All-atom multiscale simulation of cowpea chlorotic mottle virus capsid swelling.
An all-atom multiscale computational modeling approach, molecular dynamics/order parameter extrapolation (MD/OPX), has recently been developed for simulating large bionanosystems. It accelerates MD simulations and addresses rapid atomistic fluctuations and slowly varying nanoscale dynamics of bionanosystems simultaneously. With modules added to account for water molecules and ions, MD/OPX is applied to simulate the swelling of cowpea chlorotic mottle virus (CCMV) capsid solvated in a host medium in this study. Simulation results show that the N-terminal arms of capsid proteins undergo large deviations from the initial configurations with their length extended quickly during the early stage of capsid swelling. The capsid swelling is a symmetry-breaking process involving local initiation and front propagation. The capsid swelling rate is approximately 0.25 nm/ns (npn) during the early stage of the simulation, and propagation of the structural transition across the capsid is roughly 0.6 npn. The system conditions that affect swelling of the capsid are analyzed. Prospects for creating a phase diagram for CCMV capsid swelling and using predictions to guide experiments are discussed.
Miao
Yinglong
Y
Center for Cell and Virus Theory, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
Johnson
John E
JE
Ortoleva
Peter J
PJ
D017795:Bromovirus / Q000737:chemistry* / Q000302:isolation & purification / Q000648:ultrastructure; D036022:Capsid Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D014867:Water / Q000737:chemistry
D036022:Capsid Proteins; D014867:Water