Quantitative computational and informatics studies on protein-protein interaction systems based on their dynamic structures

我们新开发了V-mcmd方法，进行了比以前更有效的增强采样。将该方法与我们的新的非Ewald方法相结合用于周期体系的快速分子动力学模拟，从而基于分子体系的自由能景观对蛋白质二聚体形成的稳定性进行了定量分析，其中主链和侧链构象在结合时发生变化。此外，对蛋白质界面的局部结构和分子表面进行了详尽的研究，发现蛋白质在不同的折叠上共享许多共同的斑块。确定了常见的结构基序，定义为结构基序组合的复合基序与蛋白质的分子功能很好地对应。

We have newly developed the V-McMD method, performing much more effective enhanced sampling than before. This method has been combined with our new non-Ewald method for rapid molecular dynamics simulations for the periodic system, so that the quantitative analysis for the stability of the protein dimer formation was made based on the free energy landscape for the molecular system, where the backbone and the side-chain conformations change upon binding. In addition, the local structures and molecular surfaces of the protein interfaces were investigated exhaustively, and many common patches are found to be shared in proteins across the different folds. The common structural motifs were identified, and the composite motifs, which are defined as the combination of those structural motifs, correspond well with the molecular functions of proteins.