Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues

摘要: Physical interactions between proteins are often difficult to decipher. The aim of this paper is present an algorithm that designed recognize binding patches and supporting structural scaffolds interacting heterodimer using the Gaussian Network Model (GNM). recognition based on (self) adjustable identification kinetically hot residues their connection possible scaffolds. with lowest entropy, i.e., highest contribution weighted sum fastest modes per chain extracted via GNM. adjusts number fast in GNM’s calculation ratio predicted expected numbers target (contact neighboring first-layer residues). This approach produces very good results when applied dimers high protein sequence length ratios. protocol’s ability near native decoys was compared residue-level statistical potential Lu Skolnick Sternberg Vakser decoy sets. produced better overall results, but a cases its predicting comparable, or even inferior, prediction GNM approach. presented suggest heterodimers at least one has scaffold determined by immovable, residues. In many cases, (especially if being noticeably different sizes) either behave as rigid lock key or, presumably, exhibit opposite dynamic behavior. While surface stable, partner’s more flexible adaptable.