Work

Communication pathway analysis within protein-nucleic acid complexes

Year: 2025

Type: article

Abstract: We developed ComPASS, a large-scale computational method designed to study communication networks in protein-protein and protein-nucleic acid complexes. Recognizing the significance of dynamics in the communication of macromolecules, our approach leverages molecular dynamics (MD) simulation data to extract inter-residue key properties, including dynamical correlations, interactions, and distances. These properties are integrated to construct a weighted communication network that comprehensively represents dependencies among amino acids and nucleotides. Using ComPASS, we uncovered distinct mechanisms of signal transmission in diverse macromolecular systems, namely Cysteinyl-tRNA synthetase (1u0b), LacI repressor, Type IIF restriction endonuclease Bse634I, liver X receptor, and four nucleosome complexes (1kx5, 1kx5_L1, 1f66, ncp601). Here we share the MD trajectories for each system, as well as the ComPASS results.

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.14843517

Authors: Bheemireddy, Sneha, Gonzalez-Aleman, Roy, Bignon, Emmanuelle, Karami, Yasaman

Institutions: Laboratoire Lorrain de Recherche en Informatique et ses Applications, Centre Inria de l'Université de Lorraine, Université de Lorraine, Laboratoire de Physique et Chimie Théoriques

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: Grand Équipement National De Calcul Intensif

Awards: G3281094210, G5063110