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Open AccessReview

Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

by Yuichi Togashi 1,2,3,* and Holger Flechsig 4
1
Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
2
RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
3
Cybermedia Center, Osaka University, 5-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
4
Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2018, 19(12), 3899; https://doi.org/10.3390/ijms19123899
Received: 8 November 2018 / Revised: 28 November 2018 / Accepted: 3 December 2018 / Published: 5 December 2018
(This article belongs to the Special Issue Protein Structural Dynamics)
Elastic networks have been used as simple models of proteins to study their slow structural dynamics. They consist of point-like particles connected by linear Hookean springs and hence are convenient for linear normal mode analysis around a given reference structure. Furthermore, dynamic simulations using these models can provide new insights. As the computational cost associated with these models is considerably lower compared to that of all-atom models, they are also convenient for comparative studies between multiple protein structures. In this review, we introduce examples of coarse-grained molecular dynamics studies using elastic network models and their derivatives, focusing on the nonlinear phenomena, and discuss their applicability to large-scale macromolecular assemblies. View Full-Text
Keywords: elastic network; coarse-grained model; molecular dynamics; normal mode analysis; nonlinearity; protein; molecular machine; allostery elastic network; coarse-grained model; molecular dynamics; normal mode analysis; nonlinearity; protein; molecular machine; allostery
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Togashi, Y.; Flechsig, H. Coarse-Grained Protein Dynamics Studies Using Elastic Network Models. Int. J. Mol. Sci. 2018, 19, 3899.

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