Enhanced conformational sampling, a genetic-algorithm-guided multi-dimensional virtual-system coupled molecular dynamics, can provide equilibrated conformational distributions of a receptor protein and a flexible ligand at room temperature. The distributions provide not only the most stable but also semi-stable complex structures, and propose a ligand-receptor binding process. This method was applied to a system consisting of a receptor protein, 14-3-3&#949, and a flexible peptide, phosphorylated Myeloid leukemia factor 1 (pMLF1). The results present comprehensive binding pathways of pMLF1 to 14-3-3&#949. We identified four thermodynamically stable clusters of MLF1 on the 14-3-3&#949 surface, and free-energy barriers among some clusters. The most stable cluster includes two high-density spots connected by a narrow corridor. When pMLF1 passes the corridor, a salt-bridge relay (switching) related to the phosphorylated residue of pMLF1 occurs. Conformations in one high-density spots are similar to the experimentally determined complex structure. Three-dimensional distributions of residues in the intermolecular interface rationally explain the binding-constant changes resultant from alanine-mutation experiment for the residues. We performed a simulation of non-phosphorylated peptide and 14-3-3&#949, which demonstrated that the complex structure was unstable, suggesting that phosphorylation of the peptide is crucially important for binding to 14-3-3&#949.

中文翻译：

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14-3-3蛋白与磷酸化肽的分子相互作用机理（通过增强的构象采样得以阐明）

增强的构象采样是一种由遗传算法指导的多维虚拟系统耦合的分子动力学，可以在室温下提供受体蛋白和柔性配体的平衡构象分布。该分布不仅提供最稳定的而且提供半稳定的复杂结构，并提出了配体-受体结合过程。此方法应用于由受体蛋白14-3-3＆＃949和柔性肽磷酸化的髓样白血病因子1（pMLF1）组成的系统。结果显示了pMLF1与14-3-3＆＃949的全面结合途径。我们在14-3-3＆＃949表面上鉴定了四个热力学稳定的MLF1团簇，并且在一些团簇之间存在自由能垒。最稳定的群集包括通过狭窄走廊连接的两个高密度点。当pMLF1通过通道时，发生与pMLF1磷酸化残基有关的盐桥中继（转换）。一个高密度斑点中的构象类似于实验确定的复杂结构。分子间界面中残基的三维分布合理地解释了由丙氨酸突变实验产生的结合常数变化。我们对未磷酸化的肽和14-3-3＆＃949进行了模拟，这证明了复杂的结构是不稳定的，这表明肽的磷酸化对于结合14-3-3＆＃949至关重要。分子间界面中残基的三维分布合理地解释了由丙氨酸突变实验产生的结合常数变化。我们对未磷酸化的肽和14-3-3＆＃949进行了模拟，这证明了复杂的结构是不稳定的，这表明肽的磷酸化对于结合14-3-3＆＃949至关重要。分子间界面中残基的三维分布合理地解释了由丙氨酸突变实验产生的结合常数变化。我们对未磷酸化的肽和14-3-3＆＃949进行了模拟，这证明了复杂的结构是不稳定的，这表明肽的磷酸化对于结合14-3-3＆＃949至关重要。