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.
Int J Mol Sci. 2022 Oct 2;23(19):11674. 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.
本研究探索了在水相环境中，蛋白质球外的 3β-转角型超二级结构稳定性的维持机制。分子动力学（MD）研究确定了大量不同来源的非同源 3β-转角结构的行为多样性。我们关注了一些几何参数，如回转半径、溶剂可及面积、主要构象寿命和扭转角以及氢键的数量。最终，从 330 个结构中选择了一组 3β-转角，其均方根偏差（RMSD）小于 5Å，回转半径的变化不超过 5%，并且残基位于 Ramachandran 图谱允许区域内。在整个 MD 实验过程中，所研究的结构保留了其拓扑结构。因此，3β-转角结构在水环境中本身就具有相当的稳定性，即没有蛋白质分子的其余部分，并且可以作为蛋白质折叠的核心或“现成”构建块。3β-转角也可以被视为结构生物学领域的一个独立研究对象。
