Michael H. Peters, Ph.D., a professor in Virginia Commonwealth University (VCU), Department of Chemical and Life Science Engineering, is using powerful supercomputers at NASA's Ames Research Center in California to investigate the spike protein of the novel coronavirus that causes COVID-19.

       Through advanced computer simulations, he hopes to determine the mechanistic action of the spike protein, which plays an important role in attaching to human cells and infecting the body. He has identified a possible factor that may be able to restrict an important action of this key protein and is trying to more fully understand how this protein functions.

       Peters conducts experimental and theoretical research in the field of protein engineering with a former graduate student, Oscar Bastidas, Ph.D., now a postdoctoral research fellow at the University of Minnesota's College of Biological Sciences. Together, they are studying the dynamics of how the spike protein changes between active and inactive states. The protein's receptor binding domain has an "up" position, in which it can bind to epithelial cell molecules. But in the "down" position, it appears to be incapable of binding.

       Peters said it was remarkable that the up domain configuration is molecularly tethered to the main structure of the protein like a tethered balloon. He added, there were two molecular tethers that are stabilized or 'tied down' by so-called beta strand structural motifs in the central part of the protein and that is why he calls this virus the "It' virus" referring to the shape-shifting creature in author Stephen King's horror tale.

       He said that, they have mapped the all-atom biomolecular dynamics of the entire spike protein and believe they have discovered a possible molecular "latch" that helps to keep the spike protein down.

       Peters is able to access the supercomputers as part of the COVID-19 High Performance Computing Consortium through the Extreme Science and Engineering Discovery Environment, a virtual system that scientists can use to interactively share computing resources. The consortium is a private-public partnership that includes the White House Office of Science and Technology Policy and major tech corporations.

       "The spike protein is a true giant among proteins and difficult to attack without the best computers out there" he said and added "We need to move as fast as possible gathering intelligence and planning attacks." difficult to attack without the best computers out there" he said and added "We need to move as fast as possible gathering intelligence and planning attacks.“

Image credit: Graphical image of coronavirus

Image credit: CC0 Public Domain

Source: www.phys.org