Root Douglas D
Department of Biological Sciences, Division of Biochemistry and Molecular Biology, University of North Texas, PO Box 305220 Denton, TX 76203-5220, USA.
Cell Biochem Biophys. 2002;37(2):97-110. doi: 10.1385/CBB:37:2:097.
Several atomic models of the actomyosin interface have been proposed based on the docking together of their component structures using electron microscopy and resonance energy-transfer measurements. Although these models are in approximate agreement in the location of the binding interfaces when myosin is tightly bound to actin, their relationships to molecular docking simulations based on computational free-energy calculations are investigated here. Both rigid-docking and flexible-docking conformational search strategies were used to identify free-energy minima at the interfaces between atomic models of myosin and actin. These results suggest that the docking model produced by resonance energy-transfer data is closer to a free-energy minimum at the interface than are the available atomic models based on electron microscopy. The conformational searches were performed using both scallop and chicken skeletal muscle myosins and identified similarly oriented actin-binding interfaces that serve to validate that these models are at the global minimum. These results indicate that the existing docking models are close to but not precisely at the lowest-energy initial contact site for strong binding between myosin and actin that should represent an initial contact between the two proteins; therefore, conformational changes are likely to be important during the transition to a strongly bound complex.
基于利用电子显微镜和共振能量转移测量将肌动球蛋白界面的组成结构对接在一起，已经提出了几种肌动球蛋白界面的原子模型。尽管当肌球蛋白紧密结合到肌动蛋白时，这些模型在结合界面的位置上大致一致，但本文研究了它们与基于计算自由能计算的分子对接模拟的关系。刚性对接和柔性对接构象搜索策略都被用于确定肌球蛋白和肌动蛋白原子模型之间界面处的自由能最小值。这些结果表明，与基于电子显微镜的现有原子模型相比，由共振能量转移数据产生的对接模型更接近界面处的自由能最小值。使用扇贝和鸡骨骼肌肌球蛋白进行了构象搜索，并确定了方向相似的肌动蛋白结合界面，这有助于验证这些模型处于全局最小值。这些结果表明，现有的对接模型接近但并非精确处于肌球蛋白和肌动蛋白之间强结合的最低能量初始接触位点，该位点应代表两种蛋白质之间的初始接触；因此，在向强结合复合物转变的过程中，构象变化可能很重要。
