Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions
| Autor: | Marco Gerolin, Paolo Calligari, Daniel Abergel, Antonino Polimeno |
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| Přispěvatelé: | Dipartimento di Scienze Chimiche [Padova], Università degli Studi di Padova = University of Padua (Unipd), Structure et Dynamique des Biomolécules (LBM-E3), Laboratoire des biomolécules (LBM UMR 7203), Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universita degli Studi di Padova, Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC) |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Quantitative Biology::Biomolecules Theoretical computer science [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM] 010304 chemical physics Basis (linear algebra) Cross-correlation Chemistry Structure (category theory) Proteins Domain decomposition methods Molecular Dynamics Simulation 01 natural sciences Computer Science Applications [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry Quantitative Biology::Subcellular Processes Distance correlation 03 medical and health sciences 030104 developmental biology Protein structure 0103 physical sciences Decomposition (computer science) Physical and Theoretical Chemistry Biological system Cluster analysis |
| Zdroj: | Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation, 2016, 13 (1), pp.309-319. ⟨10.1021/acs.jctc.6b00702⟩ Journal of Chemical Theory and Computation, American Chemical Society, 2016, 13 (1), pp.309-319. ⟨10.1021/acs.jctc.6b00702⟩ |
| ISSN: | 1549-9626 1549-9618 |
| Popis: | International audience; 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 pairwise 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. |
| Databáze: | OpenAIRE |
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