Dissipative electro-elastic network model of protein electrostatics

TL;DR

This paper introduces a dissipative electro-elastic network model (DENM) that captures the dynamics and electrostatic fluctuations at active sites of proteins, integrating harmonic network theory with electrostatic charge effects.

Contribution

The model combines harmonic residue networks with overdamped dynamics and electrostatic charges, providing a new approach to study protein electrostatics and fluctuations.

Findings

Model accurately reproduces electrostatic fluctuation spectra

Matches all-atom molecular dynamics simulations results

Provides insights into protein electrostatic dynamics

Abstract

We propose a dissipative electro-elastic network model (DENM) to describe the dynamics and statistics of electrostatic fluctuations at active sites of proteins. The model combines the harmonic network of residue beads with overdamped dynamics of the normal modes of the network characterized by two friction coefficients. The electrostatic component is introduced to the model through atomic charges of the protein force field. The overall effect of the electrostatic fluctuations of the network is recorded through the frequency-dependent response functions of the electrostatic potential and electric field at the active site. We also consider the dynamics of displacements of individual residues in the network and the dynamics of distances between pairs of residues. The model is tested against loss spectra of residue displacements and the electrostatic potential and electric field at the heme's iron from all-atom molecular dynamics simulations of three hydrated globular proteins.