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Fig. 5.1 Ramachandran map for the l-alanine residue. The dark boxes enclose the regions of f,c space that may be broadly classified as right-handed helical (aR), left-handed helical (aL) and extended (b) regions. The extended b-region may be further subdivided into polyproline II (PII) and b-sheet (parallel and antiparallel) secondary structures.

are conveniently identified by a clustering of successive residues in specific regions of space (Fig. 5.1).

Figure 5.2 illustrates the distribution of non-Gly and Gly residues in a data set of high resolution protein structures [13]. Glycine is unique amongst the amino acid constituents of proteins, being the smallest in size and also the only achiral residue. These features result in a much larger region of f,c space being steri-cally accessible. The Ramachandran allowed regions are symmetric with respect to origin of the f,c map, permitting Gly residue to adopt local conformations which are sterically forbidden for the other 19 i-amino acids. The scatter plot for the non-Gly residues shows a distribution, which is largely concentrated in three broad regions denoted as aR, b/PII and aL, which correspond to the right-handed a-helical, extended strand and left-handed helical regions of f,c space, respectively. The distribution in the extended region ((f @ —130 G 50°) may be subdivided into two clusters corresponding to b strands (bf @ —120°) and polyproline II (Piif @ —60°). Most individual residues in proteins do not have a strong intrinsic preference for either the helical or extended strand regions, limiting the use of statistically determined propensities in the design of local structures. Two residues, for which conformational biases are significant, are i-Pro and i-Asn. The observed distribution for i-Pro residues in proteins (Fig. 5.2) highlights the narrow distribution of f values (f = — 60 G 20°), which results from the constraints imposed by the pyrrolidine ring. Two distinct clusters corresponding to PII (f = —60°, c = +120°) and aR (f = —60°, c = —30°) are observed. The gamma turn or C7 conformation (f = —70°, c = +70°) is sparsely populated. Amongst the genetically coded amino acids, the proline residue provides the greatest op-

Fig. 5.2 (a) Distribution of f,c values of non-Gly residues from 250 protein structures (<2.0A); (b) Distribution of f,c values of Gly residues from 250 protein structures (<2.0A). (c and d) Distribution of conformational angles of l-Pro and l-Asn residues from 538 independent protein crystal structures [13]. The protein data set used to generate this figure was derived from the Protein Data Bank using a resolution cutoff of 2.0 A and a sequence homology cutoff of 40% and contained a total of 47612 non-glycine, 4933 glycine, 4995 proline and 5503 asparagine residues.

Fig. 5.2 (a) Distribution of f,c values of non-Gly residues from 250 protein structures (<2.0A); (b) Distribution of f,c values of Gly residues from 250 protein structures (<2.0A). (c and d) Distribution of conformational angles of l-Pro and l-Asn residues from 538 independent protein crystal structures [13]. The protein data set used to generate this figure was derived from the Protein Data Bank using a resolution cutoff of 2.0 A and a sequence homology cutoff of 40% and contained a total of 47612 non-glycine, 4933 glycine, 4995 proline and 5503 asparagine residues.

portunity for directing local chain folding. The chirality of the i-amino acids in proteins greatly restricts the sterically allowed regions with positive values of f. Asn is the only chiral residue with a high propensity to occur in the left-handed helical (aL, f — +60°, c — +30°) conformations. This local feature is important in generating 'prime' turns (type 1'/II'), which in turns act as a nucleus for the formation of b-hairpin structures. A convincing theoretical rationalization of the tendency of Asn residues to favor left-handed helical conformations is still to be achieved. It may be noted that Jane Richardson, in an insightful analysis of protein structures, remarked that by virtue of its CH2-CONH2 side-chain Asn is the 'least chiral' of the amino acids [14]. An analysis of individual residue conformations in proteins suggests that conformational choices accessible to each amino acid are wide enough to result in a very large region of sterically allowed structure space, for polypeptides of even limited chain length. Control of chain folding is, thus, a formidable task. One synthetic approach to peptide and protein design involves the use of nonprotein residues to act as local directors of chain folding, restricting available conformations to limited region of Ramachandran space [15].

The use of conformationally constrained residues in the design of folded pep-tide structures is based on the simple principle that the residue choice must limit conformational excursions to a well-defined region of space. The subsequent sections of this chapter illustrate the approaches used in engineering the construction of peptide helices and hairpins, followed by their assembly into mimics of supersecondary structures.

a-Aminoisobutyric Acid (Aib) and Related Dialkyl Amino Acids

Aib is a constituent of several naturally occurring antimicrobial peptides. Notably, Aib is a major constituent of a class of linear peptide antibiotics, produced by soil

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