期刊
BIOCHIMIE
卷 160, 期 -, 页码 88-92出版社
ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
DOI: 10.1016/j.biochi.2019.02.006
关键词
Protein structures; Peptides; Protein dynamics; Molecular dynamics; Stable conformations; Local protein conformations
资金
- Russian Foundation for Basic Research [18-54-00037]
- Program for Molecular and Cellular Biology of the Russian Academy of Sciences
- Russian Science Foundation [14-14-01152]
- Ministry of Research (France)
- University Paris Diderot, Sorbonne, Paris Cite (France)
- National Institute of Blood Transfusion (INTS, France)
- National Institute of Health and Medical Research (INSERM, France)
- labex GR-Ex
- program Investissements d'avenir of the French National Research Agency [ANR-11-LABX-0051, ANR-11-IDEX-0005-02]
- Indo-French Centre for the Promotion of Advanced Research/CEFIPRA [5302-2]
The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide sequences with no more than three functional groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures of peptides by the molecular dynamics method and found that 1,225 pentapeptides over 80% of the simulation time were in a stable conformation. Clustering of these conformations revealed 54 topological types of conformationally stable pentapeptides. These conformations relate to different combined elements of the protein secondary structure. So, we obtained a minimal set of amino acid structures of conformationally stable pentapeptides, creating a complete set of different topologies that ensure the formation of pre-folded conformation of protein structures. (C) 2019 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.
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