On the Relation Between Residue Flexibility and Residue Interactions in Proteins

Hui      Yin; Yi-Zhou      Li; Meng-Long      Li

Abstract

B-factor from X-ray crystal structure can well measure protein structural flexibility, which plays an important role in different biological processes, such as catalysis, binding and molecular recognition. Understanding the essence of flexibility can be helpful for the further study of the protein function. In this study, we attempted to correlate the flexibility of a residue to its interactions with other residues by representing the protein structure as a residue contact network. Here, several well established network topological parameters were employed to feature such interactions. A prediction model was constructed for B-factor of a residue by using support vector regression (SVR). Pearson correlation coefficient (CC) was used as the performance measure. CC values were 0.63 and 0.62 for single amino acid and for the whole sequence, respectively. Our results revealed well correlations between B-factors and network topological parameters. This suggests that the protein structural flexibility could be well characterized by the inter-amino acid interactions in a protein.

Keywords: B-factors, network topological parameters, residue flexibility, SCOP, sliding window, SVR, correlation coefficient (CC), support vector regression (SVR), Residue Interactions, PDB, Support Vector Regression Prediction, GalNAc-transferase, LibSVMB-factors, network topological parameters, residue flexibility, SCOP, sliding window, SVR, correlation coefficient (CC), support vector regression (SVR), Residue Interactions, PDB, Support Vector Regression Prediction, GalNAc-transferase, LibSVM