A consensus residue analysis of loop and helix-capping residues in four- alpha-helical-bundle proteins

A statistical study was performed on a set of proteins which adopt the four-alpha-helical-bundle tertiary motif in order to determine amino acid occurrences at helix-capping and loop positions. Eight X-ray crystal structures from the Brookhaven Protein Data Bank (PDB) were examined and N", N', Ncap, Ccap, C' and C" residues were assigned. In addition, a set of 55 protein sequences for the analogous proteins from different strains and species was taken from the Protein Information Resource and Swiss-Prot databanks. The residues at the capping and loop positions in this expanded data set were deduced by aligning these sequences with those from the PDB files. Similar trends were observed in the two data sets. In general, polar residues were predominant in the loops, although aromatic residues were also fairly common. Glycine, a highly flexible residue with an excellent 'helix-breaking' ability, was very common at the Ccap, C' and C" residues. Proline, which can force sharp turns in the direction of a peptide backbone, was only common at the N" residue. Residues which can participate in the N-capping box motif were found with high frequency. Capping motifs at the helix C-termini (Schellman and alphaL motifs) were also somewhat common, while another helix N-terminal stabilizing motif, the hydrophobic stable, was not common. The data presented in this study should prove useful for applying the 'consensus residue' approach to the de novo design of loop regions in helical bundle proteins.