Geometric and amino acid type determinants for protein-protein interaction interfaces

Yongxiao Yang, Wei Wang, Yuan Lou, Jianxin Yin, Xinqi Gong

Abstract: p><i>Background</i>: Protein-protein interactions are essential to many biological processes. The binding site information of protein-protein complexes is extremely useful to obtain their structures from biochemical experiments. Geometric description of protein structures is the precondition of protein binding site prediction and protein-protein interaction analysis. The previous description of protein surface residues is incomplete, and little attention are paid to the implication of residue types for binding site prediction.</p> <p><i>Methods</i>: Here, we found three new geometric features to characterize protein surface residues which are very effective for protein-protein interface residue prediction. The new features and several commonly used descriptors were employed to train millions of residue type-nonspecific or specific protein binding site predictors.</p> <p><i>Results</i>: The amino acid type-specific predictors are superior to the models without distinction of amino acid types. The performances of the best predictors are much better than those of the sophisticated methods developed before.</p> <p><i>Conclusions</i>: The results demonstrate that the geometric properties and amino acid types are very likely to determine if a protein surface residue would become an interface one when the protein binds to its partner.</p>