Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.
Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.
复制标题
拟南芥肌动蛋白解聚因子1与肌动蛋白结合机制的计算研究
DOI：
10.1371/journal.pone.0159053
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Yao XJ
中科院分区：
文献类型：
--
作者：
Du J;Wang X;Dong CH;Yang JM;Yao XJ
肌动蛋白是一种高度保守的蛋白。它在细胞功能中起重要作用，以单体（G-肌动蛋白）或聚合形式（F-肌动蛋白）存在。肌动蛋白解聚因子（ADF）/cofilin蛋白家族的成员结合到G-肌动蛋白和F-肌动蛋白，并通过操纵丝聚合和解聚的速率在肌动蛋白动力学中发挥重要作用。拟南芥肌动蛋白解聚因子1（ADF 1）的S6 D和R98 A/K100 A突变体降低了ADF与肌动蛋白单体的结合亲和力。为了研究ADF 1-actin复合物的结合机制和动力学行为，我们基于AtADF 1的晶体结构和twinfilin C-末端ADF-H结构域与小鼠肌动蛋白单体的复合物，构建了AtADF 1-actin复合物的同源模型。然后，该模型被细化为后续的分子动力学模拟。使用分子力学广义玻恩表面积和泊松-玻尔兹曼表面积（MM-GB/PBSA）方法观察到突变系统的结合能增加。为了确定对ADF 1肌动蛋白结合亲和力有决定性贡献的残基，进行了残基分解和计算丙氨酸扫描分析，这提供了关于结合机制的更详细的信息。均方根波动和主成分分析证实，S6 D和R98 A/K100 A突变体诱导增加的构象灵活性。从本研究中获得的全面的分子见解是非常重要的了解ADF 1和G-actin的结合机制。
Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1–actin complex, we constructed a homology model of the AtADF1–actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson–Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.