Development of a structure based protein function prediction method: Calcium binding protein

Abstract

Three-dimensional local structures located near active sites are responsible for protein functions. To predict protein functions, we developed a method to extract three-dimensional structural characteristics of functions. We chose EF-hand calcium binding proteins as the model target. We defined a local structure as the structure within 12Å from an arbitrary Asp(C^α). Analysis of the amino acid propensities in the active sites showed that there were clear preferences for certain amino acids to locate at the binding sites. Furthermore, the analysis of the distributions of the distances between Asp(C^α) and any other amino acids(C^α) showed that there were preferred distances for respective amino acids. Using such structural data, we derived a DB (distance based) score and a DPB (distance and propensity based) score for the prediction of functional sites. A search for EF-hand calcium binding sites was performed to test the method. EF-hand calcium binding sites were successfully predicted. Key Words: protein local structures, calcium binding protein, EF-hand calcium binding site, amino acid propensity, distance distribution