Impact of surface charge density and motor force upon polyelectrolyte packaging in viral capsids

Abstract

By means of Langevin molecular dynamics simulations, we study the packaging dynamics of flexible and semiflexible polyelectrolytes in spherical cavities that resemble viral capsids. We employ a coarse‐grained model of the polymer–capsid complex that allows us to perform simulations of a 900mer and investigate the influence of surface charges inside the capsid and an additional motor force, acting on the polymer in the portal region of the cavity, on the packaging process. Our results indicate that it is most efficient if surface charges are present that initially promote the formation of an ordered surface layer inside the capsid. Once these charges are screened, the motor force pulls in the remaining part of the chain. Additionally, the simulations also demonstrate that the packaging dynamics depends on the counterion valence. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 1054–1065

DNA packaging in viral capsids with peptide arms

“…Undoubtedly, the motor can accelerate the packaging process, and it is the main driving force at later stages. 23 If the amount of net charges in the PA layer is sufficiently high, the DNA chain can be pulled into the capsid despite the absence of a molecular motor. As shown in Fig.…”

“…Previous theoretical and simulational studies, 2,9,10,[12][13][14][15][16][17][18][19][20][21][22][23] aiming at conformational and dynamic properties of DNA packaging, were based on simple models for the internal structure of the capsid and electrostatic features of DNA-DNA and DNA-capsid interactions. Most computational models neglect the electrostatic interaction or only consider it as a potential of mean force based on Debye-Hückel theory.…”

Fractional separation of polymers in nanochannels: Combined influence of wettability and structure

“…This has opened up a new avenue for filtration of polymers using differential mobilities based on their structures and sizes in corrugated nanochannels, the dynamics of chain transport in such channels as well as mechanism of polymer trapping and escape from a corrugation/groove . Moreover, polymers in solvated state like water, are expected to give rise to nonintuitive behavior . Irrespective of the copious amount of literature existing on the detached problems: charge‐wettability interaction in molecular fluids and polymer dynamics at nanoscale, few attempts had been made to utilize the channel wettability, charge interactions, and polymer structure in confinement toward filtration and segregation of polymers.…”

“…30 Moreover, polymers in solvated state like water, are expected to give rise to nonintuitive behavior. [23][24][25][26][27][28] Irrespective of the copious amount of literature existing on the detached problems: charge-wettability interaction in molecular fluids and polymer dynamics at nanoscale, few attempts had been made to utilize the channel wettability, charge interactions, and polymer structure in confinement toward filtration and segregation of polymers. Such mapping of selective transfer of polymers can enhance the understanding of migration of reactive species and signals in several natural processes within cellular environment.…”