Researchers at the University of Oxford have combined experimental data from X-ray crystallography, NMR spectroscopy, cryoelectron microscopy and lipidomics (the study of cellular lipid networks), and have built a 'virtual virus', a complete model of the outer envelope of influenza A virion.
This study approach is known as a coarse-grained molecular dynamics simulation, and has allowed the researchers to generate trajectories at different temperatures and lipid compositions, revealing various characteristics about the membrane components that may help them better understand how the virus survives in the wild or find new ways to combat it.
The computer simulation begins by rendering the virtual virus as a relatively large, 73-nanometer ball of loosely packed lipids, which 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. After this the viral spike proteins are embedded into the lipid envelope individually, before adding solvent to the system.
From the simulation, researchers found that the viral spike proteins protruding from the virion's membrane spread out, rather than aggregating close together. This was the 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.
With this understanding of the membrane envelope's structural dynamics, scientists have got an insight into the wide-ranging survival times of the virion in different environments, such as fresh-water rivers.