Department of Pure and Applied Physics, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, Japan.
J Am Chem Soc. 2012 May 30;134(21):8918-25. doi: 10.1021/ja301447j. Epub 2012 May 15.
Association of protein molecules constitutes the basis for the interaction network in a cell. Despite its fundamental importance, the thermodynamic aspect of protein-protein binding, particularly the issues relating to the entropy change upon binding, remains elusive. The binding of actin and myosin, which are vital proteins in motility, is a typical example, in which two different binding mechanisms have been argued: the binding affinity increases with increasing temperature and with decreasing salt-concentration, indicating the entropy-driven binding and the enthalpy-driven binding, respectively. How can these thermodynamically different binding mechanisms coexist? To address this question, which is of general importance in understanding protein-protein bindings, we conducted an in silico titration of the actin-myosin system by molecular dynamics simulation using a residue-level coarse-grained model, with particular focus on the role of the electrostatic interaction. We found a good agreement between in silico and in vitro experiments on the salt-concentration dependence and the temperature dependence of the binding affinity. We then figured out how the two binding mechanisms can coexist: the enthalpy (due to electrostatic interaction between actin and myosin) provides the basal binding affinity, and the entropy (due to the orientational disorder of water molecules) enhances it at higher temperatures. In addition, we analyzed the actin-myosin complex structures observed during the simulation and obtained a variety of weak-binding complex structures, among which were found an unusual binding mode suggested by an earlier experiment and precursor structures of the strong-binding complex proposed by electron microscopy. These results collectively indicate the potential capability of a residue-level coarse-grained model to simulate the association-dissociation dynamics (particularly for transient weak-bindings) exhibited by larger and more complicated systems, as in a cell.
蛋白质分子的相互作用构成了细胞内相互作用网络的基础。尽管其具有重要的基础性，但蛋白质-蛋白质结合的热力学方面，特别是结合过程中熵变的问题，仍然难以捉摸。肌动蛋白和肌球蛋白的结合就是一个典型的例子，对于这两种至关重要的运动蛋白，人们提出了两种不同的结合机制：结合亲和力随温度升高和盐浓度降低而增加，分别表明是熵驱动的结合和焓驱动的结合。这两种热力学上不同的结合机制怎么可能共存呢？为了解决这个普遍存在于理解蛋白质-蛋白质结合的问题，我们通过使用残基水平的粗粒化模型进行分子动力学模拟，对肌动蛋白-肌球蛋白系统进行了虚拟滴定实验，特别关注了静电相互作用的作用。我们发现虚拟和体外实验在盐浓度依赖性和结合亲和力的温度依赖性方面非常吻合。然后，我们弄清楚了这两种结合机制是如何共存的：由于肌动蛋白和肌球蛋白之间的静电相互作用，焓（enthalpy）提供了基本的结合亲和力，而熵（entropy）则在较高温度下增强了它。此外，我们还分析了模拟过程中观察到的肌动蛋白-肌球蛋白复合物结构，并获得了多种弱结合复合物结构，其中包括一个早期实验提出的不寻常结合模式和电子显微镜提出的强结合复合物的前体结构。这些结果共同表明，残基水平的粗粒化模型有潜力模拟更大、更复杂的系统（如细胞）中表现出的结合-解离动力学（特别是瞬态弱结合）。
