Nucleic Acids Research, 2001, Vol. 29, No. 4 943-954
© 2001 Oxford University Press
Protein–RNA interactions: a structural analysis
1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK, 2Department of Chemistry, Rutgers, The State University, Piscataway, NJ 08855-0939, USA and 3Department of Crystallography, Birkbeck College, Malet Street, London WC1 7HX, UK
A detailed computational analysis of 32 protein–RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein–double-stranded DNA and protein–single-stranded DNA complexes. The interface properties of the protein–RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein–RNA and protein–DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein–RNA complexes, backbone contacts were more dominant in the protein–DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.
* To whom correspondence should be addressed at: Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1 6BT, UK. Tel: +44 207 679 7048; Fax: +44 207 916 8499; Email: thornton@biochem.ucl.ac.uk
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