Related Experiment Video
Updated: Aug 8, 2025

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
Published on: April 13, 2022
The "violin model": Looking at community networks for dynamic allostery
Lalima K Madan1, Colin L Welsh1, Alexandr P Kornev2
1Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Ave., Charleston, South Carolina 29425, 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.
More Related Videos
Related Concept Videos
Cooperative Allosteric Transitions
Allosteric Regulation
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Problem-Solving: Tuning of a Guitar String
The string's wave speed can be regulated by varying the linear density. Tension is the other property that determines the speed of...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Sequence Networks of Rotating Machines
Zero-sequence current induces a voltage drop across the generator's neutral impedance and other...

