Abstract

BackgroundThe 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 these activities and aid in functional annotation, however, insufficient work has been done on the research of heme binding residues from protein sequence information.MethodsWe propose a sequence-based approach for accurate prediction of heme binding residues by a novel integrative sequence profile coupling position specific scoring matrices with heme specific physicochemical properties. In order to select the informative physicochemical properties, we design an intuitive feature selection scheme by combining a greedy strategy with correlation analysis.ResultsOur 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 tests.ConclusionsThe novel feature of an integrative sequence profile achieves good performance using a reduced set of feature vector elements.

Highlights

  • The heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression

  • The heme-protein interactions are involved in a wide range of biological processes such as electron transfer, catalysis, signal transduction and control of gene expression [1]

  • We performed a greedy feature selection approach in combination with correlation analysis to reach an optimal subset of features

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Summary

Introduction

The 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 these activities and aid in functional annotation, insufficient work has been done on the research of heme binding residues from protein sequence information. The heme-protein interactions are involved in a wide range of biological processes such as electron transfer, catalysis, signal transduction and control of gene expression [1]. To better understand the mechanism of hemeprotein interactions and aid in heme related functional annotation, it is crucial to characterize and identify the binding sites of heme proteins[2]. A pioneering method HemeBIND [3] is designed to predict heme binding residues on heme proteins. HemeBIND provides two complementary methods to distinguish heme binding

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