Protein structural models for nucleic acid interactions

It is proposed that particular segments of some ribosomal, histone and plant viral capsid proteins adopt a helical structural mode for interaction with nucleic acid. The amino acid regions were determined by three probes applied to 26 protein sequences: searches for helical wheels displaying asymmetric basic charge distributions, secondary structural predictions, and searches for primary structural homologies. In 11 of the protein sequences examined, homologous heptapeptides were found in the residue spans delineated by the three probes. A helical wheel analysis of the oligopeptide amino acids showed a distinct positive charge clustering. It is suggested that the basic amino acid side chains on the hydrophilic helical side interact with nucleic acid negative phosphate groups while the somewhat hydrophobic side is available for interaction within the protein or possibly with the major groove of double-stranded nucleic acid.