Synchronous and asynchronous response in dynamically perturbed proteins

Abstract

We present a dynamic perturbation-response model of proteins based on the Gaussian Network Model, where a residue is perturbed periodically, and the dynamic response of other residues is determined. The model shows that periodic perturbation causes a synchronous response in phase with the perturbation and an asynchronous response that is out of phase. The asynchronous component results from the viscous effects of the solvent and other dispersive factors in the system. The model is based on the solution of the Langevin equation in the presence of solvent, noise, and perturbation. We introduce several novel ideas: The concept of storage and loss compliance of the protein and their dependence on structure and frequency; the amount of work lost and the residues that contribute significantly to the lost work; new dynamic correlations that result from perturbation; causality, that is, the response of j when i is perturbed is not equal to the response of i when j is perturbed. As examples, we study two systems, namely, bovine rhodopsin and the class of nanobodies. The general results obtained are (i) synchronous and asynchronous correlations depend strongly on the frequency of perturbation, their magnitude decreases with increasing frequency, (ii) time-delayed mean-squared fluctuations of residues have only synchronous components. Asynchronicity is present only in cross correlations, that is, correlations between different residues, (iii) perturbation of loop residues leads to a large dissipation of work, (iv) correlations satisfy the hypothesis of pre-existing pathways according to which information transfer by perturbation rides on already existing equilibrium correlations in the system, (v) dynamic perturbation can introduce a selective response in the system, where the perturbation of each residue excites different sets of responding residues, and (vi) it is possible to identify nondissipative residues whose perturbation does not lead to dissipation in the protein. Despite its simplicity, the model explains several features of allosteric manipulation.