signal sequence. Specially, this sequence is detected by a signal recognition protein (SRP) causing the ribosome/nascent chain/SRP complex bind to the ER membrane. Then, the complex travels through a proteinaceous pore called Sec61 translocon which allows the polypeptide chain enter the lumen portion of the ER.

Processes in Conflict During Protein Folding:After the protein enters the ER, the proteins break up into an ensemble of folding intermediates. These intermediates take three different routes. They are either folded properly and sent to be exported out of the endoplasmic reticulum (ER) into the cytosol, aggregated or picked out for degradation. These three processes are in competition to properly secrete a protein. In order for a protein to be properly secreted, the competition between folding, aggregation and degradation must be in favor of folding, so that folding occurs faster than the other processes. This balance is termed proteostasis. The balance of proteostasis can be tipped in favor of folding by either using smaller molecules to stabilize the protein (called co-factors) or increasing the concentrations of folding factors. This ability to control proteostasis allows scientists the power to overcome some of the protein folding diseases such as cystic fibrosis.

The proteins that are folded properly are ready for anterograde transport, and secreted through the membrane of the ER into the cytosol by a cargo receptor that recognizes the properly folded protein. The proteins that are incorrectly folded are not secreted and are either targeted for degradation or aggregated. The aggregated proteins are able to re-enter the stage of protein ensembles ready to be folded so that they may try again at being folded properly.

Folding Factors in the Endoplasmic Reticulum:

Biochemical research on folding pathways has provided a comprehensive list of folding factors, or chaperones, involved with protein folding in the ER. Folding factors are categorized based on whether they catalyze certain steps or if they interact with intermediates in the folding pathway. General protein folding factors are typically separated into four different groups: heat shock proteins as chaperones or cochaperones, peptidyl prolyl cis/trans isomerases (PPIases), oxidoreductases, and glycan-binding proteins.

Many folding factors are great in that they are multi-functional. One folding factor can take care of different areas of the folding pathway. Unfortunately, this leads to redundancy due to different classes of proteins carrying out overlapping functions. This functional redundancy complicates the understanding of the specific roles of individual folding factors in aiding maturation of client proteins. Folding factors also prefer to act in concert during the maturation process, which further obscures the individual roles of each factor. Since these roles are not clear, it is difficult to confirm that even if one folding factor deals with a particular reaction in one protein, that same folding factor will carry out the same function in another.

In addition to aiding non-covalent folding and unfolding of proteins, folding factors in the ER sometimes delay interactions with the protein. This allows time for nascent proteins to fold properly and enables folded proteins to backtrack on its folding pathway, which prolongs equilibrium in a less folded state, preventing the protein from being held in a non-native state.

Folding after Endoplasmic Reticulum: Although ER provides only correctly assembled proteins to be secreted, some examples exist in which proteins change conformation in the Golgi bodies and beyond. Typically, newly folded proteins are sensitive and prone to unfolding while in the ER but resistant to unfolding after exit. In an environment without chaperones and other folding enzymes, proteins are compact and relatively resistant to change after exiting the ER. However, this doesnt necessarily mean that protein folding ends because some molecular chaperones like Hsp 70s and Hsp 90s continue to assist in protein conformation throughout the proteins existence.

A strategy for studying the folding of proteins is to unfold the protein molecules in high concentrations of a chemical denaturant like guanidinium chloride. The solution is then diluted rapidly until the denaturant concentration is lowered to a level where the native state is thermodynamically stable again. Afterwards, the structural changes of the protein folds may be observed. In theory, this sounds simple. However, such experiments are complex, since unfolded proteins have random coil states in chemical denaturants. Moreover, analyzing the structural changes taking place in a sample may is difficult, since all of the molecules may have significantly different conformations until the final stages of a reaction. As such, the analysis would have to be performed in a matter of seconds rather than days or weeks that are normally allowed to deduce the structure of a single conformation of a native protein. To avoid this problem, the disulphide bonds can be reduced after the protein is unfolded and reformed under oxidative conditions. The protein can then be identified by standard techniques such as mass spectroscopy to draw conclusions about the structure present at stages of folding where disulfide bonds are formed.

Multiple techniques are used to monitor structural changes during the refolding. For instance, in circular dichorism, UV is used from far away to provide a measurement of the appearance of the secondary structure during folding. UV at a close distance monitors the formation of the close-packed environment for aromatic residues. NMR is also a useful technique for characterizing conformations at the level of individual amino-acid residues. It can also be used to monitor how the development of structures protect amide hydrogens from solvent exchanges.

Circular Dichroism: This type of spectroscopy measures the absorption of circularly polarized light since the structures of protein such as the alpha helix and beta sheets are chiral and can absorb this sort of light. The absorption of light indicates the degree of the proteins foldedness. This technique also measures equilibrium unfolding of protein by measuring change of absorption against denaturant concentration or temperature. The denaturant melt measures the free energy of unfolding while the temperature melt measures the melting point of proteins. This technique is the most general and basic strategy for studying protein folding.

Dual Polarization Interferometry: This technique uses an evanescent wave of a laser beam confined to a waveguide to probe protein layers that have been absorbed to the surface of the waveguide. Laser light is focused on two waveguides, one that senses the beam and has an exposed surface, and one that is used to create a reference beam and to excite the polarization modes of the waveguides. The measurement of the interferogram can help calculate the protein density or fold, the size of the absorbed layer, and to infer structural information about molecular interactions at the subatomic resolution. A two-dimensional pattern is obtained in the far field when the light that has passed through the two waveguides is combined.

Mass Spectrometry: The advantages of using Mass Spectroscopy to study protein folding include the ability to detect molecules with different amounts of deuterium, which allows the heterogeneity of the protein folding reactions to be studied. It can also measure the conformation of folding intermediates bound to molecular chaperones without disrupting the complex. Mass spectrometry can also directly compare refolding properties, since mixtures of proteins can be studied without separation if the two proteins have sufficiently different molecular weights.

High Time Resolution: These are fast time-resolved techniques where a sample of unfolded protein is triggered to fold rapidly. The resulting dynamics are then studied. Ways to accomplish this include fast mixing of solutions, photochemical methods, and laser temperature jump spectroscopy.

Computational Prediction of Protein Tertiary Structure: This is a distinct form of protein structure analysis in that it involves protein folding. These programs can simulate the lengthy folding processes, provide information on statistical potential, and reproduce folding pathways.

Protein misfolding refers to the failure of a protein to achieve its tightly packed native conformation efficiently or the failure to maintain that conformation due to reduction in stability as a result of environmental change or mutation. It has been established that failure of protein folding is a general phenomenon at elevated temperatures and under other stressful circumstances. The two most common results of misfolded proteins are degradation and aggregation. When a polypeptide emerges from the cell, it may fold to the native state, degraded by proteolysis, or form aggregates with other molecules. Proteins are in constant dynamic equilibrium so even if the folding process is complete, unfolding in the cellular environment can occur. Unfolded proteins usually refold back into their native states but if control processes fail, misfolding leads to cellular malfunctioning and consequently diseases. Diseases associated with misfolding cover a wide array of pathological conditions such as cystic fibrosis where mutations in the gene encoding the results in a folding to a conformer whose secretion is prevented by quality-control mechanisms in the cell. About 50% of cancers are associated with mutations of the p53 protein that eventually lead to the loss of cell-cycle control and causing the growth of tumors. Failure of proteins to stay folded can result in aggregation, a common characteristic of a group of genetic, sporadic, and infectious conditions known as amyloidoses. Aggregation usually results in disordered species that can be degraded within the organism but it may also result in highly insoluble fibrils that accumulate in tissue. There are about twenty known diseases resulting from the formation of amyloid material including Alzheimers, Type II diabetes, and Parkinsons disease. Amyloid fibrils are ordered protein aggregates that have an extensive beta sheet structure due to intermolecular hydrogen bonds and have an overall similar appearance to the proteins they are derived from. The formation of the amyloid fibrils are the result of prolonged exposure to at least partially denatured conditions.

Alzheimer's: This neurological degeneration is caused by the accumulation of Plaques and Tangles in the nerve cells of the brain.[1] Plaques, composed of almost entirely a single protein, are aggregation of the protein beta-amyloid between the spaces of the nerve cells and Tangles are aggregation of the protein tau inside the nerve cells. Tangles are common in extensive nerve cell diseases whereas neuritic plaque is more specific to Alzheimer's. Although scientists are unsure what role Plaques and Tangles play in the formation of Alzheimer's, one theory is that these accumulated proteins impede the nerve cell's ability to communicate with each other and makes it difficult for them to survive. Studies have shown that Plaques and Tangles naturally occur as people age, but more formation is observed in people with Alzheimer's. The reasons for this increase is still unknown.

Creutzfeldt-Jakob Disease (Mad Cow Disease): This disease is caused by abnormal proteins called prions which eat away and form hole-like lesions in the brain. Prions (proteinaceous infectious virion) were discovered to be proteins with an altered conformation. Scientists hypothesize that these infectious agents could bind to other similar proteins and induce a change in their conformation as well, propagating new, infectious proteins.[2] Prions are highly resistant to heat, ultraviolet light, and radiation which makes them difficult to be eliminated. In Creutzfeldt-Jakob Disease there is an incubation period for years which is then followed by rapid progression of depression, difficulty walking, dementia and death. Currently there is no effective treatment for prion diseases and all are fatal.[3]

Parkinson's disease:A mutation in the gene which codes for alpha-synuclein is the cause of some rare cases of familial forms of Parkinson's disease. Three point mutations have been identified thus far: A53T, A30P and E46K. Also, duplication and triplication of the gene may be the cause of other lineages of Parkinson's disease.Victims of Parkinson's disease have primary symptoms that result from decreased stimulation of the motor cortex by the basal ganglia, normally caused by the insufficient formation and action of dopamine. Dopamines are produced in the dopaminergic neurons of the brain. People who suffer from this disease have brain cell loss (death of dopaminergic neurons), which may be caused by abnormal accumulation of the protein alpha-synucleinbinding to ubiquitin in the damaged cells. This makes the alpha-synuclein-ubiquitin complex unable to be directed to the proteosome. New research shows that the mistransportation of proteins between endoplasmic reticulum and the Golgi apparatus might be the cause of losing dopaminergic neurons by alpha-synuclein.

Cystic Fibrosis: Francis Collins first identified the hereditary genetic mutation in 1989. The problem occurs in the regulator cystic fibrosis transmembrane conductance regulator (CFTR), which regulates salt levels and prevents bacterial growth, when the dissociation of CFTR is disturbed as a protein regulating the chloride ion transport across the cell membrane.[4] The deleted amino acid doesn't allow bacteria in the lungs to be killed thereby causing chronic lung infections eventually leading to an early death.[5] Scientists have used nuclear magnetic resonance spectroscopy (NMR) to study Cystic Fibrosis and its effects.

Sickle Cell Anemia: Sickle-shaped red blood cells cling to walls in narrow blood vessels obstructing the flow of blood define sickle cell anemia. The shortage of red blood cells in the blood stream in addition to the lack of oxygen-carrying blood causes serious medical problems. The defect in the Hemoglobin gene is detected with the presence of two defective inherited genes. The sickle cell shape is formed as hemoglobin give up their oxygen resulting in stiff red blood cells forming rod-like structures. Some symptoms include: fatigue, shortness of breath, pain to any joint or body organ lasting for varying amounts of time, eye problems potentially leading to blindness, and yellowing of the skin and eyes which is due to the rapid breakdown of red blood cells. Luckily, sickle cell anemia can be detected by a simple blood test via hemoglobin electrophoresis. Even though there is no cure, blood transfusions, oral antibiotics, and hydroxyurea are treatments that reduce pain caused.[6]

Huntington's Disease: Also known as the trinucleotide repeat disorder, Huntington's disease results from glutamine repeats in the Huntingtin protein. Roughly 40 or more copies of C-A-G (glutamine) will result in Huntington's disease as the normal amount is between 10 and 35 copies. During the post-translational modification of mutated Huntingtin protein(mHTT), small fractions of polyglutamine expansions misfold to form inclusion bodies. Inclusion bodies are toxic for brain cell. This alteration of the Huntingtin protein does not have a definite effect except that it affects nerve cell function.[7] This incurable disease affects muscle coordination and some cognitive functions.

Cataracts: Eye lens are made up of proteins called crystallins. Crystallins have a jelly-like texture in a lens cytoplasm. The current leading cause of blindness in the world, cataracts occurs when crystallin molecules form aggregates scattering visible light causing the lens of the eye to become cloudy. UV light and oxidizing agents are thought to contribute to cataracts as they may chemically modify crystallins. In children, it has been observed that the deletion or mutation of B-crystallin facilitates cataracts formation. The likelihood of developing cataracts exponentially increases with age. Pain, Roger H. (2000). Mechanisms of Protein Folding. Oxford University Press. pp.420421. ISBN019963788. http://books.google.com/books?id=DvJygJkNCYkC&pg=PA420&lpg=PA420&dq=cataract+protein+folding&source=bl&ots=lDazpccGH2&sig=aHxuSkC1XNmcOnJYnmW4rZPuUvg&hl=en&ei=Z7rbSv3_OJG-sgOvpOGRBg&sa=X&oi=book_result&ct=result&resnum=2&ved=0CBUQ6AEwAQ#v=onepage&q=cataract%20protein%20folding&f=false. Retrieved 2009-10-18.

