Langevin dynamics simulation of DNA ejection from a phage
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Langevin dynamics simulation of DNA ejection from a phage J. P. Mahalik · B. Hildebrandt · M. Muthukumar
Received: 18 February 2013 / Accepted: 22 March 2013 / Published online: 23 April 2013 © Springer Science+Business Media Dordrecht 2013
Abstract We have performed Langevin dynamics simulations of a coarse-grained model of ejection of dsDNA from 29 phage. Our simulation results show significant variations in the local ejection speed, consistent with experimental observations reported in the literature for both in vivo and in vitro systems. In efforts to understand the origin of such variations in the local speed of ejection, we have investigated the correlations between the local ejection kinetics and the packaged structures created at various motor forces and chain flexibility. At lower motor forces, the packaged DNA length is shorter with better organization. On the other hand, at higher motor forces typical of realistic situations, the DNA organization inside the capsid suffers from significant orientational disorder, but yet with long orientational correlation times. This in turn leads to lack of registry between the direction of the DNA segments just to be ejected and the direction of exit. As a result, a significant amount of momentum transfer is required locally for successful exit. Consequently, the DNA ejection temporarily slows down exhibiting pauses. This slowing down occurs at random times during the ejection process, completely determined by the particular starting conformation created by prescribed motor forces. In order to augment our inference, we have additionally investigated the ejection of chains with deliberately changed persistence length. For less inflexible chains, the demand on the occurrence of large momentum transfer for successful ejection is weaker, resulting in more uniform ejection kinetics. While being consistent with experimental observations, our results show the nonergodic nature of the ejection kinetics and call for better theoretical models to portray the kinetics of genome ejection from phages. Keywords Genome ejection from phages
J. P. Mahalik · B. Hildebrandt · M. Muthukumar (B) Department of Polymer Science and Engineering, Department of Physics, University of Massachusetts, Amherst, MA 01003, USA e-mail: [email protected]
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1 Introduction The precise molecular mechanism of transfer of a dsDNA molecule from bacteriophages to the host cells is still not fully understood [1, 2]. The major steps comprised of recognition of proteins of the host by the phage, activation of the release of DNA from the lumen of the phage, and the eventual translocation of DNA into the host cell have been well recognized in the literature [3–6]. Each of these steps involves biochemical processes associated with protein–protein and protein–DNA interactions. In addition, there are physical forces mainly arising from the release of pressure initially generated by a motor protein in encapsidating the DNA inside the phage capsid. The release of pressure, concomitant wi
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