Washington: A "virtual virus" has helped scientists unfold the flu on a CPU, it has been revealed.
By combining experimental data from X-ray crystallography, NMR spectroscopy, cryoelectron microscopy and lipidomics (the study of cellular lipid networks), researchers at the University of Oxford have built a complete model of the outer envelope of influenza A virion for the first time.
The approach, known as a coarse-grained molecular dynamics simulation, has allowed them to generate trajectories at different temperatures and lipid compositions, revealing various characteristics about the membrane components that may help scientists better understand how the virus survives in the wild or find new ways to combat it.
The computer simulation begins by rendering the virus as a relatively large, 73-nanometer ball of loosely packed lipids. This ball then relaxes down into a smaller, 59-nanometer virion within 300 nanoseconds - an imperceptible amount of time on the macroscopic level, but roughly 1/15th of the simulation's total run time. The viral spike proteins are then embedded into the lipid envelope individually, before adding solvent to the system.
From the simulation, Tyler Reddy, a postdoctoral fellow at the University of Oxford and coworkers have found that the viral spike proteins protruding from the virion's membrane spread out, rather than aggregating close together. This was key to the strength of the interactions between influenza A virions and host cells, which are determined by the number of spike proteins that can engage with receptors.
Understanding the membrane envelope's structural dynamics also provided insight into the wide-ranging survival times of the virion in different environments, such as fresh-water rivers.
