title: DNA packaging in viral capsids with peptide arms.
abstract: Strong chain rigidity and electrostatic self-repulsion of packed double-stranded DNA in viruses require a molecular motor to pull the DNA into the capsid. However, what is the role of electrostatic interactions between different charged components in the packaging process? Though various theories and computer simulation models were developed for the understanding of viral assembly and packaging dynamics of the genome, long-range electrostatic interactions and capsid structure have typically been neglected or oversimplified. By means of molecular dynamics simulations, we explore the effects of electrostatic interactions on the packaging dynamics of DNA based on a coarse-grained DNA and capsid model by explicitly including peptide arms (PAs), linked to the inner surface of the capsid, and counterions. Our results indicate that the electrostatic interactions between PAs, DNA, and counterions have a significant influence on the packaging dynamics. We also find that the packed DNA conformations are largely affected by the structure of the PA layer, but the packaging rate is insensitive to the layer structure.
authors.affiliation: College of Mechanical and Electrical Engineering, Jiaxing University, Jiaxing 314001, P. R. China. qqcao@mail.zjxu.edu.cn and Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, GA 30602, USA. bachmann@smsyslab.org and Institut für Theoretische Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
authors.forename: Qianqian
authors.identifier: http://orcid.org/0000-0002-1207-4002
authors.initials: Q
authors.lastname: Cao
authors.affiliation: Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, GA 30602, USA. bachmann@smsyslab.org and Instituto de Física, Universidade Federal de Mato Grosso, Cuiabá (MT), Brazil and Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte (MG), Brazil.
authors.forename: Michael
authors.initials: M
authors.lastname: Bachmann
mesh_terms: D002213:Capsid / Q000737:chemistry* / Q000378:metabolism*; D042003:DNA Packaging; D004279:DNA, Viral / Q000235:genetics* / Q000378:metabolism*; D010455:Peptides / Q000378:metabolism*; D055672:Static Electricity; D013499:Surface Properties
chemical_list: D004279:DNA, Viral; D010455:Peptides