Protein misfolding caused by impairment in folding efficiency leads to a reduction in number of the proteins available to conduct its normal role and formation of amyloid fibrils, protein structures that aggregate, resulting in a cross- structure that can generate numerous biological functions. Protein aggregation can come from different processes occurring after translation including the increase in likelihood of degradation through the quality control system of the endoplasmic reticulum (ER), improper protein trafficking, or conversion of specific peptides and proteins from its soluble functional states into their highly organized aggregate fibrils.

Structures

X-ray Crystallography

From X-ray crystallography, three-dimensional crystals of amyloid fibril structures were formed and the structure of the peptide formation and how the molecule is packed together were examined. In one particular fragment, the crystal was found to contain parts of parallel -sheets where each peptide contributes one single -strand. The -strands are stacked and -sheets formed are parallel and side chains Asn2, Gln4 and Asn6 interact with each other in a way that water is kept out of the area in between the two -sheets with the rest of the side chains on the outside are hydrated and further away from the next -sheet.

Solid State Nuclear Magnetic Resonance (SSNMR)

Through solid-state nuclear magnetic resonance (SSNMR) and the help of other methods such as computational energy minimization, electron paramagnetic resonance and site-directed fluorescence labeling and hydrogen-deuterium exchange, mass spectrometry, limited proteolysis and proline-scanning mutagenesis the structure of an amyloid fibril was suggested to be four -sheets separated by approximately 10.

Through NMR with computational energy minimization, a 40-residue form of amyloid peptide at pH 7.4 and 24Celius was determined to contribute one pair of -strand to the core of the fibril which is connected by a protein loop. The amyloid peptides are stacked on each other in a parallel fashion.

From experiments of site-directed spin labeling coupled to electron paramagnetic resonance (SDSL-EPR), the molecule was found to be very structured in the fibrils and in parallel arrangement. SDSL-EPR along with hydrogen-deuterium exchange, mass spectrometry, limited proteolysis and proline-scanning mutagenesis suggests that the structure has high flexibility and exposure to solvent of N-terminal side, but is rigid in the other parts of the structure.

Experiments through SSNMR with fluorescence labeling and hydrogen-deuterium exchange determined that the C-terminals are involved in the core of the fibril structure with each molecule contributing four -strands with strands one and three forming one -sheet and strands two and four forming another -sheet about 10 apart.

Further experimentation approaching the atomic level with SSNMR techniques resulted in very narrow resonance lines in the spectra, showing that the molecules within fibrils hold some uniformity with peptides that display extended -strands with the fibrils.

Conclusion

The structures determined from X-ray crystallography or SSNMR were similar to previously proposed structures from cryo-electron microscopy (EM) formed from insulin. EM, which uses electron density maps, revealed untwisted -sheets in the structure. The similarities of the structures found in these experiments suggest a lot of amyloid fibrils can have similar characteristics such as the side-chain packing, aligning of -strands and separation of the -sheets.[8] Annu. Rev. Biochem. 2006.75:333-366. http://www.annualreviews.org. Retrieved 24 Oct 2011

Formation

The capability to form amyloidal protein structures that are considered to be genetic is from the findings that an increasing number of proteins show no signs of protein related diseases. It has been found that amyloidal proteins can be converted from its own protein that has a function rather than disease- related characteristics in living organisms.

In these protein mutations, different factors that affect the formation of amyloid fibril formation and different chains form amyloid fibrils at different speeds. In different polypeptide molecules, hydrophobicity, hydrophillicity, changes in charge, degree of exposure to solvent, the number of aromatic side chains, surface area, and dipole moment can affect the rate of aggregation of protein. It has been found that the concentration of protein, pH and ionic strength of the solution the protein is in as well as the amino acid sequence it is in determines the aggregation rate from the unstructured, non-homologous protein sequences.

As the hydrophobicity of the side chains increases or decreases can change the tendency for the protein to aggregate.

Charge in a protein can create aggregations through interaction of the polypeptide chain with other macromolecules around it. Also, the low tendency for -sheets to form along with the high tendency for -helixes to form contributes in facilitating amyloid formation.

It was found that the degree in which the protein sequence are exposed to solvent tend to affect the formation of amyloids. Proteins that are exposed to solvent seem to promote aggregation. Even though some other parts of the protein that had a high tendency to aggregate were not involved in the aggregation, they seem to at least be partially unexposed to the solvent but other regions that were exposed to solvent that were not involved in the aggregation had a low tendency to form amyloid fibrils.

It has even been raised that protein sequences have evolved over time to avoid forming clusters of hydrophobic residues by alternating the patterns of hydrophobic and hydrophillic regions to lower the tendency for protein aggregation to occur.[8]

The Affects of Sequence on the Formation of Amyloid Proteins

Amyloid formation arises mostly from the properties of the polypeptide chain that are similar in all peptides and proteins, but sometimes, the sequence affects the relative stabilities of the conformational states of the molecules. In that case, the polypeptide chains with different sequences form amyloid fibrils at various rates. Sequence difference affects the behavior of the protein aggression instead of affecting the stability of the protein fold. Various physicochemical factors affect the formation of amyloid structure by unfolded polypeptide chains.

Hydrophobicity of the side chains affects the aggregation of unfolded polypeptide chains. The amino acid in the regions of the aggregation site can change the ability of aggregation of a sequence when they increase or decrease the hydrophobicity at the site of the mutation or folding site. Over time, sequences have evolved to avoid creating clumps of hydrophobic residues by alternating hydrophobic areas of the protein.

Charge affects the aggregation of amyloid protein folding. A high net charge can have the possibility of impeding self association of the protein. Mutations in decreasing the positive net charge may result in the opposite effect of aggregate formation as increasing the positive net charge. It has been seen found that polypeptide chains can be run by interactions with highly charged macromolecules, displaying the importance of charge of a protein aggregation.

Secondary structures of proteins affect the amyloid aggregation as well. Studies show that a low probability to form -helix structures and a high probability to form -sheet structures are contributive factors to amyloid formation. However, it has been found that -sheet formation is not particularly favored by nature since there are little alternation of hydrophilic and hydrophobic residue sequence patterns to be found.

The characteristics of the amino acid sequences affect the amyloid fibril structure and rate of aggregation. Different mutations, including changes in the number of aromatic side chains, the amount of exposed surface area and dipole moment, have been said to change the aggregation rates of lots of polypeptide chains.

Unfolded regions play vital roles in promoting the aggregation of partially folded proteins. Some regions that were found to be flexible or exposed to solvent were fond of aggregation. Other regions that are not involved in the aggregation were found to not be exposed, but rather half buried even though they have high possibility of aggregating while the exposed regions of the structure that are not involved in the aggregation have a low probability of aggregating amyloid fibrils. The fibrils tend to come together by association of unfolded polypeptide segments rather than by docking the structural elements.

Overall, it has been found that unfolded proteins have lower less hydrophobicity and higher net charge than that of a folded protein. Residues that tend not to form the secondary structure of -sheet structured proteins seem to inhibit the occurrence of amyloid aggregation. Concentration of protein, pH and ionic strength were found to be associated with the amino acid sequence, which affects the rate of aggregation.

[8]

It is understood that the primary structure (the amino acid sequence) of a protein predisposes the protein for a specific three dimensional structure and how it will fold from the unfolded form to the native state. The concentration of salts, the temperature, the nature of the primary solvent, macromolecular crowding, and the presence of chaperones are all factors that affect the mechanism of folding and the ratio of unfolded proteins to those in the native state. More than anything, these environmental factors affect the likelihood of any single protein reaching the correct final structure.

Isolated proteins placed in proper environments (specific solvent, solute concentrations, pH, temperature, etc.) tend to self-fold into the correct native conformation. Altering any of these environmental characteristics can disrupt the structure and/or interfere with the folding mechanism. A pH outside the normal range of a given protein can ionize specific amino acids or interfere with both polar and dipole-dipole intramolecular forces that would otherwise stabilize the structure. Excess heat (cooking) proteins can break hydrogen bonds essential to the secondary structure of proteins.

Extreme environments or the presence of chemical denaturants (such as reducing agents that can break disulfide bonds) can cause proteins to denature and lose its secondary and tertiary structure, forming into a random coil. Under certain conditions fully denatured proteins can return to their native state. Intentional denaturing is used in various methods to analyze biomolecules.

The complex environments within cells often necessitate chaperones and other biomolecules for proteins to properly form the native state.

Protein is an essential part of living thing. The development of human body is needed to be parallel with the development of protein. But protein contains so many mysteries that we did not discovery yet. For example, that is protein folding. Folding is a necessary activity of proteins. They need to fold to continue their biological activity. Folding is also a process that very protein goes through to have a stable conformation. But sometimes this process is happened incorrectly, and the scientist call this problem is protein misfolding. The results of protein folding incorrectly are so many bad diseases happening for human, animals and living things such as Alzheimers disease and Mad Cow disease. Because of this reason, the researches about protein folding and misfolding become very important. During the process of discovering about protein, folding, misfolding and its affects, the scientists have been collecting many successes; the mystery about protein is unraveled gradually. As a scientist, W. A. (Bill) Thomasson records many importance things about protein in the article Unraveling the Mystery of Protein Folding; in this article, he make the points about Alzheimers disease and Mad Cow disease and some affects of protein misfolding beside the successes of science about them.Dr Thomasson begins his article by introduce generally about protein folding and misfolding. First of all, proteins consists the sequences of amino acid. The scientists have discovered 20 amino acids appearing in proteins. The protein structure is known with 2 basic shapes which are _helix and _sheet. Most of proteins probably go through several intermediate states on their way to a stable conformation (Campbell and Reece, 79). Proteins need to fold to continue its activity. The scientists have listed 3 type of protein folding; the protein can be folded, partial folded or misfolded. In the process of folding, the proteins called chaperones are associated with the target protein; however once folding is complete (or even before) the chaperone will leave its current protein molecule and go on to support the folding of another (Thomasson). The author of the article records the very important conclusion of Anfinsen about protein misfolding. In his point of view, the misfolding is occurred in the process of folding when the folding goes wrong. The research of protein misfolding is focus on the temperature sensitive mutation; the scientists observe the bacteriophage P22 with the changing of temperature to cause the mutation. And they conclude that the mutant proteins are less stable than the normal. It means, they give a conclusion is that in the tailspike of bacteriophage the misfolded proteins is less stable than the correctly folded proteins and they are difficult to reach the properly folded state. When the protein misfolding occurs, it results many bad disease. The aggregation can appear along with the appearance of misfolding and it is at the brain to cause Alzheimers disease and Mad Cow disease as many scientists consider. One affect of protein misfolding on human life that is Alzheimers disease. This is a disease of the elderly. According to the research of scientist, this disease is occurred when the amyloid precursor protein is misfolding. This protein is processed into a soluble peptide A. The scientists have not known exactly the reason of this disease yet. But the main reason causing the misfolding is the protein apolipoprotein E (apoE) inside our blood stream. The protein apoE has three forms such as apoE2, apoE3 and apoE4. The affects of each form of apoE on the A is not discovered yet but the scientists consider that the apoE can bind to the A. In the process of misfolding, the -amyloid is formed to make neuritic plaque in the Alzheimers patient. This disease is just happened with the older people because in the amyloid process, a nucleus is formed very slowly. The mutation of this protein is not stable and causes the disease. The studying about apoE is still a secret because some scientists show that one form of this protein is developing the disease but another form is decreasing the development of the disease. Finally, the research about Alzheimers disease is continued in order to affirm the results of protein apoE on A and to find the treatment for this disease successfully. Another affect from the protein misfolding is the Mad Cow disease. This is a very dangerous disease because it can be transmitted from animals to human. This disease causes by the misfolding of prions. The process of misfolding is the self-replicating of the prions. Prions are protein particles containing DNA and RNA. The mutation appear in the process of folding, the prions self-replicate and cause the misfolding of the proteins. They contain DNA and RNA. This is a special situation of the protein; it can be served as its chaperons. Because of the replicating, the prion was multiplied very quickly along with the increasing of normal proteins. This disease shows that the protein folding can be occurred without the genetics such as the experiment on the sheep. Dr. Thomasson continues his article by some more information about the misfolding and the way of the scientist to prove the mystery. He gives the information about the protein p53 and its mutation. It can cause the cancer, it also one type of protein misfolding. The point Dr. Thomasson wants to make that is his idea about the drug that can make the protein misfolding becoming more stable and minimize the misfolding of protein. This idea seems very good but its results are like a mystery as the mystery of protein folding. The research about the protein folding is very important to our lives. The misfolding is one of the main reasons causing so many dangerous disease but we did not have a successful treatment yet. The study of protein folding is more and more successful to help the human to be able to destroy the disease causing by misfolding. The disease caused by protein misfolding has become one problem of human that need to be solved.

