3β-Corner Stability by Comparative Molecular Dynamics Simulations

• Published in: International journal of molecular sciences 2022-10, Vol.23 (19), p.11674
• Main Authors: Rudnev, Vladimir R., Nikolsky, Kirill S., Petrovsky, Denis V., Kulikova, Liudmila I., Kargatov, Anton M., Malsagova, Kristina A., Stepanov, Alexander A., Kopylov, Arthur T., Kaysheva, Anna L., Efimov, Alexander V.
• Format: Article
• Language: English
• Subjects: Amino acids; Aqueous environments; Comparative analysis; Dynamic stability; Experiments; Gyration; Hydrogen bonding; Hydrogen bonds; Molecular dynamics; Protein folding; Proteins; Structural stability; Topology
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms231911674

This study explored the mechanisms by which the stability of super-secondary structures of the 3β-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 3β-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 3β-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 3β-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 3β-corner can also be considered as an independent object for study in field of structural biology.