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Polymers 2016, 8(9), 343; doi:10.3390/polym8090343

Particle-Based Modeling of Living Actin Filaments in an Optical Trap

1
D3-Computation, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
2
Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
3
IAC, CNR, Via dei Taurini, Rome 00185, Italy
4
Department of Physics, University of Rome “La Sapienza”, P.le Aldo Moro 2, Rome 00185, Italy
5
School of Physics, University College Dublin, Belfield, Dublin 4, D04 V1W8, Ireland
6
Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio 10, L’Aquila 67100, Italy
7
Department of Physics, Université Libre de Bruxelles (ULB), Campus Plaine, CP 223, Brussels B-1050, Belgium
*
Authors to whom correspondence should be addressed.
Academic Editor: Martin Kröger
Received: 13 July 2016 / Revised: 19 August 2016 / Accepted: 6 September 2016 / Published: 19 September 2016
(This article belongs to the Special Issue Semiflexible Polymers)
View Full-Text   |   Download PDF [1087 KB, uploaded 19 September 2016]   |  

Abstract

We report a coarse-grained molecular dynamics simulation study of a bundle of parallel actin filaments under supercritical conditions pressing against a loaded mobile wall using a particle-based approach where each particle represents an actin unit. The filaments are grafted to a fixed wall at one end and are reactive at the other end, where they can perform single monomer (de)polymerization steps and push on a mobile obstacle. We simulate a reactive grand canonical ensemble in a box of fixed transverse area A, with a fixed number of grafted filaments N f , at temperature T and monomer chemical potential μ 1 . For a single filament case ( N f = 1 ) and for a bundle of N f = 8 filaments, we analyze the structural and dynamical properties at equilibrium where the external load compensates the average force exerted by the bundle. The dynamics of the bundle-moving-wall unit are characteristic of an over-damped Brownian oscillator in agreement with recent in vitro experiments by an optical trap setup. We analyze the influence of the pressing wall on the kinetic rates of (de)polymerization events for the filaments. Both static and dynamic results compare reasonably well with recent theoretical treatments of the same system. Thus, we consider the proposed model as a good tool to investigate the properties of a bundle of living filaments. View Full-Text
Keywords: biofilaments; actin networks; molecular simulation biofilaments; actin networks; molecular simulation
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Hunt, T.A.; Mogurampelly, S.; Ciccotti, G.; Pierleoni, C.; Ryckaert, J.-P. Particle-Based Modeling of Living Actin Filaments in an Optical Trap. Polymers 2016, 8, 343.

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