Exploring Residue Component Contributions to Dynamical Network Models of Allostery

Abstract

Allosteric regulation in biological systems is of considerable interest given the vast number of proteins that exhibit such behavior. Network models obtained from molecular dynamics simulations have been shown to be powerful tools for the analysis of allostery. In this work, different coarse-grain residue representations (nodes) are used together with a dynamical network model to investigate models of allosteric regulation. This model assumes that allosteric signals are dependent on positional correlations of protein substituents, as determined through molecular dynamics simulations, and uses correlated motion to generate a signaling weight between two given nodes. We examine four types of network models using different node representations in Cartesian coordinates: the (i) residue α-carbons, (ii) the side chain center of mass, (iii) the backbone center of mass, and the entire (iv) residue center of mass. All correlations are filtered by a dynamic contact map that defines the allowable interactions between nodes based on physical proximity. We apply the four models to imidazole glycerol phosphate synthase (IGPS), which provides a well-studied experimental framework in which allosteric communication is known to persist across disparate protein domains (e.g., a protein dimer interface). IGPS is modeled as a network of nodes and weighted edges. Optimal allosteric pathways are traced using the Floyd Warshall algorithm for weighted networks, and community analysis (a form of hierarchical clustering) is performed using the Girvan–Newman algorithm. Our results show that dynamical information encoded in the residue center of mass must be included in order to detect residues that are experimentally known to play a role in allosteric communication for IGPS. More broadly, this new method may be useful for predicting pathways of allosteric communication for any biomolecular system in atomic detail.

Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities

“…Allosteric networks were characterized using a community network analysis approach previously applied to investigate allostery in tRNA-protein complexes and other protein systems (24,31,32). This approach constructs a dynamic contact map consisting of a network graph in which each residue is treated as a "node" connected by edges to other nodes when two residues are deemed to be "in contact."…”

From local to global changes in proteins: a network view

“…using Floyd Warshall algorithm, Girvan-Newman algorithm) to identify nodes or links which are central to the communication in the network (betweenness, closeness, etc.). Such measures are used in protein allostery [22][23][24][25][26][27][28][29]. They are relevant only to networks whose communication seeks the shortest available routes (e.g.…”

MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations

“…A number of specialized methods have been proposed to address this issue (10)(11)(12)(13)(14)(15). Another approach that has been widely used in recent years is to analyze standard MD simulations with network theory (16)(17)(18)(19)(20)(21)(22). This approach involves modeling the protein as a graph, with residues mapped to network nodes, thus yielding a coarse-grained representation of the system.…”