Paper Citing NAMD - Abstract
Roberts, Jason A.; Kuiper, Michael J.; Thorley, Bruce R.; Smooker, Peter M.; Hung, Andrew
Investigation of a predicted N-terminal amphipathic et-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:165-173, SEP 2012
The wild type 1 poliovirus capsid was first described in atomic detail in 1985 using X-ray crystallography. Numerous poliovirus capsid structures have been produced since, but none resolved the spatial positioning and conformation of a predicted N-terminal a-helix of the capsid protein VP1, which is considered critical to virus replication. We studied the helical structure under varying conditions using in silica reconstruction and atomistic molecular dynamics (MD) simulation methods based on the available poliovirus capsid atom coordinate data. MD simulations were performed on the detached N-terminal VP1 helix, the biologically active pentamer form of the pre-virion structure, reconstructed empty virus capsids and a full virion containing the poliovirus RNA genome in the form of a supercoiled structure. The N-terminal a-helix structure proved to be stable and amphipathic under all conditions studied. We propose that a combination of spatial disorder and proximity to the genomic RNA made this particular structure difficult to resolve by X-ray crystallography. Given the similarity of our in silico model of poliovirus compared to X-ray crystallography data, we consider computational methods to be a useful complement to the study of picornaviruses and other viruses that exhibit icosahedral symmetry. (C) 2012 Elsevier Inc. All rights reserved.
