Manipulation of conformational change in proteins by single residue perturbations

TL;DR

This study uses perturbation-response scanning to identify key residues in proteins that can induce conformational changes, revealing diverse mechanisms and correlating well with experimental data, with implications for understanding protein dynamics.

Contribution

The paper demonstrates that PRS can effectively identify residues controlling conformational changes, showing that multiple relevant modes can be triggered by single residue perturbations.

Findings

PRS identifies residues that induce conformational change in proteins.

Perturbation effects vary from scattered to localized residues.

Correlations with experimental displacements are high, validating PRS.

Abstract

Using the perturbation-response scanning (PRS) technique, we study a set of 23 proteins that display a variety of conformational motions upon ligand binding (e.g. shear, hinge, allosteric). In most cases, PRS determines residues that may be manipulated to achieve the resulting conformational change. PRS reveals that for some proteins, binding induced conformational change may be achieved through the perturbation of residues scattered throughout the protein, whereas in others, perturbation of specific residues confined to a highly specific region are necessary. Correlations between the experimental and calculated atomic displacements are always better or equivalent to those obtained from a modal analysis of elastic network models. Furthermore, best correlations obtained by the latter approach do not always appear in the most collective modes. We show that success of the modal analysis depends on the lack of redundant paths that exist in the protein. PRS thus demonstrates that several relevant modes may simultaneously be induced by perturbing a single select residue on the protein. We also illustrate the biological relevance of applying PRS on the GroEL and ADK structures in detail, where we show that the residues whose perturbation lead to the precise conformational changes usually correspond to those experimentally determined to be functionally important.