Molecular Chaperones are known mainly for assisting the folding of proteins. Chaperones are not just involved in the initial stages of a proteins life. Molecular Chaperones are involved in producing, maintaining, and recycling the structure and units of protein chaperones. Chaperones are present in the cytosol but are also present in cellular compartment such as the membrane bounded mitochondria and endoplasmic reticulum. The role or necessity of chaperones to the proper folding of proteins varies. Many prokaryotes have few chaperones and less redundancy in the types of chaperones and whereas eukaryotes have large families of chaperones containing some redundancy. It is hypothesized that some chaperones are essential to proper protein folding such as the example of the prokaryote which has less variations of a chaperone family available. Other chaperones play less of an essential role such as in eukaryotes where more variations within a family of chaperones exist and gradients of efficiency or affinity are produced. This redundancy or existence of less efficient chaperones may exist in one state but the effectiveness of chaperones is also a function of their environment. The pH, space, temperature, protein aggregation and other external factors may render a chaperone that was once ineffective into a more essential chaperone. These environmental factors show why it is important to simulate cellular in vivo conditions, or native states, in order to grasp the conditions that require use of chaperones. This briefly summarizes the difficulties in analyzing and comparing chaperone function in vivo vs. in vitro.Simulating in vivo, or the environment within the cell, is important not just because of physical factors such as pH or temperature but also because the time in which the chaperone begins to conform the polypeptide. Some chaperones are nearby the ribosome and attach immediately to the polypeptide to prevent misconformation. Other chaperones allow the polypeptide to begin folding by itself and attach later on. Thus the role of each chaperone becomes specific to its vicinity to the polypeptide and time and place in which it assists folding. Recent research has implicated that chaperones within the nucleolus not only catalyze protein folding but also catalyze other functions important to maintain a healthy cell. These nucleolar chaperones are called Nucleolar Multitasking Proteins (NoMP's). Heat shock proteins, for example, not only help other proteins fold but also act during moments of stress to regulate protein homeostatis. Furthermore, there is evidence that chaperones work together in networks to oversee certain functions like dealing with toxins, starvation or infection.

The nucleolar chaperone network is divided into different branches that have specific functions. The network is dynamic and can vary in concentration or location of the network components depending on changes in the physiology and environment of the cell. Heat shock proteins (HSPs), which are classified based on their molecular weights, are integral components of the chaperone network. HSP 70s and 90s maintain proteostasis by ensuring that proteins are properly folded and preventing proteotoxicity, which is the damage of a cell function due to a misfolded protein. HSP70s help to fold recently synthesized proteins, while HSP90s help later in the folding process. The nucleolar network also contains chaperones that are part of ribosome biogenesis, or the synthesis of ribosomes in the cells. Proteins in the HSP70 and DNAJ families, which help to process pre-rRNA, are regularly found in protein complexes that process pre-rRNA in Saccharomyces cerevisiae (a species of yeast). Other HSPs are important in ribosome biogenesis as well, including HSP90 which works together with TAH1 and PIH1 to create small nucleolar ribonucleoproteins. The nucleolar chaperone network provide the organization and assistance needed to complete the biological taks necessary for cell survival, and if it does not function properly there can be many problems. For instance, when cancer cells have increased levels of rRNA synthesis, ribosome biogenesis is increased. Scientists are researching the compound CX-3543, which can stop nucleolin from binding with rDNA and impede RNA synthesis, leading to cell death. It is possible to potentially use drugs designed to target specific branches of the nucleolar chaperone network in malfunctioning cells. Other networks of chaperones include networks that specifically participate in de novo protein folding, meaning they help to fold newly made proteins, and the refolding of proteins that have been damaged. One chaperone network that exists in tumor cell mitochondria contains HSP90 and TRAP1, which protect the mitochondria and prevent cell death, allowing the cancer cells to continue to spread uncontrollably.[9]

HSP 70 is a protein in the Heat Shock Protein family along with HSP 90. It works together with HSP 90 to support protein homeostasis. It binds to newly synthesized proteins early in the folding process. It has three major domains, the N-terminal ATPase domain, the Substrate binding domain, and C-terminal domain. The N-terminal ATPase binds and hydrolyzes ATP, the substrate binding domain hold an affinity for neutral, hydrophobic amino acid residues up to seven residues in length while the c-terminal domain acts as a sort of lid for the substrate binding domain. This lid is open when HSP 70 is ATP bound and closes when hsp 70 is ADP bound. HSP70, or DnaK, are bacterial chaperones and can help in folding by clamping down on a peptide.[10]

GroEL and GroES, or 60kDa and 10kDa, are both bacterial chaperones. Both GroEL and GroES are structured so that they are a stacked ring with an empty center. The protein fits in this hollow center. Conformational changes within the chamber can then change the shape and folding of the protein.[10]

HSP 90 is a protein in the Heat Shock Protein family. This particular protein, however, is different from other chaperones in that HSP90 is limited in the folding aspect of molecular chaperones. Instead, Hsp 90 is vital to study and understand because many cancer cells have been able to take over and utilize the Hsp 90 in order to survive in many virulent surroundings. Therefore, if one were to structurally study and somehow target Hsp90 inhibitors, then there could be a way to stop cancer cells from spreading. Furthermore, many studies have been performed in order to test whether or not the Hsp 90 chaperone cycle is driven by ATP binding and hydrolysis or some other factor. But after much research by Southworth and Agard, there was enough evidence to state that HSP90 protein could conformationally change without nucleotide binding but rather the stabilization of an equilibrium is the factor that will change the Hsp90 to a closed or compact or open state. The three conformations of the Hsp90 were found through x-ray crystallography and also through single electron particle microscopy and by studying the three-state conformational changes in yeast Hsp90, human Hsp90 and bacteria Hsp 90 (HtpG) it was clear that there are distinct conformational changes for specific species. Overall, Hsp90 is a chaperone that is more involved with maintaining homeostasis within a cell rather than the involvement of protein folding. Hsp90 has rising potential in the area of drug development in the future since it plays such an essential role in aiding the survival for cancer cells.

This is the first chaperone to interact with the nascent chain as it exits the ribosome tunnel. Without the nascent chain, the TF cycles on and off but once the nascent chain is present, it binds onto the chain, forming a protecting cavity around. In order to do its function, TF scans for any exposed hydrophobic segment of the nascent chain and it can also re-associate with the chain. Folding is found to be more efficient in the presence of the TF, however, this is done at the expense of speed, it can stay with the chain for more than 30 seconds. The release of the chain is triggered when the hydrophobic portions is buried as the folding progresses toward the native state.

YidC, Alb3, and Oxa1 are proteins that facilitate the insertion of proteins in the plasma membrane. YidC is a protein that has only two polypeptide chains. The formation of its structure has been supported by particular phospholipids. YidC proteins can be found in Gram-negative and Gram-positive bacteria. Oxa1 can be found in the inner membrane of the mitochondria. Alb3 locates in the membrane of the thylakoid inside the chloroplast. Experiments showed that YidC protein actively contributes to the insertion of Pf3 coat protein. In addition, YidC also has direct contact with the hydrophobic segment of Pf3 coat protein. Although Oxa1 can only be found in the mitochondria it can also facilitate the insertion of membrane proteins in the nucleus. The role of YidC and Alb3 seems to be interchangeable because Alb3 can replace YidC in E. coli. Moreover, YidC, Oxa1, and Alb3 all support the insertion of Sec-independent proteins. Oxa1 only supports the insertion of Sec-independent proteins because the mitochondria in yeast cell do not have Sec proteins.

Nucleotide-binding domains that are leucine- rich (NLR) provide a pathogen-sensing mechanism that is present in both plants and animals. They could either be triggered directly or indirectly by a derivation of pathogen molecules via elusive mechanisms. Researches show that molecular chaperones like HSP90, SGT1, and RAR1 are main stabilizing components for NLR proteins. HSP90 can monitor the function of its corresponding clients that apply to NLR proteins in three practical ways: promotion of steady-state of functional threshold, activating stimulus-dependent activity, and raising the capacity to evolve.

Plants contain many NLR genes that considered being polymorphic in the LRR domain in order to be familiar with the highly diversified pathogen effectors. The NLR sensor stability will be the mechanism that will determine the pathogen recognition. The HSP90 system is advantageous for plants because it will couple metastable NLR proteins and stabilize them in a signaling competent condition. This will allow for the masking of mutations that would be detrimental.

It is known that chaperones work together to aid in the folding of protein in order to prevent misfolding. However, the mechanism of how chaperones help in protein folding was not fully understood. Recent studies on Hsp40 and Hsp70 have provided more insights into the mechanism of chaperones and their substrate. The Hsp40 family consists of many Hsp40 with different J-domain. Different J-domain will carry out different Hsp70 ATPase activities when Hsp40 binds to Hsp70. In protein folding, an unfolded polypeptide binds to a Hsp40 co-chaparone. From there, the J-domain of Hsp40 binds to the nucleotide-binding domain (NBD) of Hsp70. A conformation change in the Hsp70 substrate-binding domain occurs when the hydrolysis of ATP to ADP takes place on the HSP70 NBD. This causes Hsp70 to have a higher affinity for the polypeptide substrate and unbind the substrate from Hsp40. When ADP is exchange for ATP, the polypeptide substrate is released from Hsp40. Studies have shown that nucleotide exchange factors make changes to the lobe on the Hsp70 ATPASE domain in way that decreases Hsp70s affinity for ADP. Once the polypeptide is released from Hsp70, it can fold to its native state or it can be refolded by the chaperones if there is a misfolding. If a polypeptide that is bounded to Hsp70 is recognized by E3 ubiquitin ligase CHIP, it will be degraded.[11]

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Food for the soul: Traditional gyza makers and eaters in Utsunomiya try to keep the dumplings rolling – The Japan Times

UTSUNOMIYA, TOCHIGI PREF. Albert Kuwano Bakonyvari beckons me inside his factorys steam chamber, where hundreds of plump, white, crescent-shaped gyza dumplings are neatly lined on stacks of trays fitted in steel racks, waiting to be sent to the freezer.

Want to try one? I bet you havent eaten gyza at this stage of production, says the tall Hungarian-American with a goatee.

As I bite into the chewy dough, the warm juice from the ground meat and finely chopped cabbage, chives and leeks spill into my mouth as the scent of garlic hits. Unlike some of the gyza Ive had in Tokyo eateries, its surprisingly flavorful even without dabbing it in the typical soy sauce, vinegar and chili oil (ryu) combination, a characteristic I later learn is part of what defines the gyza made in Utsunomiya, Tochigi Prefecture, where some restaurants advise against the overuse of condiments to avoid killing the flavor of the dumplings.

Weve put a lot of time and energy into the dough and I think the texture of our gyza is unique its firm but its delightful to eat at the same time, it doesnt fall apart but still has a softness, Kuwano, 54, says.

For the filling of the gyza, we use domestic ingredients. The meat, leeks and chives are from Tochigi Prefecture. We use garlic from Aomori Prefecture and cabbage from the Kanto area. We try to keep the flavor relatively simple so the taste of the vegetables can shine through.

This is the heart of gyza country, at the gyza capital of Japan that boasts the highest annual household expenditure on the finger-sized dumplings.

A successful branding campaign led by the city and local gyza restaurants and makers, combined with word-of-mouth recommendations and media exposure, has made Utsunomiya synonymous with the comfort food. Its a studied example of machiokoshi (town promotion), so successful, perhaps, that protecting the brand has become an occasional source of contention.

AQ Foods, founded by Hisashi and Ayako Kuwano in 1965 as Eikyu Shokuhin, has been running one of the citys largest wholesale gyza businesses, with its products being distributed to department stores and supermarkets across the nation. While the couple is now in semi-retirement, the business was handed down to their son-in-law, Albert, who arrived in Japan in 1991 and married the Kuwanos only daughter.

AQ now produces more than a dozen varieties of gyza and manj dumplings, with its flagship product being a hand-made jumbo gyza that weighs 50 grams more than double the size of a regular gyza.

You cant make quality gyza of that size using machines. Perhaps 35 grams is the limit, says Koichi Chiba, the manager of one of AQs factories in Utsunomiya, a land-locked city with a population of around 520,000. In an age of automation, Chiba says AQ is a rarity in that it still produces hand-made gyza alongside the machine-made variety.

A former itamae chef and a relative of Ayako Kuwano, Chiba and his brother joined AQ around two decades ago. The two apprenticed under the founding couple, with Chiba specializing in the art of making a balanced, flavorful filling that has just the right amount of salt, while his brother oversees the production of gyza wrappers from scratch.

For the jumbo gyza, we have people wrapping them individually and packing them in containers to be shipped, he says. Gyza this size requires real people folding the pleats to seal them. Its not a skill that can be learned overnight, he says, typically taking three months of training before the technique is mastered.

Gyza is made all over Japan, but the ones made in Utsunomiya are the best and I strive to improve our product everyday so I can say ours is No. 1.

Gyza traces its roots to Chinas jiaozi dumplings, which are thought to have originated during the Tang Dynasty (618-907), according to Hideaki Otsuka, a Tsukuba University researcher and expert on Chinese culture.

