Abstract
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.