title: Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids.
abstract: We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (approximately 10) low-frequency modes that are global and cooperative.
authors.affiliation: Department of Physics, Center for Biological Physics, Arizona State University, Tempe, Arizona 85287-1504, USA.
authors.forename: Eric C
authors.initials: EC
authors.lastname: Dykeman
authors.forename: Otto F
authors.initials: OF
authors.lastname: Sankey
mesh_terms: D001696:Biomechanical Phenomena; D002213:Capsid / Q000737:chemistry*; D004583:Electrons; D006801:Humans; D008958:Models, Molecular; D012997:Solvents / Q000737:chemistry; D013059:Spectrum Analysis, Raman; D014732:Vibration
chemical_list: D012997:Solvents