Dried jiaozi (mummified jiaozi, so to speak), had been excavated from the ruins of Dunhuang. Scholars were surprised to learn that a food so similar to todays jiaozi, with the typical features of the folded dumpling with pleats, a semicircular shape and pointed edges, was eaten in the Tang Dynasty (618-907), he said in a lecture he delivered at a food culture seminar hosted by soy sauce manufacturer Kikkoman Corp.s Tokyo headquarters.

Otsuka says an Edo Period (1603-1868) cookbook introduced three cooking methods for gyza deep-frying, pan-frying and steaming but at the time it was still seen as a Chinese dish and was not a common food.

Chinese cuisine, including jiaozi, began to be served in the Chinatowns of Yokohama, Kobe and other cities during the Meiji Era (1868-1912), but gyzas status wasnt elevated to that of fast food of choice until after World War II, when the repatriation of many Japanese from mainland China who were used to eating jiaozi sparked a gyza boom. But whereas boiled jiaozi is common in China, its birthplace, pan-fried gyza became the norm in Japan.

The first gyza restaurant in Utsunomiya is believed to have opened near Utsunomiya Station in 1952, followed by the predecessor to famed gyza chain Minmin. Other legendary gyza houses that still serve to this day followed, including Masashi and Koran.

Its unclear why gyza shops concentrated in Utsunomiya, although it may have to do with how the city produces many of the dishs essential ingredients of gyza, including pork, flour, cabbage and chives. In any case, Utsunomiya residents embraced the dumplings since 1987, when the then-Management and Coordination Agency began including foodstuff in its annual survey of consumer habits, the city has been repeatedly ranked as the nations top gyza consumer despite the fact that the results excluded gyza eaten in restaurants. The survey is based on average annual expenditure per household on ready-made gyza bought and taken home from supermarkets and gyza restaurants. That means if the figure included gyza consumed at the numerous gyza restaurants dotting the city, the number will likely be substantially higher.

An Utsunomiya city official saw the stats and came up with a plan to promote gyza as a tourist attraction, says Hoshimi Kawazu, a spokeswoman for the Utsunomiya Gyoza Association, an organization formed in 1993 with 38 gyza restaurants. The group became a cooperative association in 2001, and now boasts more than 90 gyza eateries and manufacturers as members.

Until gyza became Utsunomiyas buzzword, the primary tourist draw was the Oya stone mine, Kawazu says, but the quarry that once supplied the Oya stone used for numerous structures in Japan collapsed in 1989, and the city needed an alternative attraction.

In 1993, a TV Tokyo variety show ran a series of programs on Utsunomiyas love affair with gyza. Coupled with the launch of an annual gyza festival and the erection of the Venus of Gyza statue in 1994, Utsunomiya and its culinary pride were soon pushed into the national spotlight.

Utsunomiyas decades-long battle with rival Hamamatsu, Shizuoka Prefecture, over the title of No. 1 gyza-consuming city has also become an annual media event. Hamamatsu beat Utsunomiya in 2018, with households spending an average 3,501 annually on gyza, compared to 3,241 in Utsunomiya.

Until I moved to Utsunomiya 10 years ago, I wasnt aware how much gyza is a part of peoples lives, Kawazu says. I also think what distinguishes us from other regional revitalization projects is how we work hand in hand with the city office.

As the associations influence grew, however, it also began implementing stronger measures to protect its brand. The Utsunomiya Gyza Association was trademarked in 2001, followed by Utsunomiya gyza being trademarked in 2002. These actions were aimed at clamping down on low-quality gyza calling themselves Utsunomiya gyza despite being produced and sold in other prefectures, Kawazu says.

Legal action ensued over the usage of the brand name, and association members were asked to follow strict orders when utilizing the trademarked brand.

In 2017, the operator of Utsunomiya gyza chain Umaiya which isnt a member reached a settlement with the association after being sued for using Utsunomiya gyza in its logo. Umaiya offered to take down the word ganso, or original, from its product logo and apply for membership.

Then in May, Kuwanos AQ Foods was removed from the gyza association, despite being one of the oldest gyza manufacturers in the city.

We were asked to join the association to promote Utsunomiya gyza and make it a thing, Kuwano says. We had already been selling it all over the country as Utsunomiya gyza, and the founder of the association knew that and was eager for us to join since he wanted to use our connections.

For a long time, the partnership was fruitful, Kuwano says, as Utsunomiya cemented its status as the gyza mecca, drawing hordes of hungry tourists.

Unfortunately, all good things like that end up having people with different priorities, and eventually the association started to control the name of Utsunomiya and a lot of our salespeople who used to sell our products as Utsunomiya gyza were not allowed to do that anymore. The association started to say the name should only be used in Utsunomiya and not around the country, whereas our business is promoting it all across the country.

We just had very different paths that we ultimately took, so yeah, were not part of the association anymore.

Without discussing specific issues, Kawazu of the gyza association says these rules are aimed at controlling quality and to prevent outside makers from using the brand to lure customers.

Utsunomiya gyza is such a broad term that it makes it difficult to trace who the producer is when issues surface if its used indiscriminately.

Dumplings are universal, as seen in their many variations, including the South Asian samosa and momo, and European pierogi and ravioli, says Izumi Kitta, a voice actress and gyza specialist who also serves as a special ambassador for Utsunomiya gyza.

So, in a sense, it was only natural for it to acquire comfort food status in Japan, she says, adding that she believes Utsunomiyas public relations campaign helped raise its national prominence.

Kitta, who is currently studying in the United Kingdom, says there were times she would eat gyza three times a day back in Japan. I think I was eating around 400 meals of gyza in 365 days, she says. Now that she lives in England, she goes out hunting for restaurants serving gyza and hosts gyza parties with friends. It made me want to spread the gospel of gyza across the world, she says.

Gyza has come a long way from its humble beginnings to become firmly embedded in Japans culinary psyche. For Hisashi and Ayako Kuwano, their encounter with gyza was life-changing.

Hisashi, 82, met Ayako, 84, when he was employed as a chef at a Japanese restaurant in Ishinomaki, Miyagi Prefecture. The two soon fell in love and ran off together to Tokyo, where Hisashi hopped around eateries. They ran a food stall, and at one point even cruised around the capital selling fish on a bicycle, but decided to settle down in Tochigi Prefecture, where Hisashi hails from, when their daughter was born.

The couple opened a restaurant in Utsunomiya in 1963 that served popular standard fare such as ramen and chhan fried rice. One of the regulars was a factory manager for Utsunomiya-based ice cream maker Futaba Foods Co. who suggested the restaurant serve frozen gyza dumplings Futaba was making to compensate for the fall in ice cream sales during the winter season.

However, Futaba would halt the production of frozen gyza once spring came, so we decided to make our own to satisfy our customers needs, Ayako says. The couples gyza was a hit, and they eventually began selling them to other restaurants, and later established a factory.

It wasnt all smooth sailing, however, and at one point the business was on the verge of collapsing when the price of cabbage soared.

We fell from the mountaintop to the bottom of the canyon, Ayako says. My husband suggested we get a divorce so I wont have to be burdened by debt, but I couldnt imagine my family being separated. In the end, we somehow managed to crawl back up.

The business persevered, and the number of employees grew. Albert, a California native, married the Kuwanos daughter in 1997 and later took over the gyza business.

I think my father-in-law stumbled upon the perfect product because gyza has every major food group you get your carbs, protein, vegetables and it happens to taste very good, Albert says. Its very satisfying but not expensive, so it kind of hits every point.

In 2012, Kuwano launched a craft beer importing business called AQ Bevolution, and opened the Titans Craft Beer Taproom & Bottle Shop in Tokyos Otsuka neighborhood to showcase the beer the company imports and, guess what? AQ Foods gyza.

We have our gyza and beer at one location, Kuwano says. And, as you may know, gyza and beer go well together.

The laid-back American may be an unlikely heir to a Japanese family-run gyza business, but Ayako and Hisashi appreciate his efforts to keep the company going despite the occasional ups and downs.

Asked whether he had any reservations having a foreign national marry their only daughter, Hisashi shakes his head.

Really? Ive heard you didnt want her to marry a gangster or a foreigner, Albert quips.

Hmm, perhaps, Hisashi says with a grin, his eyes wandering as if to recall a distant memory. However, he doesnt forget to add, Were grateful to have you.

Read the rest here:

Food for the soul: Traditional gyza makers and eaters in Utsunomiya try to keep the dumplings rolling - The Japan Times

Molecular Biology 02: ‘Thermodynamics of protein folding’

These are my notes from lecture 02 of Harvards BCMP 200: Molecular Biology course, delivered by Joe Loparo on September 5, 2014.

Continued from lecture 01. is always 0 or +180. If you plot and you find only a few clusters are well-represented: a range of -helix combinations, a -sheet area, and a third rarer area (called L and populated by left-handed -helices). is ususally found in the trans conformation due to steric hindrance of the consecutive side chains, however, proline because it is anchored to the backbone has a unique twist that enables a cis conformation.

-helices and -sheets are two ways of allowing the NH and C=O groups on the backbone to form hydrogen bonds. -helices contain 3.6 residues per rotation, or in other words, each residue spans 100 of rotation. Consecutive rungs of an -helix turns are separated by 5.4. -helices are almost exclusively right-handed. In a right-handed -helix, you turn counter-clockwise as you go up. In a left-handed -helix you turn clockwise as you go up. Side chains point outward from the helix. If you plot out where each residue falls on the helix based on the 3.6 residues/turn rule, you find that amphipathic, half-buried helices have all the hydrophobic residues on one side and the hydrophilic ones on the other side. A fully buried helix will be all hydrophobic residues and a fully exposed helix will be all hydrophilic residues.

In -sheets, all potential H-bonds are satisfied except for the flanking strands at either end of the sheet. About 20% of -sheets found in nature are mixed parallel and anti-parallel, the other 80% are pure one or the other. -sheets are not flat, but pleated.

A single sheet or helix is not stable in water. Tertiary structure is the packing of these elements, and loops connecting them, onto each other.

There are two fundamental problems in protein folding:

As an example, consider the metalloprotease cleaveage of Notch to create the Notch intracellular domain (NICD), which then translocates to the nucleus and affects transcription. The proteolytic site of Notch is protected by Lin12/Notch repeats which are connected to the EGF repeats that interact with Notchs ligand. The ligand is believed to apply a force that unfolds this region, allowing cleavage. Mutations which destabilize this fold and result in constitutive activation cause tumors.

Thermodynamics can only describe whether a chemical reaction will occur spontaneously or not, not how fast it will occur (see Biochemistry 01).

The energy of a system is its capacity to do work.

U = q + w

Where U is internal energy, q is heat and w is work.

q := heat = C(Tf-Ti)

Where C is the heat capacity and f and i mean final and initial.

w := work = Fxx

Where F is force and x is displacement along the x axis.

If you dissolve urea in water at a 4M solution, it will dissolve spontaneously and the solution will become cold (just like guanidine, as I learned here).

Gibbs free energy is defined as:

G = H - TS

Where G, H, T and S are Gibbs free energy, enthalpy, temperature and entropy respectively.

G = H - TS

If G < 0 the reaction will proceed spontaneously.

In the urea example, H > 0 because energy is required to pull apart the interacting urea molecules, using heat from the water. Yet the reaction still occurs spontaneously because S > 0 by a lot - the urea solution is much more entropic than urea and water separately.

For the reaction A + B C + D, we define:

Keq = ([C]eq[D]eq)/([A]eq[B]eq)

Keq = e-G/RT

ATP is a special molecule: its hydrolysis into ADP is spontaneous at physiological concentrations of the reactants and products, i.e. G < 0 for this reaction:

ATP + H2O ADP + Pi

Le Chateliers principle says you could drive the reaction in reverse, making ATP spontaneously, simply by increasing the concentrations of the procuts. However [Pi] never gets high enough in the cell for ATP to be spontaneously generated from ADP. The unfavorable production of ATP is instead created via a coupled reaction with favorable reactions such as the release of protons across the mitochondrial membrane (see Biochemistry 08).

H := Enthalpy = U + PV

Where U, P and V are internal energy, pressure and volume.

In physiological conditions, changes in pressure and volume are almost always negligible, so H and U are closely coupled. In other words, in most biological systems, the enthalpy is equal to the internal energy.

People have developed molecular dynamics simulations of the fundamental atomic forces that determine a proteins enthalpy (dihedral angles, Van der Waals interactions, electrostatic interactions, etc) and attempt to minimize the energy to determine a proteins fold. But there are so many degrees of freedom that computational expense prohibits running the simulation long enough to find the lowest energy state. Still there are attempts, such as Folding@Home, Foldit, and D.E. Shaws Anton. Anton holds the record for the longest molecular dynamics simulation - it ran for some untold amount of time, calculating the energy a protein would have at every femtosecond or something, in order to simulate 1 millisecond of the proteins movement. Obviously, the time that Anton took to simulate that millisecond was more than a millisecond.

