Journal Article

Functionally important residues from graph analysis of coevolved dynamic couplings

Garnett, James A, Xu, Manming, Dantu, Sarath Chandra, Haider, Shozeb, Bonomo, Robert A, Pandini, Alessandro

2025

Overview

The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins’ performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue–residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings—residue pairs with critical dynamical interactions that have been preserved during evolution—DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.

• Publisher: eLife Sciences Publications Ltd
• Subject: Antibiotic resistance / Antibiotics / beta-Lactamases - chemistry / beta-Lactamases - genetics / beta-Lactamases - metabolism / Catalysis / Coevolution / Computational Biology - methods / Computer applications / Drug development / DyNoPy / Enzymes / Evolution / Evolution, Molecular / molecular dynamics / Molecular Dynamics Simulation / Mutation / Proteins / Proteins - chemistry / Proteins - genetics / Proteins - metabolism / Simulation / β Lactamase