3ß-Corner Stability by Comparative Molecular Dynamics Simulations.
Int J Mol Sci
; 23(19)2022 Oct 02.
Article
em En
| MEDLINE
| ID: mdl-36232976
ABSTRACT
This study explored the mechanisms by which the stability of super-secondary structures of the 3ß-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3ß-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3ß-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3ß-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or "ready-made" building block in protein folding. The 3ß-corner can also be considered as an independent object for study in field of structural biology.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Água
/
Simulação de Dinâmica Molecular
Idioma:
En
Revista:
Int J Mol Sci
Ano de publicação:
2022
Tipo de documento:
Article
País de afiliação:
Federação Russa