S := Entropy = kbln(W)

Where kb is Boltzmanns constant and W is the number of microstates that give rise to the macrostate of interest.

My favorite explanation of this is that given by Richard Feynman. When I read it, I understood for the first time how physical entropy and information entropy are the same concept:

So we now have to talk about what we mean by disorder and what we mean by order. Suppose we divide the space into little volume elements. If we have black and white molecules, how many ways could we distribute them among the volume elements so that white is on one side and black is on the other? On the other hand, how many ways could we distribute them with no restriction on which goes where? Clearly, there are many more ways to arrange them in the latter case. We measure disorder by the number of ways that the insides can be arranged, so that from the outside it looks the same. The logarithm of that number of ways is the entropy. The number of ways in the separated case is less, so the entropy is less, or the disorder is less.

Richard Feynman, quoted here

In biology, entropy is very often the driving force, for instance for the burial of hydrophobic protein domains. Imagine a water molecule in a tetrahedron. The tetrahedron has four corners, and the water has two hydrogens, so you can place the molecule in 4 choose 2 = 6 orientations. If you add a nonpolar group of a neighboring molecule at one corner of the tetrahedron, only three of the six states remain favorable (by still allowing hydrogen bonding). So Shydrophobic = kbln(3) - kbln(6) < 0, meaning that entropy has decreased.

Consider the mixing of epoxy and hardener into cured epoxy. This reaction has S < 0 because the solid has fewer microstates than the liquids did. Yet the reaction occurs spontaneously at room temperature, so it must be true that H < 0. Heat is therefore released - in fact, the reaction is extremely exothermic. Joe measured the temperature of 5-minute epoxy and it rose from 21C to >40C at the 5 minute mark.

An incorrect and simplistic view of protein folding is as follows. An unfolded protein has high configurational entropy but also high enthalpy because it has few stabilizing interactions. A folded protein has far less entropy, but also far less enthalpy. There is a tradeoff between H and S here. Note that because G = H - TS, increased temperature weights the S term more heavily, meaning that higher temperature favors unfolding.

That entire explanation only considers the energy of the protein and not that of the solvent. In fact, hydrophobic domains of a protein constrain the possible configurations of surrounding water (see explanation above), and so their burial upon folding increases the waters entropy. Moreover, it turns out that the hydrogen bonding of polar residues and the backbone is satisfied both in an unfolded state (by water) and in a folded state (by each other). Therefore enthalpy is zero sum, and protein folding is driven almost entirely by entropy.

Here is a description of a technique called differential scanning calorimetry. You apply equal amounts of heat to two solutions, one with only buffer and the other with buffer and protein, and you measure the temperature in each solution. Eventually the protein reaches its melting temperature Tm, where the protein is 50% folded and 50% unfolded and G = 0. At Tm, the melting of the protein aborbs lots of the applied heat, and so the temperature does not rise as much as it does in the buffer-only solution.

Another technique for measuring protein stability is the force required to unfold it using single molecule atomic force microscopy.

Common denaturants are urea and guanidine hydrochloride. Amazingly, we still do not know how they work. It is thought that they stabilize all constituent parts of the unfolded protein. Guanidine may surround those unfavorable hydrophobic domains of the protein but then expose its own hydrophilic side to water, so that the movement of the water is not constrained.

Continued here:

Molecular Biology 02: 'Thermodynamics of protein folding'

Geroscience and it’s Impact on the Human Healthspan: A podcast with John Newman – GeriPal – A Geriatrics and Palliative Care Blog

Ok, I'll admit it. When I hear the phrase "the biology of aging" I'm mentally preparing myself to only understand about 5% of what the presenter is going to talk about (that's on a good day). While I have words like telomeres, sirtuins, or senolytics memorized for the boards, I've never been able to see how this applies to my clinical practice as it always feels so theoretical. Well, today that changed for me thanks to our podcast interview with John Newman, a "geroscientist" and geriatrician here at UCSF and at the Buck Institute for Research on Aging.

In this podcast, John breaks down what geroscience is and how it impacts how we think about many age-related conditions and diseases. For example, rather than thinking about multimorbidity as the random collection of multiple different clinical problems, we can see it as an expression of the fundamental mechanisms of aging. This means, that rather than treating individuals diseases, targeting aging pathways may be a better way to prevent or ameliorate multimorbidity. We talk with John about this, and current trials underway to test this hypothesis, along with so much more!

If you're interested in taking a deeper dive in the subject, take a look at these papers that John co-authored:

You can also find us onYoutube!

Listen to GeriPal Podcasts on:

Alex: This is Alex Smith.

Eric: Alex, we have someone in our studio audience ... our office studio? Our studio-

Alex: Our office studio? We have John Newman, who's a geriatrician and geroscientist-

Eric: A gero-what?

Alex: A geroscientist-

Eric: A gero-what?

Alex: A geroscientist who has held a joint appointment between UCSF and the Buck Institute for Aging Research. Welcome to the GeriPal PodCast, John.

John: Thanks, guys. Thanks, Alex. Thanks, Eric.

Eric: I'm really interested in figuring out what a geroscientist is. But before we do that, can we have a little song request for Alex?

John: Yeah, what should we sing about? Do you know a little song called Who Wants to Live Forever?

Alex: Ah, more Queen.

Eric: Boy, you can never get enough Queen.

Alex: Maybe our audience can. (singing).

Eric: John Newman does, right? John Newman wants all of us to live forever. At least that's why I am currently, those who are watching this on YouTube, can see I am getting fresh stem cells from my baby farm that I get infused every day, so I can live forever.

John: We're transfusing you as we speak.

Eric: As we speak.

John: As we speak.

Eric: Yeah, I give John hefty amounts of money for those baby transfusions.

John: Hey, that deal's just for you, Eric. Don't go advertising me.

Eric: So John, geroscience. What is this field, and is it about living forever?

John: It is not about living forever. It's about living healthier, longer, and staying independent. So what is geroscience?

Eric: That, I have no idea.

Alex: That's, I don't know.

John: I thought I was here, so you guys would tell me.

Alex: Gero ... Gero-

Eric: Gero- so, older.

Alex: Ger, Jerry, Ben and Jerry's.

John: Aging ... aging science.

Alex: Aging science.

John: Aging science with a flavor of people.

Eric: So what is the difference between you and Alex? You're both researchers. Is Alex a geroscientist?

John: Well, geroscience is a, it's a made-up word which was coined for a new field, and a whole new idea, which is now reality. Which is going to sound a little crazy. Taking what we know about the biological mechanisms that drive aging. The biology of aging.

John: And not only understanding that, which itself sounds a little crazy. But actually turning that into therapies, to help to treat or prevent disease, or help to improve the lives, especially of older adults.

John: Geroscience is the idea of translational geriatrics, taking what we know about the basic science of the processes that drive aging. And turning it into therapies and helping to improve people's lives.

Eric: The processes that ... Okay. As I age, I start developing some chronic medical conditions. They start building up. I have more and more medical conditions. If only I could just focus on making sure I don't develop those, or I treat these well; like diabetes, COPD. Would I prevent aging? Is that the goal here?

John: Well, one place this comes from is, what's that common underlying factor that's putting you at risk for COPD and for diabetes and for Alzheimer's disease and for cardiovascular disease and for strokes? And for osteoarthritis and osteoporosis? And for almost everything that we treat.

Eric: Nacho cheese Doritos?

John: That's a big one! That's a big one.

Eric: But there's more.

John: But what's the common variable for all of those? We call these age-related chronic conditions or age-related diseases.

Eric: Yeah.

John: Because they're all driven by aging. The key thing is that's not an accident or it's not just like a probability thing or it's not just time passing. But it's actually the biological mechanisms that change in our bodies as we get older that make us what we perceive as older. There's a biology there. And that biology puts you at risk for all these different chronic diseases.

John: You could try to treat or prevent all of these individually. But, if you're not changing, if you're not affecting the aging that's driving all of them, there's a limit to how far you can go with that, or how effective it's going to be.

John: You prevent diabetes, but you get cancer. You cure Alzheimer's disease, which would be amazing, but then you have a stroke. But if you intervene on the aging that's behind all of this, then maybe you can slow or delay or prevent all of these together. That's the great hope of geroscience.

Alex: Is delay or preventing aging ... Earlier, you said that it's not so much about living longer, as it is improving healthy years of life. And yet, but what you just said was, "delay or prevent aging." I'm a little lost there. Can you help me out?

John: Well, delay or prevent all of the diseases and conditions that are driven by aging. So, targeting aging as the underlying biology that causes or contributes to diabetes, dementia, cancer, heart disease, and all of that.

John: All of that might wind up helping you live longer; who knows. But that's not the goal.

Alex: Ah.

John: The goal is to be healthier for longer.

Alex: Oh.

John: To spend, so we all can spend more years independent and being able to do the things we want to do in a state of better health.

Alex: It's like the principle of the double effect. For those palliative care listeners, right, the primary ... right? We're relating the subject to you.

Alex: The primary intended target in the principle of double effect in palliative care is often opioids for pain relief. And yet, as a secondary effect, if the patient dies sooner, that's acceptable.

Alex: Your primary intended effect is to treat the disease that are associated with aging; the conditions that are associated with aging. As a secondary effect, if people end up living longer, then that's fine too. But it's not the primary target of geroscience?

John: I love that analogy. Living longer may wind up being a side effect of being healthier longer. But when you talk about ... Aging is a weird subject, right? Because it's this, it's not a disease. It's not a bad thing. There are many many positive elements of aging. I am happier now than I was 20 years. Hopefully I'll be even happier 20 years from now, even if I can't jump as high.

John: Aging is not a disease. It's not a bad thing. And yet we're trying to target, almost to treat it. The goal is if we can slow or reduce the bad aspects of aging, the parts of aging that give rise to chronic disease. And you're living healthier longer, you'll probably live longer, too, in good health.

John: When I go to a room and I ask people, "We're talking about aging as a target for therapies. Who wants to live to be 200?"

John: Not a whole lot of people raise their hands, because most of them are thinking, "I'm not sure how I'm going to feel when I'm 95 or 85 or 75. You extrapolate that out, and what am I going to feel like when I'm 200?"

Alex: Right.

John: That doesn't seem like a great choice. But if you ask people, "What if you could have the health that you have now, or the health that you had when you're 60, or the health you had when you're 50? And just keep that for longer?"

Alex: Uh-huh.

John: Most people would volunteer for that.

Alex: Interesting.

Eric: I just want to make sure that when you ... When I hear "aging," I think probably the common definition is, I'm getting older.

Eric: When you hear the word "aging," what do you mean by aging? Especially as we're targeting aging? I can't target the clock; I guess I could target my clock and just turn it around. What do you mean when you say "aging"?

John: Well, here's the geriatrician's perspective. How do we know what "old" is, what an older adult is, for making a clinical decision, for example?

Eric: Yeah.

John: For thinking about prognosis, for example. There's someone I know who's done a lot of work around prognosis and how to estimate someone's life expectancy.

Alex: I don't know who you're talking about [laughter].

John: Yeah, the name, it's right on the tip of my tongue. So how do we know? Of course, we know that someone's birthday doesn't really help a whole lot with that stuff. There's 85-year-olds who are very fit and active and healthy and young. And there are 85-year-olds who are not very young. What makes that difference?

John: In geriatrics, we think of things like functional assessments. Mobility and ADL function, idea function, frailty, trying to get that certain aspect of what does it mean to be older, to have an advanced stage of aging? Geroscience and aging biology is sort of the molecular reflection of that.

John: If we know that you have two 85-year-olds, and one of them needs help with ADLs, they're going to be at risk for complications from surgery. But not necessarily because they need help with ADLs, but because that reflects their biology. The stage of their aging.

Alex: Right.

John: We're learning more and more about what that biology really is.

Alex: Right.

John: Is it their telomeres, for example? Like Eric said earlier. Or how many senescent cells they have in their body. Or what is their NAD reserve? What is the state of their chronic inflammation? How are their proteins folding? What is their proteostatic resilience?

John: We're getting closer to be able to understand what all of these biological aspects are, so we can look at someone who we think, "Is this person an old 85-year-old or a young 85-year-old?" And know what their biology tells us.

Alex: I don't want to ... I mean, I don't want to belabor this point. But I know some of our listeners are probably skeptics. We have one skeptic, a nurse practitioner on our hospice and palliative care service. Patrice Villars. We mentioned we were doing this podcast.

Alex: And she said, "Is it," something along the lines of, "is it morally responsible to focus on helping people to live longer, given the current burden of climate change that humans are placing on the planet currently, much less if we were to live longer lives?"

John: I love that question. I love ... Aging is a really unusual field to study, because it's, again, it's not a disease. It's something universal that happens to all of us. That does make it a little bit different, and opens up these really interesting questions about not only how to study it, and what our goals should be; but also how to ...

John: If we have therapies that effectively target aging, target mechanisms of aging, who gets them? How do we decide how to use them? How do we decide who should have them and who doesn't get them? Is that different from the way that we decide who gets other treatments? These are really interesting questions.

