December 23, 2014

A picture of a membrane protein called cysZ determined with Phenix software using data that could not previously be analyzed. (Credit: LANL)

Brett Smith for redOrbit.com Your Universe Online

Tiny molecular machines are expected to play a major role be the next generation of medicine as researchers at Los Alamos National Laboratory (LANL) in New Mexico have announced a new technique that allows for the first-ever 3D imaging of these miniscule machines, according to a report in the journal Nature Methods.

Inside each cell in our bodies and inside every bacterium and virus are tiny but complex protein molecules thatsynthesize chemicals, replicate genetic material, turn each other on and off, and transport chemicals acrosscell membranes, said Tom Terwilliger, a Los Alamos National Laboratory scientist. Understanding how all these machines work is the key to developing new therapeutics, fortreating genetic disorders, and for developing new ways to make useful materials.

Past research on molecular machines has taken advantage of the fact that any incorporated metal atoms diffract X-rays differently than a machines other atoms, which are typically carbon, hydrogen, nitrogen and oxygen. Computers could be used to seize on these differences and any machines without metal atoms had to be studied by incorporating metal into them.

Through the newly developed imaging method, the LANL team was able to show that robust statistical procedures might be used to locate metal atoms in molecular machines even if they dont spread X-rays differently than carbon and other atoms. The technique allows for metal atoms like sulfur, normally part of many proteins, to be discovered and used to produce a three-dimensional image of a protein. Also, the new technique makes it easy to see a three-dimensional image of a protein without unnaturally integrating metal atoms into them, which means a lot more molecular machines can be analyzed.

The updated procedure starts with scientists generating billions of copies of a particular protein machine, dissolving them in water and growing crystals of the protein. Next, the scientists aim a stream of X-rays at a crystal and assess the brilliance of all of the thousands of diffracted X-ray spots that are generated. Then, scientists use a software program called Phenix to assess the diffraction spots and generate a three-dimensional image of an individual protein machine. This image shows the scientists just how the protein machine is assembled.

One such machine that was recently investigated was the Cascade machine, which happens to be in bacteria and is used to identify DNA that comes from viruses that infect bacteria. Looking somewhat like a seahorse, Cascade is composed of 11 proteins and an RNA molecule, with the RNA molecule winding through the entire body of the seahorse. If a bit of foreign DNA is able to interlock with the RNA molecule, Cascade hold the foreign viral DNA in place as a different machine comes by and destroys it, keeping the bacterium from infection. A report on Cascade was published in the journal Science over the summer.

In addition to investigating Cascade, the Phenixsoftware has allowed scientists to determine three-dimensional configurations of more than 15,000 different protein machinesand has already been cited by more than 5000 scientific publications.

View original post here:

First-ever 3D images of "molecular machines" produced