Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks

• Published in: Biochimica et biophysica acta. General subjects
• Main Authors: Astl, Lindy, Verkhivker, Gennady M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 19.07.2019
• Subjects: Allosteric modulators; Allosteric proteins; case studies; coevolution; Coevolutionary networks; combination drug therapy; Functional dynamics; Protein kinases; protein structure; proteins; Residue coevolution; Residue interaction networks; signal transduction; Allosteric modulators; Allosteric proteins; Coevolutionary networks; Functional dynamics; Residue coevolution; Protein kinases; Residue interaction networks
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2019.07.008

Computational studies of allosteric interactions have witnessed a recent renaissance fueled by the growing interest in modeling of the complex molecular assemblies and biological networks. Allosteric interactions in protein structures allow for molecular communication in signal transduction networks. In this work, we performed a large scale comprehensive and multi-faceted analysis of >300 diverse allosteric proteins and complexes with allosteric modulators. By modeling and exploring coarse-grained dynamics, residue coevolution, and residue interaction networks for allosteric proteins, we have determined unifying molecular signatures shared by allosteric systems. The results of this study have suggested that allosteric inhibitors and allosteric activators may differentially affect global dynamics and network organization of protein systems, leading to diverse allosteric mechanisms. By using structural and functional data on protein kinases, we present a detailed case study that that included atomic-level analysis of coevolutionary networks in kinases bound with allosteric inhibitors and activators. We have found that coevolutionary networks can form direct communication pathways connecting functional regions and can recapitulate key regulatory sites and interactions responsible for allosteric signaling in the studied protein systems. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of known regulatory hotspots in protein kinases. This study has shown that allosteric inhibitors and allosteric activators can have a different effect on residue interaction networks and can exploit distinct regulatory mechanisms, which could open up opportunities for probing allostery and new drug combinations with broad range of activities. [Display omitted] •Allosteric proteins produce small world interaction networks.•Allosteric inhibitors and activators have a different effect on residue interaction networks.•Allosteric activators induce mobility of highly coevolving residues.•Allosteric changes are sequence-encoded through residue coevolution.•Hubs in coevolutionary networks define allosteric regulatory centers.