Protein token: a dynamic unit in protein interactions

TL;DR

This paper introduces 'protein tokens' as a new dynamic structural unit for understanding protein-protein interactions, emphasizing their role in conformational changes and interaction specificity.

Contribution

The study proposes a novel concept of protein tokens that are based on cooperative conformational changes rather than traditional structural units, offering new insights into protein interaction mechanisms.

Findings

Identified various protein tokens in Ras GTPases superfamily.

Distinct token combinations correlate with different regulatory interactions.

Protein tokens may explain the multiplexer property of Ras proteins.

Abstract

In this study, we introduced a new unit, named "protein token", as a dynamic protein structural unit for protein-protein interactions. Unlike the conventional structural units, protein token is not based on the sequential or spatial arrangement of residues, but comprises remote residues involved in cooperative conformational changes during protein interactions. Application of protein token on Ras GTPases revealed various tokens present in the superfamily. Distinct token combinations were found in H-Ras interacting with its various regulators and effectors, directing to a possible clue for the multiplexer property of Ras superfamily. Thus, this protein token theory may provide a new approach to study protein-protein interactions in broad applications.