Eric: In the work that you do, I'm guessing ... because I think this is a really fascinating thing to do, like if you extend the life, even 20 years, the ethical issues that come up. Even from a population density standpoint, can our earth even handle that? Then who gets all these treatments? In the field of geroscience, are there ethicists in that field, too, that are looking at these questions?

John: Yeah. This is a brand-new field, an emerging field. There are ethicists who are particularly thinking about these questions. Not very many, in the same way there's not very many clinician scientists who are helping to develop and study these therapies.

John: But there are people who are just starting to really think about, because these questions; even five years ago, this would have felt like a really academic philosophical kind of discussion. Therapies that target aging. Sure, let's maybe 10 years, 20 years down the line.

John: But the crazy thing is the first clinical trial that takes a drug in this case, that targets a cellular mechanism of aging, was given to older adults to treat a chronic syndrome of aging. That clinical trial, that first clinical trial has already been done.

Eric: What are they doing?

John: This was a drug that targets protein quality control. It's a drug called Rapamycin and its related drugs. We can talk about how this fits into the bigger scheme of mechanisms of aging. But it helps to activate pathways in your cells that clean up misfolded proteins and help your cells to make proteins that are more functional.

John: This drug and a related drug were first given to older adults before flu vaccine, to see if it would improve response to the flu vaccine. And it did. Then the next step, they did a clinical trial where they treated people with these drugs for just a month, and then gave them a flu vaccine, and saw that it improved their response to a flu vaccine.

John: But then over the next six months, they saw how often they got respiratory or other infections. What they actually found was that the people who received this treatment just for a month had about a third fewer infections over the next six months. So it had this really interesting long-lasting effect on their immune function in these older adults. It was helping to ameliorate what we call immunosenescence, the decline in function of our immune systems as we get older.

John: It's a really small, limited thing. One drug, some older people, flu vaccine, it was just looking at infections. Doesn't seem like a big deal, and it's not. Except it was the first randomized controlled trial of a drug like this that targets mechanisms of aging in older adults, to improve syndromes of older adults.

Alex: And it's already happened.

John: And it's already happened.

Eric: I guess that's probably the hard part with this is that I would imagine you can't do a randomized controlled trial with this drug for 20-year-olds and wait 90 years to see what happens to them. And then market that drug after a hundred years.

John: Exactly. I mean, hey, the average R01 lasts for five years.

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Geroscience and it's Impact on the Human Healthspan: A podcast with John Newman - GeriPal - A Geriatrics and Palliative Care Blog

Protein Folding – Anfinsen’s Experiment ~ Biology Exams 4 U

How Protein folds? During translation, the linear chain of amino acids formed will be gradually released from the ribosome, and these amino acids should fold properly to make a functional protein, the ultimate nano machines in the cells. Protein folding is undoubtedly the most critical events that determine the ability of that given protein to work properly.

How protein folds? Is it a random process? It shouldnt be, as folding determines the function.

Definition:

Protein folding refers to the set of ordered pathways by which protein folds into their native functional confirmation.

Protein folding is primarily driven by hydrophobic forces.

Anfinsen's Experiment

First step..

The first insight to this question was provided by Christian Anfinsen at the NIH. He was working on the properties of ribonuclease A (a single chain protein of 124 amino acids with 4 di-sulphide bonds). He unfolded (denatured) ribonuclease A using urea and mercaptoethanol (denaturants). The protein lost its function. Then he allowed to renature ribonuclease A by removing denaturants, and found out that ribonuclease A folded spontaneously and become functional. He concluded that Ribonuclease A can self assemble into its 3D functional structure.

Protein Folding inside the Cell

Inside the cell, protein folding is assisted by different proteins collectively called as accessory proteins.

The importance of studying protein folding?

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Protein Folding - Anfinsen's Experiment ~ Biology Exams 4 U

Protein Folding – an overview | ScienceDirect Topics

8 INHIBITORS OF HEAT-SHOCK PROTEINS (HSP 90)

Protein folding is catalysed in vivo by isomerases and chaperone proteins. Molecular chaperones are ubiquitous proteins that assist folding, assembly, transport, and degradation of proteins within the cell. The first identified chaperones were heat-shock proteins (HSPs), whose names is derived from the elevated levels produced when cells are grown at higher-than-normal temperatures. HSPs stabilize other proteins during their synthesis and assist in protein folding by binding and releasing unfolded or misfolded proteins using an ATP-independent mechanism. Proteins unable to maintain their proper shape are broken down by the proteasome (see Section 1 of Chapter 10) and eliminated, as shown in Fig. 9.33. These events may be favourable if the proteins are previously mutated and hence dangerous for the survival of the cell, but they become a problem if the proteins are necessary for its normal functioning.

Figure 9.33. Function of heat-shock proteins.

HSP 90 is the best known of HSPs and its activity is coupled to an ATPase cycle that is controlled by several cofactors. It has three major domains, namely a highly conserved N-terminal ATPase domain, a middle domain, and a C-terminal dimerization domain. The crystal structure of HSP 90 bound to ATP has shown how this nucleotide is hydrolysed,135 but the detailed mechanism of protein folding remains unknown.

HSP 90 has emerged as an attractive cancer target because its inhibition blocks a large number of cancer-related signalling pathways since a large number of intra-cellular signalling molecules require association with HSP 90 to achieve their active conformation, correct cellular location, and stability.136 These include steroid hormone receptors, transcription factors like the tumor suppressor protein p53 and kinases like Src-kinase.

The conformational changes that take place in HSP 90 after binding and hydrolysis of ATP regulate the stabilization and maturation of client proteins, including hypoxia-inducible factor-1 (HIF-1), a relevant anticancer target.137 This ATP site is known by X-ray crystallography to be very different from that of kinases, allowing the design of inhibitors with high selectivity with regard to other ATP-binding proteins.

The design and study of selective inhibitors of HSP 90 was initially controversial because this protein is critical for the survival of both normal and sick cells. However, HSP does not have much activity under normal conditions. When the cell is under stress by genetic mutations or environmental changes such as heat or infection HSP 90 activity is increased as an emergency response that stabilizes partially unfolded proteins and helps them to achieve their correct shape. This activity also assists the survival of cancer cells despite an abundance of misfolded and unstable proteins, and this is one of the reasons to study HSP 90 as an anticancer target.

The main strategy employed in the design of HSP 90 inhibitors is based in the synthesis of analogues of the natural antitumor geldanamycin, a benzoquinone derivative belonging to the ansamycin class, although some companies working in this field are designing entirely synthetic molecules not related to this compound.

Geldanamycin was originally believed to be a TK inhibitor, but it was later identified as an ATP-competitive inhibitor of HSP 90. It could not be advanced to the clinical stage because it showed unacceptable hepatotoxicity, probably associated with the presence of the electrophilic methoxybenzoquinone moiety. For this reason, displacement of the 17-methoxy group by nucleophiles led to less toxic analogues such as tanespimycin (17-allylaminogeldanamycin, 17-AAG).138 Another problem associated with geldanamycin is its very low solubility, which was solved with the development of the water-soluble analogue alvespimycin (17-dimethylaminoethylaminogeldanamycin, 17-DMAG).139 Both analogues were better tolerated than the parent natural product and are under clinical trials. In another approach, the problematic quinone moiety of 17-AAG was reduced to the hydroquinone stage. The resulting compound, IPI-504, can be formulated as a soluble salt that is suitable for intravenous or oral formulations. It has shown encouraging results in Phase I trials in patients with gastrointestinal stromal tumors that were resistant to imatinib, although further clinical development is necessary.

See more here:

Protein Folding - an overview | ScienceDirect Topics

Rett Syndrome Tied to Altered Protein Levels in Brain in Early Study – Rett Syndrome News

Lack of a functional MeCP2 protein leads toRett syndrome by altering levels of brain proteins associated with energy metabolism and protein regulation, a study in a mouse model suggests.

These altered protein levels might also predict Rett syndromes progression, the investigators said.

The study, Brain protein changes in Mecp2 mouse mutant models: Effects on disease progression of Mecp2 brain specific gene reactivation, was published in theJournal of Proteomics.

Rett syndrome is caused by mutations in the MECP2gene that result in a missing functional MeCP2 protein, a regulator of gene expression. Despite prior studies in animal models, little research has focused on the effects of MeCP2 deficiency in the levels of other proteins in the brain, as well as in Rett syndromes progression.

Researchers from Italy used a mouse model of Rett to address this gap. They did a proteomic analysis of the brains of mice both before and after they developed symptoms, and compared the data to controls withoutMECP2mutations. (Proteomics is the large-scale study of proteins, conducted to draw more global conclusions than possible if assessing proteins one-by-one.)

Results showed abnormal levels of 20 brain proteins in symptomatic mice with Rett syndrome. Twelve of these proteins were overproduced, while eight were at lower levels compared to non-diseased control mice.

Notably, eight (40%) of these 20 proteins were involved in energy metabolism (the process by which cells get energy), and six (30%) were involved in proteostasis, which refers to cellular processes to ensure proper production and folding of proteins.

Presymptomatic mice showed abnormal levels in 18 proteins; 10 at low levels and 8 at high levels compared to controls. Similar to symptomatic mice, these proteins were primarily involved in energy metabolism and proteostasis.

The team then looked at mice that had been engineered to turn the MECP2 gene on in the brain, which was associated with mild symptoms and a longer life than otherwise expected.

By comparing animals lacking functional MeCP2 to mice with so-called MECP2 gene reactivation, the researchers worked to identify the proteins most directly impacted by missing MeCP2.

They found 12 proteins whose levels were normalized by gene reactivation. Seven of these proteins were at low levels and five at high levels without functional MeCP2 protein. Again, most were associated with energy metabolism and proteostasis, while two proteins were involved in how cells respond to oxidants reactive molecules that can damage DNA and cellular structures that is called redox regulation.

Only two of these 12 proteins, PYL2 and SODC, had been previously associated with Rett syndrome via earlier animal model studies that recorded altered levels in the brain.

Our findings suggest that RTT [Rett syndrome] is characterized by a complex metabolic dysfunction strictly related to energy metabolism, proteostasis processes pathways and redox regulation mechanisms, the researchers wrote.

Alteration in the evidenced cellular processes, brain pathways and molecular mechanisms [suggest] the possibility of the use of proteins as predictive biomarkers, they added.

Marisa holds an MS in Cellular and Molecular Pathology from the University of Pittsburgh, where she studied novel genetic drivers of ovarian cancer. She specializes in cancer biology, immunology, and genetics. Marisa began working with BioNews in 2018, and has written about science and health for SelfHacked and the Genetics Society of America. She also writes/composes musicals and coaches the University of Pittsburgh fencing club.

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Rett Syndrome Tied to Altered Protein Levels in Brain in Early Study - Rett Syndrome News

Denaturation and Protein Folding | Introduction to Chemistry

Each protein has its own unique sequence of amino acids and the interactions between these amino acids create a specify shape. This shape determines the proteins function, from digesting protein in the stomach to carrying oxygen in the blood.

If the protein is subject to changes in temperature, pH, or exposure to chemicals, the internal interactions between the proteins amino acids can be altered, which in turn may alter the shape of the protein. Although the amino acid sequence (also known as the proteins primary structure) does not change, the proteins shape may change so much that it becomes dysfunctional, in which case the protein is considered denatured. Pepsin, the enzyme that breaks down protein in the stomach, only operates at a very low pH. At higher pHs pepsins conformation, the way its polypeptide chain is folded up in three dimensions, begins to change. The stomach maintains a very low pH to ensure that pepsin continues to digest protein and does not denature.

Because almost all biochemical reactions require enzymes, and because almost all enzymes only work optimally within relatively narrow temperature and pH ranges, many homeostatic mechanisms regulate appropriate temperatures and pH so that the enzymes can maintain the shape of their active site.

It is often possible to reverse denaturation because the primary structure of the polypeptide, the covalent bonds holding the amino acids in their correct sequence, is intact. Once the denaturing agent is removed, the original interactions between amino acids return the protein to its original conformation and it can resume its function.

However, denaturation can be irreversible in extreme situations, like frying an egg. The heat from a pan denatures the albumin protein in the liquid egg white and it becomes insoluble. The protein in meat also denatures and becomes firm when cooked.

Chaperone proteins (or chaperonins) are helper proteins that provide favorable conditions for protein folding to take place. The chaperonins clump around the forming protein and prevent other polypeptide chains from aggregating. Once the target protein folds, the chaperonins disassociate.

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Two years in the making, Pizza Hut tests a round pizza box – Fast Company

This week, Pizza Hut is using one Phoenix location to test two innovations. First up is a trial of plant-based Italian sausage as a pizza topping on a Garden Specialty Pizza, complemented by banana peppers, onions, and mushrooms. The sausage is made by Kelloggs incomparably named Incogmeato brand. Pizza toppings made from plant-based meat are still rather novel; in the United States, only Little Casears has tested an Italian sausage crumble from Impossible last spring.

But while the protein may top a lot of the headlines, the real potential for change is in its second move here: a round pizza box.

According to Pizza Hut,the new box keeps pizzas crispier, and it relies on less overall packaging compared with a typical square pizza box. The companys chief customer and operations officerNicolas Burquier says Pizza Hut worked with the startup Zume, best known for robotic pizza trucks, for more than two years on this design.

