Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein-RNA complexes is presented, A number of physical and chemical properties of the intermolecular interfa ces are calculated and compared with those observed in protein-double-stran ded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding site s. van der Waals contacts played a more prevalent role than hydrogen bond c ontacts, and preferential binding to guanine and uracil was observed. The p ositively charged residue, arginine, and the single aromatic residues, phen ylalanine and tyrosine, all played key roles in the RNA binding sites, A co mparison between protein-RNA and protein-DNA complexes showed that whilst b ase and backbone contacts (both hydrogen bonding and van der Waals) were ob served 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 betwe en the two types of nucleic acid binding protein at the atomic contact leve l.