Multiscale modeling of cellular actin filaments: From atomistic molecular to coarse-grained dynamics

被引:25
作者
Deriu, Marco A. [1 ]
Shkurti, Ardita [2 ]
Paciello, Giulia [2 ]
Bidone, Tamara C. [1 ]
Morbiducci, Umberto [1 ]
Ficarra, Elisa [2 ]
Audenino, Alberto [1 ]
Acquaviva, Andrea [2 ]
机构
[1] Politecn Torino, Dept Mech, I-10129 Turin, Italy
[2] Politecn Torino, Dept Control & Comp Engn, I-10129 Turin, Italy
关键词
actin; biomechanics; coarse grain; multiscale; cytoskeleton; molecular dynamics; Brownian dynamics; F-ACTIN; THERMAL FLUCTUATIONS; COFILIN INCREASES; NETWORK MODEL; SIMULATIONS; FLEXIBILITY; POLYMERIZATION; NUCLEOTIDE; PROTEINS; MECHANICS;
D O I
10.1002/prot.24053
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
In this article, we present a computational multiscale model for the characterization of subcellular proteins. The model is encoded inside a simulation tool that builds coarse-grained (CG) force fields from atomistic simulations. Equilibrium molecular dynamics simulations on an all-atom model of the actin filament are performed. Then, using the statistical distribution of the distances between pairs of selected groups of atoms at the output of the MD simulations, the force field is parameterized using the Boltzmann inversion approach. This CG force field is further used to characterize the dynamics of the protein via Brownian dynamics simulations. This combination of methods into a single computational tool flow enables the simulation of actin filaments with length up to 400 nm, extending the time and length scales compared to state-of-the-art approaches. Moreover, the proposed multiscale modeling approach allows to investigate the relationship between atomistic structure and changes on the overall dynamics and mechanics of the filament and can be easily (i) extended to the characterization of other subcellular structures and (ii) used to investigate the cellular effects of molecular alterations due to pathological conditions. Proteins 2012. (c) 2012 Wiley Periodicals, Inc.
引用
收藏
页码:1598 / 1609
页数:12
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