Nov. 22 — It sounds like something out of the Borg in Star Trek. Nano-sized robots self-assemble to form biological machines that do the work that keeps one alive. And yet something like this really does go on.

Every cell in our body – be they flesh and blood, brain and everything in between – has identical DNA, the twisted staircase of nucleic acids uniquely coded to each organism. Complex assemblages that resemble molecular machines take pieces of DNA called genes and make a brain cell when needed, instead of, say, a bone cell. These molecular machines are so complex, yet so tiny, that scientists today are just starting to understand their structure and function using the latest microscopes and supercomputers. Biological molecular machines could lay the foundation for developing cures to diseases like cancer. How small can one see, and what will one find?

Cryo-electron microscopy combined with supercomputer simulations have created the best model yet, with near atomic-level detail, of a vital molecular machine, the human pre-initiation complex (PIC). A science team from Northwestern University, Berkeley National Laboratory, Georgia State University, and UC Berkeley published their results on the PIC May 2016 in the journal Nature.

“For the first time, structures have been detailed of the complex groups of molecules that open up human DNA,” said study co-author Ivaylo Ivanov, associate professor of chemistry at Georgia State University. Ivanov led the computational work that modeled the atoms of the different proteins that act like cogs of the PIC molecular machine.

The PIC finds genes associated with making a specific protein, such as an antibody or an enzyme. There the PIC pulls apart the two strands of DNA and feeds the coding strand to the workhorse enzyme RNA polymerase II. This starts transcription, where DNA bits are copied by RNA polymerase II into a single strand of messenger RNA. The RNA makes its way to ‘protein factories’ in the cell called ribosomes that take them as orders for which protein to make. If DNA is like the blueprint of a new house, RNAs are instructions to the ‘contractors’ at the ribosome work station. The manufactured proteins are like the nails, wood, plaster, and just about everything else in the house.

The experiment began with images painstakingly taken of PIC. They were made by a group led by study co-author Eva Nogales, a professor in the Department of Molecular and Cellular Biology at UC Berkeley and also Senior Faculty Scientist at the Lawrence Berkeley National Laboratory and Howard Hughes Medical Investigator.

Nogales’ group used cryo-electron microscopy (cryo-EM), a rising star in lab techniques. They cryogenically froze human PIC bound to DNA. The freezing kept it in a chemically-active, near-natural environment. Next they zapped it with electron beams. Thanks to recent advances in direct electron detector technology, cryo-EM can now image at near atomic resolution large and complicated biological structures that have proven too difficult to crystalize. The go-to technique, X-ray crystallography, requires crystallized specimens, and cryo-EM avoids this hard step.

Over 1.4 million cryo-EM ‘freeze frames’ of PIC were processed using supercomputers at the National Energy Research for Scientific Computing Center to sift out background noise and reconstructed three-dimensional density maps that show details in the shape of the molecule that had never been seen before.

“Cryo-EM is going through a great expansion as are all the computer software used to generate both the density maps and also to interpret them like we’ve done in this study,” Nogales said. “It is allowing us to get higher resolution of more structures in different states so that we can describe not just one picture of how they look, but several pictures showing how they are moving. We don’t see a continuum, but we see snapshots through the process of action.”

Study scientists next built an accurate model that made physical sense of the density maps of PIC using XSEDE, the eXtream Science and Engineering Discovery Environment, funded by the National Science Foundation. XSEDE allows scientists to interactively share computing resources, data and expertise via a single virtual system. Ivaylo Ivanov’s team has run over four million core hours of simulations on the Stampede supercomputer at the Texas Advanced Computing Center to model complex molecular machines, including those for this study. Ivanov’s broader molecular machine work also includes an XSEDE allocation of 1.7 million core hours on the Comet supercomputer at the San Diego Supercomputing Center.

“I have been using XSEDE resources for more than 12 years now,” Ivanov said. “Without the availability of XSEDE resources, all of our research would have been much more limited in terms of the systems that we can address. For us, XSEDE has been absolutely essential.”

The entire article can be found here.

Source: Jorge Salazar, TACC