Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties

Abstract

Heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression. The knowledge of heme binding residues can provide crucial clues to understand the mechanism of heme-protein interactions and aid in functional annotation. In the present work, we propose a sequence-based approach for the accurate prediction of heme binding residues by a novel integrative sequence profile coupling position specific scoring matrices with heme specific physicochemical properties. Particularly, we design an intuitive feature selection scheme for informative physicochemical properties. As shown in the primary results, our integrative sequence profile approach for prediction of heme binding residues outperforms the conventional methods using amino acid and evolutionary information on the 5-fold cross validation and the independent test.