دورية أكاديمية
3β-Corner Stability by Comparative Molecular Dynamics Simulations.
العنوان: | 3β-Corner Stability by Comparative Molecular Dynamics Simulations. |
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المؤلفون: | Rudnev VR; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia.; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia., Nikolsky KS; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Petrovsky DV; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Kulikova LI; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia.; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia., Kargatov AM; Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia., Malsagova KA; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Stepanov AA; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Kopylov AT; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Kaysheva AL; Biobanking Group, Branch of Institute of Biomedical Chemistry 'Scientific and Education Center', 109028 Moscow, Russia., Efimov AV; Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia. |
المصدر: | International journal of molecular sciences [Int J Mol Sci] 2022 Oct 02; Vol. 23 (19). Date of Electronic Publication: 2022 Oct 02. |
نوع المنشور: | Journal Article |
اللغة: | English |
بيانات الدورية: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Basel, Switzerland : MDPI, [2000- |
مواضيع طبية MeSH: | Molecular Dynamics Simulation* , Water*, Amino Acids ; Protein Structure, Secondary ; Solvents/chemistry |
مستخلص: | 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. |
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معلومات مُعتمدة: | 2021-2030 Russian Federation Fundamental Research Program for the long-term period for |
فهرسة مساهمة: | Keywords: 3β-corner; folding nuclei; structure stability; super-secondary structure |
المشرفين على المادة: | 0 (Amino Acids) 0 (Solvents) 059QF0KO0R (Water) |
تواريخ الأحداث: | Date Created: 20221014 Date Completed: 20221017 Latest Revision: 20221019 |
رمز التحديث: | 20231215 |
مُعرف محوري في PubMed: | PMC9570037 |
DOI: | 10.3390/ijms231911674 |
PMID: | 36232976 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1422-0067 |
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DOI: | 10.3390/ijms231911674 |