Vibrational density of states capture the role of dynamic allostery in protein evolution

TL;DR

This study introduces a method to visualize protein evolution by analyzing vibrational density of states, revealing how dynamic allostery influences functional changes in proteins over time.

Contribution

It demonstrates that VDOS profiles can track protein evolution and highlight the role of dynamic allostery, including flexibility changes without amino acid substitutions.

Findings

VDOS profiles differ between ancestral and extant proteins in the terahertz region.

Dynamic allostery plays a key role in protein functional evolution.

VDOS of individual positions can indicate flexibility changes without amino acid substitutions.

Abstract

Previous studies of the flexibilities of ancestral proteins suggests that proteins evolve their function by altering their native state ensemble. Here we propose a more direct method of visualizing this by measuring the changes in the vibrational density of states (VDOS) of proteins as they evolve. Through analysis of VDOS profiles of ancestral and extant proteins we observe that $\beta$-lactamase and thioredoxins evolve by altering their density of states in the terahertz region. Particularly, the shift in VDOS profiles between ancestral and extant proteins suggests that nature utilize dynamic allostery for functional evolution. Moreover, we also show that VDOS profile of individual position can be used to describe the flexibility changes, particularly those without any amino acid substitution.