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. |
| References: | Structure. 1994 Nov 15;2(11):999-1002. (PMID: 7881910) Nature. 1976 Jun 17;261(5561):552-8. (PMID: 934293) J Mol Biol. 2017 Feb 3;429(3):348-355. (PMID: 27914894) Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2362-7. (PMID: 15677316) Int J Mol Sci. 2021 May 31;22(11):. (PMID: 34073028) Biochemistry. 1982 Aug 17;21(17):3955-65. (PMID: 6751382) Prog Biophys Mol Biol. 1993;60(3):201-39. (PMID: 8372226) Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15915-20. (PMID: 15520391) Biochemistry. 1996 Oct 1;35(39):12723-32. (PMID: 8841116) Biophys J. 2017 May 9;112(9):1829-1840. (PMID: 28494954) PLoS One. 2009 Dec 02;4(12):e8140. (PMID: 19956577) J Mol Biol. 1995 Apr 7;247(4):536-40. (PMID: 7723011) Structure. 2019 Jan 2;27(1):6-26. (PMID: 30393050) Proteins. 1997 Jun;28(2):241-60. (PMID: 9188741) FEBS Lett. 1984 Jan 23;166(1):33-8. (PMID: 6692923) Biophys J. 2008 Feb 1;94(3):726-36. (PMID: 17890394) Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W500-2. (PMID: 15215436) J Mol Biol. 1973 May 15;76(2):241-56. (PMID: 4737475) J Phys Chem B. 2012 Jun 7;116(22):6311-25. (PMID: 22587454) Protein Sci. 2016 Jul;25(7):1227-40. (PMID: 26610273) Nat Struct Biol. 1994 Jun;1(6):388-98. (PMID: 7664053) Proteomes. 2022 Feb 11;10(1):. (PMID: 35225987) Int J Mol Sci. 2021 Nov 02;22(21):. (PMID: 34769310) J Mol Biol. 1994 Mar 11;236(5):1382-400. (PMID: 8126727) Biopolymers. 1983 Dec;22(12):2577-637. (PMID: 6667333) |
| 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 |
Full Text Finder | تدمد: | 1422-0067 |
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| DOI: | 10.3390/ijms231911674 |