The goal was to design a box that simply makes our pizza taste even betterhotter pizza, crispier crust, says Burquier. This box will improve the pizza-eating experience for our customers and simplify operations for our team members.

The new round box has grooves to help catch grease and prevent soggy crust, and the top latches to keep heat in. It also interlocks easily to stack compactly, cutting out the employee effort that typically must be devoted to folding pizza boxes.

It may be innovative, but Pizza Hut is hardly the first to cut the corners off its pizza boxes. Back in 2010, Apple actually filed a patent for a round pizza box of its own, then touted it in a fun, three-minute ad called The Underdogs back in April.

In 2018, sustainable packaging company World Centric unveiled its own version of the round box. And even way back in 2004, a round pizza box called the Presseal was introduced by an inventor named John Harvey. None managed to catch on at a scale that even comes close to threatening the dominance of the almighty square.

ButBurquier is confident that could change.

One day in the future well reminisce about the idea of round pizzas in square boxes and laugh,says Burquier. The company plans to evaluate how the limited rollout in Phoenix goes, and look for ways to expand it across the country.

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Two years in the making, Pizza Hut tests a round pizza box - Fast Company

Insights into Parkinson’s Onset May Lie in New Model of Cell Aging and Damage – Parkinson’s News Today

A newly created model helps to clarify the processes by which cells grow old and die, and which are known to be involved in the onset of neurodegenerative disorders likeAlzheimers and Parkinsons disease.

The study describing this model, Proteostasis collapse is a driver of cell aging and death, was published in PNAS.

To remain healthy, cells must be able to produce proteins and chaperone them: keeping proteins correctly folded, and destroying those that arent.

But as cells age, oxidative stress an imbalance between reactive and inflammatory free radicals andthe ability of cells to detoxify them slowly leads to the accumulation of irreparably damaged proteins inside cells that eventually overwhelm their quality control mechanisms.

Irreparably damaged proteins accumulate with age, increasingly distracting the chaperones from folding the healthy proteins the cell needs. The tipping point to death occurs when replenishing good proteins no longer keeps up with depletion from misfolding, aggregation, and damage, the researchers wrote.

Investigators with the Laufer Center for Physical & Quantitative Biology at Stony Brook University created a model that is able to predict the lifespan of the round worm Caenorhabditis elegans, an animal model often used in aging studies, based on its protein quality controlmechanisms.

In their study, scientists showed their models predictions matched the results of experiments they performed on round worms to assess the effects of oxidative damage on the animals lifespan.

In one experiment, they found that animals raised at a temperature of 20 degrees Celsius (about 68 degrees Farhenheit) had an average lifespan of 20 days. Worms were raised at higher temperatures and in the presence of free radicals (byproducts of oxidative stress), however, had lifespans of only a few hours.

As the cell is stressed by heat, proteins unfold, misfold, and aggregate. Chaperones are recruited, but with age, the synthesis [production] of good protein and the chaperoning of those spontaneously unfolding ultimately succumb to damage levels, at which bad protein becomes overwhelming, the researchers said.

Their work also found that mutant animals with more chaperones or proteasomes a complex of enzymes responsible for the destruction of unnecessary or damaged proteins lived longer.

All these findings were in agreement with the foundations of their model, which stated that oxidative stress and protein instability increase with age and are the root cause of cell degeneration.

This modeling is unique by being mathematically detailed and describing a broad range of cellular processes across the cells whole proteome [all proteins found in a cell], Ken A. Dill, PhD, a distinguished professor and director of the Laufer Center for Physical & Quantitative Biology, and a study co-author, said in a news release.

Often, aging-related studies look at the effects of one or two proteins at a time, rather than seeking, more generally, the cellular aging mechanism itself, Dill added.

This study also sets the foundation for future research into the molecular origins of aging disorders associated with protein misfolding, such as Parkinsons.

Joana holds a BSc in Biology and a MSc in Evolutionary and Developmental Biology from Universidade de Lisboa. She is currently finishing her PhD in Biomedicine and Clinical Research at Universidade de Lisboa. Her work has been focused on the impact of non-canonical Wnt signaling in the collective behavior of endothelial cells cells that made up the lining of blood vessels found in the umbilical cord of newborns.

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Ana holds a PhD in Immunology from the University of Lisbon and worked as a postdoctoral researcher at Instituto de Medicina Molecular (iMM) in Lisbon, Portugal. She graduated with a BSc in Genetics from the University of Newcastle and received a Masters in Biomolecular Archaeology from the University of Manchester, England. After leaving the lab to pursue a career in Science Communication, she served as the Director of Science Communication at iMM.

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Insights into Parkinson's Onset May Lie in New Model of Cell Aging and Damage - Parkinson's News Today

UT molecular evolution professor named 2019 American Physical Society Fellow – UT The Daily Texan

The American Physical Society recently recognized a UT professor of molecular evolution as one of their 2019 fellows.

Claus Wilke said he was nominated by the Division of Biological Physics within the society and was given the fellowship in October. Associate physics professor Vernita Gordon said Wilke got his nomination for his studies of protein biophysics and molecular evolution.

Gordon said half of 1% of society members receive fellowships every year based on notable research findings in their field of study. Gordon also said 168 fellows were selected this year, and seven of these fellows were nominated within the biophysics field.

(Wilke) is really deserving of this award, Gordon said. Theres stuff to back up why they have made contributions at a level significant enough that they should be recognized as an APS fellow.

Wilke said his research identifying the primary driver of protein sequences, or sequences of organic compounds known as amino acids, kick-started his nomination from the division. He said his research combined physics and biology to showcase the functions of protein folding and the advancement of genetic sequences.

Wilke said he researched genetic mutations and patterns visible in the evolution of genomes, or an organisms genetic material, related to mutation structures. He said he studied the areas where more harm is caused from mutation and how it would affect the shape of protein sequences.

Everybody knows Jenga, Wilke said. So theres pieces that you just take out, and nothing is going to happen because the tower is stable, but theres other pieces that after a while you cant touch them because the whole thing would fall. So, what Im doing is a lot like that. Im trying to figure out which are the (proteins) that can be changed and which parts cant.

Nursing freshman Margarita Ramirez said she is becoming aware of the topics Wilke researched and how they compare to previous biophysics research.

Its good that he got awarded for (sequences) because its something having to do with evolution, and not a lot of people are looking into proteins, Ramirez said. His study is very unique compared to other biological professionals because its not just looking at DNA. Its looking deeper.

Wilke will be presented with the award in March 2020 during an annual ceremony where the society hosts fellows and other contributors to the study of physics.

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UT molecular evolution professor named 2019 American Physical Society Fellow - UT The Daily Texan

Christopher Dobson: chemist whose work on proteins advanced research into neurodegenerative diseases – The BMJ

Christopher Dobson, master of St Johns College, Cambridge, whose work on proteins advanced research into diseases such as Parkinsons and Alzheimers, died at the Royal Marsden Hospital, Surrey, at the age of 69.

Born in Rinteln, Germany, the son of Arthur Dobson, an army officer, and Mabel, ne Pollard, Christopher Dobson was educated at Hereford Cathedral Junior School, Abingdon School (where he was a rowing cox), and Keble College, Oxford, where he took a first in chemistry before going on to take a DPhil at Merton College. Both his parents were originally from Bradford in Yorkshire and had left school aged 14. He had two elder siblings, Graham and Gillian. Because of his fathers postings, Dobsons early life was fairly nomadic. He grew up in Nigeria in the formative part of his childhood, which created a lifelong fascination with different cultures, said his son, William. He first wanted to be an architect but owing to inspirational science teachers at Abingdon, he instead chose to study chemistry at university.

Dobson devoted his life to researching diseases such as Parkinsons and Alzheimers and understanding the chemical processes that disrupt the production of healthy proteins and instead trigger their aggregation into toxic clumps. He became one of the worlds leading experts on protein folding and aggregation, and its links to neurodegenerative conditions. Alzheimers disease is a new plague, already affecting 40 million people worldwide, he said. Its one of a group of non-infectious diseases that terrifies us.

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Christopher Dobson: chemist whose work on proteins advanced research into neurodegenerative diseases - The BMJ

Diseases Folding@home

The Folding@home project (FAH) is dedicated to understanding protein folding, the diseases that result from protein misfolding and aggregation, and novel computational ways to develop new drugs in general. Here, we briefly describe our goals, what we are doing, and some highlights so far.

A distributed computing project must not only run calculations on millions of PCs, but such projects must produce results, especially in the form of peer-reviewed publications, public lectures, and other ways that disseminate the results from FAH to the greater scientific community. In the sidebar, you will find links to our progress in different areas.

You will also find updates about our work, advancements and new projects in the main Folding@home blog.

Proteins are necklaces of amino acids, long chain molecules. They are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions that make biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome the blueprint for all of the proteins in biology but how can we understand what these proteins do and how they work?

However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carry out their function (e.g. as enzymes or antibodies), they must take on a particular shape, also known as a fold. Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called folding.

Diseases such as Alzheimers disease, Huntingtons disease, cystic fibrosis, BSE (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding. When proteins misfold, they can clump together (aggregate). These clumps can often gather in the brain, where they are believed to cause the symptoms of Mad Cow or Alzheimers disease.

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Diseases Folding@home

DeepMind timeline: The history of the UK’s pioneering AI firm – Techworld.com

DeepMind timeline: The history of the UK's pioneering AI firm | Startups | TechworldThe London startup has made headlines for both breakthroughs and controversies since it was founded in 2010

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DeepMind's efforts to achieve artificial general intelligence have won the firm both plaudits and critics since it was founded in 2010. The firm's research into deep learning techniquesconvinced the search engine giant Googleto spend 400 million on the company in 2014, but it has since incurred heavy losses and while its scientific discoveries have earned acclaim, DeepMind has also been rebuked for itslaissez faire approach to data privacy and security practices.

Read next: Google DeepMind: the story behind the world's leading AI startup

Here's our timeline of DeepMind's short but eventful history.

DeepMind was founded in London by machine learning researcher Shane Legg and childhood friends Demis Hassabis and former consultant Mustafa Suleyman. The cofounders all metat University College London, where Legg was a research associate and Hassibis was studying for a PhD in cognitive neuroscience.

The trio declared a grand ambition for their new company: "To solve intelligence and then to use that to solve everything else."

They initially pursued this lofty goal through video games. A 16-year-old Hasabis had co-developed the hit simulation game Theme Park, and at 22 was running his own games studio. He combined this experience with his neuroscience PhD to create AIprogrammesthat could master video games.One ofthese systemstaught itself how to play 49 different Atari games, including Pong and Space Invaders, just byviewing the score and pixels on the screen.

These experiments with video games led DeepMind to focus on an AI technique called deep reinforcement learning, which combines the pattern recognition of deep learning with the reward signals for completing tasks achieved through reinforcement learning.

DeepMind announced the technique in a research paper about its Atari trials, which it called "the first deep learning model to successfully learn control policies directly from high-dimensional sensory input using reinforcement learning."

The technique was responsible for DeepMind'smost impressive achievements, but the company's relentless focus on the technique has been questioned by some AI experts. In August 2019, Gary Marcus, the founder of Robust.AI and a professor of psychology and neural science at NYU, noted inWiredthat the company was still yet to find a large-scale commercial application of deep reinforcement learning.

"Ten years from now we will conclude that deep reinforcement learning was overrated in the late 2010s, and that many other important research avenues were neglected," he wrote. "Every dollar invested in reinforcement learning is a dollar not invested somewhere else, at a time when, for example, insights from the human cognitive sciences might yield valuable clues."

Google made DeepMind one of its biggest-ever European acquisitions when it splashed out 400 million on the London-based startup.Googleagreed to establish an AIethics boardas part of the deal, but the members and workings of the board have never been made clear.

A DeepMind-created system became the first AI to beat a professional Go player when AlphaGo routed European champion Fan Hu by a score of five to zero.Later that year, the system defeatedKe Jie, the world's number one player of the ancient and highly complex board game.

DeepMind began its controversial relationship with the Royal Free hospital in London when the two organisationssigned a deal that gave the Google subsidiary access to healthcare dataon 1.6 million patients. DeepMind later announced that the partnership hadyieldedan app called Streams that would help clinicians monitor patients for early signs of kidney disease.

DeepMind turned its ambition to use AI to improve healthcare into a separate division of the company:DeepMindHealth.Suleyman, whose mother was an NHS nurse, who chosen to lead the unit.

Suleymanwent on to sign further NHS dealswithTaunton & Somerset Foundation Trust,Yeovil District Hospital,University College London Hospital,Imperial College Healthcare and Moorfields Eye Hospital to apply AI to various medical challenges.

The Information Commissioner's Office (ICO), theUK's data regulator, ruled that the Royal Free"failed" to comply with data protection rules when it provided DeepMind with patient data as it didn't properly inform patients about how their details would be used.

Read next: DeepMind report fails to justify NHS use, claim privacy campaigners

The Royal Free accepted the findings and was not fined. The Trust announced that it hadstarted to address the concerns.

