The 'violin model': Looking at community networks for dynamic allostery

Autor:	Lalima K. Madan, Colin L. Welsh, Alexandr P. Kornev, Susan S. Taylor
Rok vydání:	2023
Předmět:	General Physics and Astronomy Physical and Theoretical Chemistry
Zdroj:	The Journal of Chemical Physics. 158:081001
ISSN:	1089-7690 0021-9606
Popis:	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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_________::f2778b54357d46982eaf9f23cf00b90a https://doi.org/10.1063/5.0138175 Zobrazit plný text záznamu