Coarse-Grained Protein Dynamics Studies Using Elastic Network Models

• Main Authors: Yuichi Togashi, Holger Flechsig
• Format: Article
• Language: English
• Published: MDPI AG 2018-12-01
• Series: International Journal of Molecular Sciences
• Subjects: elastic network; coarse-grained model; molecular dynamics; normal mode analysis; nonlinearity; protein; molecular machine; allostery
• Online Access: https://www.mdpi.com/1422-0067/19/12/3899

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.