This study characterises the interaction between the type IV pilus assembly PilB ATPase of a versatile electroactive microbe, Shewanella oneidensis MR-1, and ATP using in silico tools. PilB ATPase, which is associated with different cellular activities, is a protein subunit of type IV pili. A composite model of the protein was generated using the I-TASSER Web server and its stereochemical quality was evaluated using PROCHECK. Loop modeling was performed using the InteractiveRosetta tool to refine the structure of the model and the COACH server was used to identify the functional binding site. The nature of binding, with the native ligand ATP, was determined using Autodock Vina and Discovery Studio Visualizer. Molecular dynamics simulations were carried out, with the bound and unbound states of the protein, for a period of 100 ns using GROMACS. Favorable root mean square deviation (0.75±0.10 nm) and radius of gyration (2.78±0.05 nm) values pointed to the stability of the modeled protein structure. Root mean square fluctuation and solvent accessible surface area analyses indicated a conformational change upon the ligand binding which occurred without a corresponding reorganization of secondary structures as evidenced by definition of secondary protein analysis. Molecular mechanics/Poisson–Boltzmann surface area analysis revealed the presence of a loop critical to the formation of stable interactions with ATP.

本研究描述了多功能电活性微生物Shewanella oneidensis MR-1 的 IV 型菌毛组装 PilB ATPase 与计算机工具中使用的 ATP之间的相互作用。PilB ATPase 是 IV 型菌毛的蛋白质亚基，与不同的细胞活动相关。使用 I-TASSER Web 服务器生成蛋白质的复合模型，并使用 PROCHECK 评估其立体化学质量。使用InteractiveRosetta工具进行循环建模以细化模型的结构，并使用COACH服务器来识别功能结合位点。使用 Autodock Vina 和 Discovery Studio Visualizer 确定与天然配体 ATP 的结合性质。使用 GROMACS 对蛋白质的结合和非结合状态进行了 100 ns 的分子动力学模拟。良好的均方根偏差（0.75±0.10 nm）和回转半径（2.78±0.05 nm）值表明模型蛋白质结构的稳定性。均方根波动和溶剂可及表面积分析表明配体结合时发生构象变化，而这种变化没有相应的二级结构重组，如二级蛋白质分析的定义所证明的。分子力学/泊松-玻尔兹曼表面积分析表明存在一个对于与 ATP 形成稳定相互作用至关重要的环。