Modeling truncated hemoglobin vibrational dynamics

TL;DR

This study investigates the vibrational dynamics of truncated hemoglobins using a Gaussian network model, revealing functional motions and ligand pathways with implications for understanding protein function.

Contribution

Introduces a beta Gaussian model incorporating effective beta carbons to analyze the collective dynamics of truncated hemoglobins, highlighting functional motions and ligand pathways.

Findings

Identifies anti-correlated motions between functionally relevant sites.

Reveals a tunnel-cavity system facilitating ligand binding.

Estimates relaxation times of slowest vibrational modes.

Abstract

We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides C-alphas for all residues but glycines in the coarse-graining procedure, without leading to an increase in the degrees of freedom (betaGaussian Model). Normalized covariance matrix and deformation along slowest modes with collective character are analyzed, pointing out anti-correlations between functionally relevant sites for the proteins under study. In particular we underline the functional motions of an extended tunnel-cavity system running inside the protein matrix, which provide a pathway for small ligands binding with the iron in the heme group. We give a rough estimate of the order of magnitude of the relaxation times of the slowest two overdamped modes and compare results with previous studies on globins.