Kumar R Pravin, Roopa L, Nongthomba Upendra, Sudheer Mohammed M M, Kulkarni Naveen
Research and Development Centre, Bharathiar University, Coimbatore, India; Polyclone Bioservices, Bangalore, India.
Research and Development Centre, Bharathiar University, Coimbatore, India.
J Mol Graph Model. 2016 Jan;63:29-37. doi: 10.1016/j.jmgm.2015.11.007. Epub 2015 Nov 23.
CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the β-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable "tense" state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin.
已知葫芦素E（CurE）可与F-肌动蛋白共价结合并抑制解聚。然而，CurE与F-肌动蛋白的结合模式以及由此导致的F-肌动蛋白动力学变化尚未得到研究。通过对F-肌动蛋白和CurE对接复合物进行分子动力学（MD）模拟后，利用量子力学/分子力学（QM/MM）和密度泛函理论（DFT）模拟，提出了迈克尔反应的详细过渡态（TS）模型。TS模型显示，Cys257的硫原子对CurE的迈克尔受体的β-碳进行亲核攻击，产生一种烯醇中间体，该中间体与CurE形成共价键。MD结果表明，游离形式的F-肌动蛋白结构与与CurE复合的F-肌动蛋白结构之间存在明显差异。CurE影响核苷酸结合口袋的构象，增加F-肌动蛋白与ADP之间的结合亲和力，进而可能影响核苷酸交换。CurE的结合还限制了F-肌动蛋白相对灵活的结构域1的相关位移，导致蛋白质保持扁平结构并转变为稳定的“紧张”状态。这种结构转变可能会抑制F-肌动蛋白的解聚。总之，CurE通过变构调节ADP并稳定F-肌动蛋白结构，从而影响F-肌动蛋白的核苷酸交换和解聚。
