Motifs in proteins: Disulfide constraints and their applications to protein engineering and peptide modelling

Abstract

By carrying out a detailed data analysis of 175 PP motifs in proteins, sequence–structure relationships were identified for linking loops 1–5 residues long. Conformational families were recognized in 1-, 2-, 3-, and 4-residue linking segments in 3P motifs. A marked clustering of linking residue conformation was observed for one- and two-residue linkers. A model calculation performed on two 9-residue L-Ala strands linked by a single Gly/Ala residue revealed no stereochemical restrictions on the linking residues, other than those which correspond to the classical Ramachandran contact restrictions. The presence of the linking residue in the right-handed helix region (?, ? space) results in an orthogonal or ‘L’-shaped orientation of the two ?-strands, whereas ?-conformation results in a ?-hairpin. Examples with ‘L’-shaped PP motifs were subjected to an explicit analysis. A vast majority have only a single residue as the linking element. Analysis of the conformational angles at the bend region in these motifs revealed the frequent presence of Type VIII ?-turn and also that Type II ?-turn is quite common. A study of these orthogonal PP motifs to find out if they were in-register with other ?-strands in the protein showed that some of them remain isolated. It is conceivable that isolated ‘L’-motifs may not contribute significantly to the stabilization of the overall fold, but may in fact be an artifact, a kind of molecular fossil, of the folding process. The data and the analysis that have been presented in this chapter should prove useful in the design, modification, and modeling of linker regions of motifs, in general.