The “violin model”: Looking at community networks for dynamic allostery

Author:

Madan Lalima K.12ORCID,Welsh Colin L.1ORCID,Kornev Alexandr P.3ORCID,Taylor Susan S.34

Affiliation:

1. Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina 1 , 173 Ashley Ave., Charleston, South Carolina 29425, USA

2. Hollings Cancer Center, Medical University of South Carolina 2 , 173 Ashley Ave., Charleston, South Carolina, 29425, USA

3. Department of Pharmacology, University of California San Diego 3 , 9500 Gilman Drive, San Diego, California, 92093, USA

4. Department of Chemistry and Biochemistry, University of California San Diego 4 , 9500 Gilman Drive, San Diego, California, 92093, USA

Abstract

Allosteric regulation of proteins continues to be an engaging research topic for the scientific community. Models describing allosteric communication have evolved from focusing on conformation-based descriptors of protein structural changes to appreciating the role of internal protein dynamics as a mediator of allostery. Here, we explain a “violin model” for allostery as a contemporary method for approaching the Cooper–Dryden model based on redistribution of protein thermal fluctuations. Based on graph theory, the violin model makes use of community network analysis to functionally cluster correlated protein motions obtained from molecular dynamics simulations. This Review provides the theory and workflow of the methodology and explains the application of violin model to unravel the workings of protein kinase A.

Funder

National Institute of General Medical Sciences

Publisher

AIP Publishing

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

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