title: Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions.
abstract: In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed.
authors.affiliation: Dipartimento di Scienze Chimiche, Università di Padova , via Marzolo, 1, I-35131 Padova, Italy.
authors.forename: Paolo
authors.identifier: 0000-0001-7614-8931
authors.initials: P
authors.lastname: Calligari
authors.affiliation: Dipartimento di Scienze Chimiche, Università di Padova , via Marzolo, 1, I-35131 Padova, Italy.|Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM) , 24 rue Lhomond, 75005 Paris, France.
authors.forename: Marco
authors.initials: M
authors.lastname: Gerolin
authors.affiliation: Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM) , 24 rue Lhomond, 75005 Paris, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Abergel
authors.affiliation: Dipartimento di Scienze Chimiche, Università di Padova , via Marzolo, 1, I-35131 Padova, Italy.
authors.forename: Antonino
authors.initials: A
authors.lastname: Polimeno
mesh_terms: D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins