title: Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins.
abstract: A protein can interact with DNA or RNA molecules to perform various cellular processes. Identifying or analyzing DNA/RNA binding site amino acid residues is important to understand molecular recognition process. It is quite possible to accurately model DNA/RNA binding amino acid residues in experimental protein-DNA/RNA complex by using the electron density map whereas, locating/modeling the binding site amino acid residues in the predicted three dimensional structures of DNA/RNA binding proteins is still a difficult task. Considering the above facts, in the present work, we have carried out a comprehensive analysis of dihedral angle preferences of DNA and RNA binding site amino acid residues by using a classical Ramachandran map. We have computed backbone dihedral angles of non-DNA/RNA binding residues and used as control dataset to make a comparative study. The dihedral angle preference of DNA and RNA binding site residues of twenty amino acid type is presented. Our analysis clearly revealed that the dihedral angles (φ, ψ) of DNA/RNA binding amino acid residues prefer to occupy (-89° to -60°, -59° to -30°) bins. The results presented in this paper will help to model/locate DNA/RNA binding amino acid residues with better accuracy.
authors.affiliation: Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India.
authors.forename: Karthe
authors.initials: K
authors.lastname: Ponnuraj
authors.affiliation: Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India. Electronic address: saravananbioinform@gmail.com.
authors.forename: Konda Mani
authors.initials: KM
authors.lastname: Saravanan
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins; D012313:RNA; D004247:DNA
keywords: Binding site; Conformation change; DNA and RNA binding; Dihedral angles; Ramachandran map