Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals

Abstract

An analysis on the nature of α-helix stop signals has been carried out, using a dataset of 1057 helices identified from 250 high resolution (≤2.0 A), non-homologous, protein crystal structures. The backbone dihedral angles (φ, ψ) of the terminating residue (T) were found to cluster either in the left-handed helical region (α_L: φ = 20° to 125° and ψ = -45° to 90°; 469 helices (44%)) or in the extended region (E: φ = -180° to -30° and ψ = 60° to 180° and -180° to -150°; 459 helices (43%)) of the Ramachandran map. These two broad categories of helix stop signals, α_L and E-terminated helices, were further examined for sequence preferences. Gly residues were found to have an overwhelming preference to occur as the "α_L-terminator (T)" resulting in the classical Schellman motif, with a strong preference for hydrophobic residues at position T - 4 and T + 1. In the case of E-terminated helices His, Asn, Leu and Phe were found to occur with high propensity at position T. Quite remarkably Pro residues, with single exception, were absent at position T, but had the highest propensity at position T + 1. Examination of the frequencies of hydrophobic (h) and polar (p) residues at positions flanking Gly/Pro permitted delineation of exclusive patterns and predictive rules for Gly-terminated helices and Pro-terminated helices. The analysis reveals that Pro residues flanked by polar amino acids have a very strong tendency to terminate helices. Examination of a segment ranging from T - 4 to T + 3 appeared to be necessary to determine whether helix termination or continuation occur at Gly residues. The two types of helix termination (α_L, E) signals also differed dramatically in their solvent accessibility. Gly and Pro residues at helix termini appeared to be strongly conserved in homologous sequences.