title: Construction of a novel coarse grain model for simulations of HIV capsid assembly to capture the backbone structure and inter-domain motions in solution.
abstract: We show the construction of a novel coarse grain model for simulations of HIV capsid assembly based on four structural models of HIV capsid proteins: isolated hexamer 3H47.pdb, tubular assembly 3J34.pdb, isolated pentamer 3P05.pdb and C-terminus dimer 2KOD.pdb. The data demonstrates the derivation of inter-domain motions from all atom Molecular Dynamics simulations and comparison with the motions derived from the analysis of solution NMR results defined in 2M8L.pdb. Snapshots from a representative Monte Carlo simulation with 128 dimeric subunit proteins based on 3J34.pdb are shown in addition to the quantitative analysis of its assembly pathway. Movies of the assembly process are compiled with snapshots of representative simulations of four structural models. The methods and data in this article were utilized in Qiao et al. (in press) [1] to probe the mechanism of polymorphism and curvature control of HIV capsid assembly.
authors.affiliation: Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Qiao
authors.affiliation: Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
authors.forename: Jaekyun
authors.initials: J
authors.lastname: Jeon
authors.affiliation: Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
authors.forename: Jeff
authors.initials: J
authors.lastname: Weber
authors.affiliation: Department of Physics, Indiana University - Purdue University Indianapolis, IN, USA.
authors.forename: Fangqiang
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Department of Physics, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Chen
keywords: Capsid assembly; Coarse grain simulations; HIV