School of Life Sciences, Henan University, JinMing Road, Kaifeng, 475000, China.
Institute of Biochemistry and Biophysics, University of Tehran, Enquelab Avenue, P.O. Box 13145-1384, Tehran, Iran.
Sci Rep. 2019 Mar 13;9(1):4353. doi: 10.1038/s41598-019-40892-0.
The conformational lock was a bio-thermodynamic theory to explain the characteristics of interfaces in oligomeric enzymes and their effects on catalytic activity. The previous studies on superoxide dismutases (Cu, Zn-SODs) showed that the dimeric structure contributed to the high catalytic efficiency and the stability. In this study, steered molecular dynamics simulations were used firstly to study the main interactions between two subunits of Cu, Zn-SODs. The decomposition process study showed that there were not only four pairs of hydrogen bonds but also twenty-five residue pairs participating hydrophobic interactions between A and B chains of SOD, and van der Waals interactions occupied a dominant position among these residue pairs. Moreover, the residue pairs of hydrogen bonds played a major role in maintaining the protein conformation. The analysis of the energy and conformational changes in the SMD simulation showed that there were two groups (two conformational locks) between A and B chains of SOD. The first group consisted of one hydrogen-bond residues pair and seven hydrophobic interactions residues pairs with a total average energy of -30.10 KJ/mol, and the second group of three hydrogen-bond residues pair and eighteen hydrophobic interactions residues pairs formed with a total average energy of -115.23 KJ/mol.
构象锁是一种生物热力学理论，用于解释寡聚酶界面的特性及其对催化活性的影响。先前关于超氧化物歧化酶（Cu，Zn-SOD）的研究表明，二聚体结构有助于提高催化效率和稳定性。在这项研究中，首次使用定向分子动力学模拟来研究 Cu，Zn-SOD 两个亚基之间的主要相互作用。分解过程研究表明，SOD 的 A 链和 B 链之间不仅存在四对氢键，还有二十五对残基对参与疏水相互作用，范德华相互作用在这些残基对中占据主导地位。此外，氢键残基对在维持蛋白质构象方面起着主要作用。SMD 模拟中能量和构象变化的分析表明，SOD 的 A 链和 B 链之间有两组（两个构象锁）。第一组由一个氢键残基对和七个疏水相互作用残基对组成，平均总能量为-30.10 KJ/mol，第二组由三个氢键残基对和十八个疏水相互作用残基对组成，平均总能量为-115.23 KJ/mol。
