X-ray studies on some proline containing peptides

Abstract

The imino acid proline plays a crucial role in determining the conformation of proteins, peptides, and peptide antibiotics. Understanding the intrinsic propensities of prolyl residues to assume different characteristic conformations in various environments is therefore of considerable importance. X?ray analyses of several short proline?containing peptides—with all?L and mixed L,D sequences, as well as those containing unusual amino acids—have been carried out by several workers with this objective. This thesis embodies the author’s contribution to this area.

The first chapter provides a brief survey of the known structural characteristics of prolyl residues. Topics discussed include the occurrence of cis peptide units, pyrrolidine?ring conformations, and the presence of prolyl residues in regular helical structures and ??turns in proteins and peptides. Peptides containing D?residues and/or unusual amino acids are also considered.

Earlier studies have shown that even tri? and tetraproline tend to assume a collagen?like polyproline II conformation. The X?ray analysis of benzyloxycarbonyl?L?prolyl?L?proline was undertaken to determine whether this tendency persists when the degree of polymerisation is reduced to the minimum possible value of two. This analysis, presented in Chapter 2, confirms that the main?chain dihedral angles indeed correspond to polyproline II. The linkage between the protecting group and the first prolyl residue adopts a cis configuration, while the peptide bond linking the two prolyl residues is trans. The pyrrolidine ring of the first prolyl residue adopts a C??exo conformation, whereas that of the second residue adopts a C??endo–C??exo conformation.

Chapter 3 presents the crystal structure of benzyloxycarbonyl?L?alanyl?D?phenylalanyl?L?proline monohydrate, a tripeptide with an LDL sequence. The X?ray analysis proved somewhat difficult despite the moderate size of the molecule. All peptide units are trans, and the prolyl residue adopts a C??exo conformation. A single water molecule is hydrogen?bonded to the carbonyl oxygen of the benzyloxycarbonyl group and to one oxygen atom of the terminal carboxyl group. This internal water bridge—observed for the first time in a linear peptide—provides a model for water?mediated chain reversal. An interesting feature of the structure is the presence of an antiparallel sheet involving the alanyl and phenylalanyl residues.

Chapter 4 reports the X?ray crystal?structure analysis of pivaloyl?D?prolyl?L?prolyl?L?alanyl?N?methylamide. All peptide bonds are trans, and both prolyl residues adopt the C??exo conformation. The molecule assumes a highly folded conformation in which a Type II? DL ??turn is followed by a Type I LL ??turn, both stabilised by intramolecular 4?1 hydrogen bonds. This conformation, observed for the first time, is of interest in relation to the structure of gramicidin S.

??Aminoisobutyric acid (Aib) is an unusual, highly conformationally restrictive amino acid found in antibiotics such as alamethicin, suzukacillin, and emerimicins. Chapter 5 reports the X?ray crystal structure of benzyloxycarbonyl?(??aminoisobutyryl?L?prolyl)??ethyl ester, a tetrapeptide containing both Aib and proline. The analysis presented several difficulties. The peptide backbone is entirely trans. One prolyl residue adopts a C??exo conformation, while the other is in the C??endo conformation. Aib(1) and Pro(2) occupy the corner positions of a Type I ??turn stabilised by a 4?1 hydrogen bond between the urethane carbonyl and the amino group of Aib(3). The main?chain dihedral angles of Aib(3) and Pro(4) are close to those characteristic of a left?handed ??helix and the polyproline II structure, respectively.

The Appendix presents the crystal structure of a peptide oxazolone derived from benzyloxycarbonyl???aminoisobutyryl???aminoisobutyric acid, obtained as a by?product during peptide synthesis involving Aib. The structure—difficult to solve—consists essentially of three planar groupings: the five?membered oxazolone ring, a peptide?like urethane group, and a phenyl ring. The lactone group exhibits its expected structural features.

Part of the work described in this thesis has been published in the following papers:

The crystal structure of a peptide oxazolone, Acta Cryst. (1980), B36, 1498 (with M. Vijayan).

X?ray crystal structure of pivaloyl?D?prolyl?L?prolyl?L?alanyl?N?methylamide: observation of a consecutive ??turn conformation, J.C.S. Chem. Commun. (1979), 1183 (with Y. V. Venkatachalapathi, M. Vijayan, and P. Balaram).

The crystal structure of pivaloyl?D?prolyl?L?prolyl?L?alanyl?N?methylamide, J.C.S. Perkin Trans. II (1980), in press (with M. Vijayan).