title: Modeling HIV-1 viral capsid nucleation by dynamical systems.
abstract: There are two stages generally recognized in the viral capsid assembly: nucleation and elongation. This paper focuses on the nucleation stage and develops mathematical models for HIV-1 viral capsid nucleation based on six-species dynamical systems. The Particle Swarm Optimization (PSO) algorithm is used for parameter fitting to estimate the association and dissociation rates from biological experiment data. Numerical simulations of capsid protein (CA) multimer concentrations demonstrate a good agreement with experimental data. Sensitivity and elasticity analysis of CA multimer concentrations with respect to the association and dissociation rates further reveals the importance of CA trimer-of- dimers in the nucleation stage of viral capsid self- assembly.
authors.affiliation: Department of Mathematics, Colorado State University, Fort Collins, CO 80523-1874, USA. Electronic address: sadre@math.colostate.edu.
authors.forename: Farrah
authors.initials: F
authors.lastname: Sadre-Marandi
authors.affiliation: School of Mathematics and Statistics, Wuhan University, Wuhan 430072, Hubei, China. Electronic address: yuewuliu@whu.edu.cn.
authors.forename: Yuewu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Mathematics, Colorado State University, Fort Collins, CO 80523-1874, USA. Electronic address: liu@math.colostate.edu.
authors.forename: Jiangguo
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Mathematics, Colorado State University, Fort Collins, CO 80523-1874, USA. Electronic address: tavener@math.colostate.edu.
authors.forename: Simon
authors.initials: S
authors.lastname: Tavener
authors.affiliation: School of Mathematics and Statistics, Wuhan University, Wuhan 430072, Hubei, China. Electronic address: xfzou@whu.edu.cn.
authors.forename: Xiufen
authors.initials: X
authors.lastname: Zou
mesh_terms: D000465:Algorithms; D002213:Capsid / Q000737:chemistry / Q000502:physiology; D036022:Capsid Proteins / Q000737:chemistry / Q000502:physiology; D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry / Q000502:physiology*; D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry / Q000502:physiology; D055641:Mathematical Concepts; D008954:Models, Biological; D008958:Models, Molecular; D055503:Protein Multimerization; D019065:Virus Assembly / Q000502:physiology*
chemical_list: D036022:Capsid Proteins; D054298:Human Immunodeficiency Virus Proteins
keywords: Capsid; Dimers; Dynamical systems; HIV-1; Hexamers; Sensitivity analysis