DeepMind revealedit had attracted a major client in the US when it announced that itwas teaming up with the US Department of Veterans Affairs to predict patient deterioration by analysing patterns in medical records.

Read next: DeepMind researcher says AI agents should cooperate for social good

The project also involves researching ways to improve the algorithmsDeepMind uses to detect acute kidney injury.

Privacy campaigners raised alarm whenDeepMind announcedthat its healthcare subsidiary was being absorbed into Google. The arrangement meant that the group would no longer operate as an independent unit but instead merge with the newly-formed Google Health team, led by former Geisinger CEO David Feinberg.

Critics argued that the shift betrayed DeepMind's promise never to share data with its parent company. DeepMind claimed that all patient data would remain separate from Google services and projects.

DeepMind made its biggest scientific breakthrough yet when its AlphaFold system won a competitionto predict the 3D shapes of proteins based on their genetic codes.The victory suggested that AI could help understand the protein-folding puzzle that plays a key role in the development of new drugs.

This is a lighthouse project, our first major investment in terms of people and resources into a fundamental, very important, real-world scientific problem, DeepMind CEO Demis Hassabistold the Guardian.

DeepMind continued its long history of applying AI tovideo games by introducing AlphaStar, a programme that can play strategy game StarCraft II. The system went on to defeat some of the world's best StarCraft II players.

DeepMind announced that Mustafa Suleyman, the company'scofounder and head of applied artificial intelligence,was leaving the company for an indefinite period that the company said would likelyend later the same year.DeepMindclaimedthat the decision was mutual andnotrelated to his performance,but rumours spread that his departure was related to the company's various healthcare controversies.

Read next:Google DeepMind loses its cofounder Mustafa Suleyman indefinitely

On September 18, Dr Dominic King, the UK site lead at Google Health, announced in a blogpost that Google had completed its takeover of DeepMind's health division.

"It's clear that a transition like this takes time," he wrote."Health data is sensitive, and we gave proper time and care to make sure that we had the full consent and cooperation of our partners. This included giving them the time to ask questions and fully understand our plans and to choose whether to continue our partnerships. As has always been the case, our partners are in full control of all patient data and we will only use patient data to help improve care, under their oversight and instructions.

The Royal Free,University College London Hospitals,Imperial College Healthcare, Moorfields Eye Hospital, Taunton & Somerset, and University College London Hospitals NHS Foundation Trust all went on to release statementsconfirming that theircontractual arrangements had been moved to Google.

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Protein Structures: Primary, Secondary, Tertiary, Quaternary …

Proteins are the largest and most varied class of biological molecules, and they show the greatest variety of structures. Many have intricate three-dimensional folding patterns that result in a compact form, but others do not fold up at all (natively unstructured proteins) and exist in random conformations. The function of proteins depends on their structure, and defining the structure of individual proteins is a large part of modern Biochemistry and Molecular Biology.

To understand how proteins fold, we will start with the basics of structure, and progress through to structures of increasing complexity.

Peptide Bonds

To make a protein, amino acids are connected together by a type of amide bond called a peptide bond. This bond is formed between the alpha amino group of one amino acid and the carboxyl group of another in a condensation reaction. When two amino acids join, the result is called a dipeptide, three gives a tripeptide, etc. Multiple amino acids result in a polypeptide (often shortened to peptide). Because water is lost in the course of creating the peptide bond, individual amino acids are referred to as amino acid residues once they are incorporated. Another property of peptides is polarity: the two ends are different. One end has a free amino group (called the N-terminal) and the other has a free carboxyl group (C-terminal).

In the natural course of making a protein, polypeptides are elongated by the addition of amino acids to the C-terminal end of the growing chain. Conventionally, peptides are written N-terminal first; therefore gly-ser is not the same as ser-gly or GS is not the same as SG. The connection gives rise to a repeating pattern of NCC-NCC-NCC atoms along the length of the molecule. This is referred to as the backbone of the peptide. If stretched out, the side chains of the individual residues project outwards from this backbone.

The peptide bond is written as a single bond, but it actually has some characteristics of a double bond because of the resonance between the C-O and C-N bonds:

This means that the six atoms involved are coplanar, and that there is not free rotation around the CN axis. This constrains the flexibility of the chain and prevents some folding patterns.

Primary Structure of Proteins

It is convenient to discuss protein structure in terms of four levels (primary to quaternary) of increasing complexity. Primary structure is simply the sequence of residues making up the protein. Thus primary structure involves only the covalent bonds linking residues together.

The minimum size of a protein is defined as about 50 residues; smaller chains are referred to simply as peptides. So the primary structure of a small protein would consist of a sequence of 50 or so residues. Even such small proteins contain hundreds of atoms and have molecular weights of over 5000 Daltons (Da). There is no theoretical maximum size, but the largest protein so far discovered has about 30,000 residues. Since the average molecular weight of a residue is about 110 Da, that single chain has a molecular weight of over 3 million Daltons.

Secondary Structure

This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups. Various types of secondary structure have been discovered, but by far the most common are the orderly repeating forms known as the a helix and the b sheet.

An a helix, as the name implies, is a helical arrangement of a single polypeptide chain, like a coiled spring. In this conformation, the carbonyl and N-H groups are oriented parallel to the axis. Each carbonyl is linked by a hydrogen bond to the N-H of a residue located 4 residues further on in the sequence within the same chain. All C=O and N-H groups are involved in hydrogen bonds, making a fairly rigid cylinder. The alpha helix has precise dimensions: 3.6 residues per turn, 0.54 nm per turn. The side chains project outward and contact any solvent, producing a structure something like a bottle brush or a round hair brush. An example of a protein with many a helical structures is the keratin that makes up human hair.

The structure of a b sheet is very different from the structure of an a helix. In a b sheet, the polypeptide chain folds back on itself so that polypeptide strands like side by side, and are held together by hydrogen bonds, forming a very rigid structure. Again, the polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the a helix, these bonds are formed between neighbouring polypeptide (b) strands. Generally the primary structure folds back on itself in either a parallel or antiparallel arrangement, producing a parallel or antiparallel b sheet. In this arrangement, side chains project alternately upward and downward from the sheet. The major constituent of silk (silk fibroin) consists mainly of layers of b sheet stacked on top of each another.

Other types of secondary structure. While the a helix and b sheet are by far the most common types of structure, many others are possible. These include various loops, helices and irregular conformations. A single polypeptide chain may have different regions that take on different secondary structures. In fact, many proteins have a mixture of a helices, b sheets, and other types of folding patterns to form various overall shapes.

What determines whether a particular part of a sequence will fold into one or the other of these structures? A major determinant is the interactions between side chains of the residues in the polypeptide. Several factors come into play: steric hindrance between nearby large side chains, charge repulsion between nearby similarly-charged side chains, and the presence of proline. Proline contains a ring that constrains bond angles so that it will not fit exactly into an a helix or b sheet. Further, there is no H on one peptide bond when proline is present, so a hydrogen bond cannot form. Another major factor is the presence of other chemical groups that interact with each other. This contributes to the next level of protein structure, the tertiary structure.

Tertiary Structure

This level of structure describes how regions of secondary structure fold together that is, the 3D arrangement of a polypeptide chain, including a helices, b sheets, and any other loops and folds. Tertiary structure results from interactions between side chains, or between side chains and the polypeptide backbone, which are often distant in sequence. Every protein has a particular pattern of folding and these can be quite complex.

Whereas secondary structure is stabilized by H-bonding, all four weak forces contribute to tertiary structure. Usually, the most important force is hydrophobic interaction (or hydrophobic bonds). Polypeptide chains generally contain both hydrophobic and hydrophilic residues. Much like detergent micelles, proteins are most stable when their hydrophobic parts are buried, while hydrophilic parts are on the surface, exposed to water. Thus, more hydrophobic residues such as trp are often surrounded by other parts of the protein, excluding water, while charged residues such as asp are more often on the surface.

Other forces that contribute to tertiary structure are ionic bonds between side chains, hydrogen bonds, and van der Waals forces. These bonds are far weaker than covalent bonds, and it takes multiple interactions to stabilize a structure.

There is one covalent bond that is also involved in tertiary structure, and that is the disulfide bond that can form between cysteine residues. This bond is important only in non-cytoplasmic proteins since there are enzyme systems present in the cytoplasm to remove disulfide bonds.

Visualization of protein structures Because the 3D structures of proteins involve thousands of atoms in complex arrangements, various ways of depicting them so they are understood visually have been developed, each emphasizing a different property of the protein. Software tools have been written to depict proteins in many different ways, and have become essential to understanding protein structure and function.

Structural Domains of Proteins

Protein structure can also be described by a level of organization that is distinct from the ones we have just discussed. This organizational unit is the protein domain, and the concept of domains is extremely important for understanding tertiary structure. A domain is a distinct region (sequence of amino acids) of a protein, while a structural domain is an independently-folded part of a protein that folds into a stable structure. A protein may have many domains, or consist only of a single domain. Larger proteins generally consist of connected structural domains. Domains are often separated by a loosely folded region and may create clefts between them..

Quaternary Structure

Some proteins are composed of more than one polypeptide chain. In such proteins, quaternary structure refers to the number and arrangement of the individual polypeptide chains. Each polypeptide is referred to as a subunit of the protein. The same forces and bonds that create tertiary structure also hold subunits together in a stable complex to form the complete protein.

Individual chains may be identical, somewhat similar, or totally different. As examples, CAP protein is a dimer with two identical subunits, whereas hemoglobin is a tetramer containing two pairs of non-identical (but similar) subunits. It has 2 a subunits and 2 b subunits. Secreted proteins often have subunits that are held together by disulfide bonds. Examples include tetrameric antibody molecules that commonly have two larger subunits and two smaller subunits (heavy chains and light chains) connected by disulfide bonds and noncovalent forces.

In some proteins, intertwined a helices hold subunits together; these are called coiled-coils. This structure is stabilized by a hydrophobic surface on each a helix that is created by a heptameric repeat pattern of hydrophilic/hydrophobic residues. The sequence of the protein can be represented as abcdefgabcdefgabcdefg with positions a and d filled with hydrophobic residues such as A, V, L etc. Each a helix has a hydrophobic surface that therefore matches the other. When the two helices coil around each other, those surfaces come together, burying the hydrophobic side chains and forming a stable structure. An example of such a protein is myosin, the motor protein found in muscle that allows contraction.

Protein Folding

How and why do proteins naturally form secondary, tertiary and quaternary structures? This question is a very active area of research and is certainly not completely understood. A folded, biologically-active protein is considered to be in its native state, which is generally thought to be the conformation with least free energy.

Proteins can be unfolded or denatured by treatment with solvents that disrupt weak bonds. Thus organic solvents that disrupt hydrophobic interactions, high concentrations of urea or guanidine that interfere with H-bonding, extreme pH or even high temperatures, will all cause proteins to unfold. Denatured proteins have a random, flexible conformation and usually lack biological activity. Because of exposed hydrophobic groups, they often aggregate and precipitate. This is what happens when you fry an egg.

If the denaturing condition is removed, some proteins will re-fold and regain activity. This process is called renaturation. Therefore, all the information necessary for folding is present in the primary structure (sequence) of the protein. During renaturation, the polypeptide chain is thought to fold up into a loose globule by hydrophobic effects, after which small regions of secondary structure form into especially favorable sequences. These sequences then interact with each other to stabilize intermediate structures before the final conformation is attained.

Many proteins have great difficulty renaturing, and proteins that assist other proteins to fold are called molecular chaperones. They are thought to act by reversibly masking exposed hydrophobic regions to prevent aggregation during the multi-step folding process. Proteins that must cross membranes (eg. mitochondrial proteins) must stay unfolded until they reach their destination, and molecular chaperones may protect and assist during this process.

Protein families/Types of proteins

Proteins are classified in a number of ways, according to structure, function, location and/or properties. For example, many proteins combine tightly with other substances such as carbohydrates (glycoproteins), lipids (lipoproteins), or metal ions (metalloproteins). The diversity of proteins that form from the 20 amino acids is greatly increased by associations such as these. Proteins that are tightly bound to membranes are called membrane proteins. Proteins with similar activities are given functional classifications. For example, proteins that break down other proteins are called proteases.

Because almost all proteins arise by an evolutionary process, ie. new ones are derived from old ones, they can be classified into families by their relatedness. Proteins that derive from the same ancestor are called homologous proteins. Studying the sequences of homologous proteins can give clues to the structure and function of the protein. Residues that are critical for function do not change on an evolutionary timescale; they are referred to as conserved residues. Identifying such residues by comparing amino acid sequences often helps clarify what a protein is doing or how it is folded. For example the proteases trypsin and chymotrypsin are members of the serine protease family; so-named because of a conserved serine residue that is essential to catalyze the reaction. Trypsin and chymotrypsin contain very similar folding patterns and reaction mechanisms. Recognizing a pattern of conserved residues in protein sequences often allows scientists to deduce the function of a protein.

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Protein Structures: Primary, Secondary, Tertiary, Quaternary ...