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

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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.