Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches

Author:

Shin Woong-Hee,Kumazawa Keiko,Imai Kenichiro,Hirokawa Takatsugu,Kihara Daisuke

Abstract

Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer.

Funder

National Institutes of Health

Directorate for Biological Sciences

Division of Information and Intelligent Systems

Division of Civil, Mechanical and Manufacturing Innovation

National Research Foundation of Korea

Japan Society for the Promotion of Science

Japan Agency for Medical Research and Development

Publisher

Frontiers Media SA

Subject

Biochemistry, Genetics and Molecular Biology (miscellaneous),Molecular Biology,Biochemistry

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