Conformational studies of heterochiral peptides with diastereoisomeric residues: crystal and molecular structures of linear dipeptides derived from leucine, isoleucine, and allo-isoleucine.

The x-ray diffraction analyses of three N- and C-terminally blocked L,D dipeptides, namely t-Boc-D-Leu-L-Leu-OMe (1), t-Boc-L-Ile-D-aIle-OMe (2), and t-Boc-D-aIle-L-Ile-OMe (3) containing enantiomeric or diastereomeric amino acid residues have been carried out. The structures were determined by direct methods and refined anisotropically to final Rf actors of 0.077, 0.058, and 0.072 for (1), (2), and (3), respectively. Peptides 1-3 all assume a similar U-shaped structure with phi and psi torsion angles corresponding to one of the possible calculated minimum energy regions (regions E and G for L residues, and F*, D* and H* for D residues). The peptide backbones of 1-3 are almost superimposable [provided that the appropriate inversion of the chiral centers of (2) is made]. Side-chain conformations of Leu residues in peptide (1) are g- (tg-) for the L-Leu residue and the mirrored g+ (tg+) for the D-Leu residue; however, in peptides (2) and (3) the conformations of the isoconfigurational side chains of the Ile or allo-Ile residues are (g-t) t and (tg+) t for the L-Ile and the D-allo-Ile moieties, respectively. In all cases, these conformations correspond to the more populated conformers of beta-branched residues statistically found in crystal structures of small peptides. The results seem to indicate that, at least in short peptides with enantiomeric or diastereoisomeric residues, the change in chirality in the main-chain atoms perturbs the backbone conformation to a lesser extent and the side chain conformation to a greater extent.

Conformation and structure of linear peptides with regularly alternating L- and D-residues: structure of the blocked hexapeptide tert-butyloxycarbonyl-(D-alloisoleucyl-L-isoleucyl)3 methyl ester monohydrate.

Peptides with a regular sequence of enantiomeric residues (L and D) along the chain have received considerable attention because of their accessibility to unique conformations and because they are model compounds for the naturally occurring peptide gramicidin A, which shows monovalent cation selective transmembrane transport. The solid-state structure of the linear hexapeptide t-Boc-(D-alle-L-Ile)3-OMe has been determined by X-ray diffraction techniques and refined to a final R factor of 0.068. The molecule shows a bent U-shaped conformation stabilized by three intramolecular H-bonds of the N-H...O = C type: a type II beta-bend (4-->1 bend or C10 ring structure) with L-Ile2 and D-aIle3 at positions 2 and 3 of the bend, an alpha-turn (5-->1 bend or C13 ring structure) and a 1-->5 bend or C17 ring structure. The first two 10-membered and 13-membered bends are enclosed in the latter 17-membered hydrogen-bonded ring structure. This structural motif is common to hepta- and octa-peptide cyclic molecules, showing that ring closure is not required to achieve a particular topology in the molecular design of specific bended conformations.

A crystal structure with features of an antiparallel alpha-pleated sheet.

A single-crystal x-ray diffraction analysis of Boc-L-Ala-D-aIle-L-Ile-OMe has been carried out. The analysis has shown (a) that the tripeptide molecules have in part an alpha-extended conformation, the torsion angles of the L-Ala and D-aIle residues being psi 1 = -75.1 degrees and psi 1 = -25.8 degrees and psi 2 = 67.3 degrees and psi 2 = 44.1 degrees, respectively, and (b) that the molecules are organized in rippled planes where they occur in relative antiparallel orientation linked together side by side by H bonds. This molecular organization of the tripeptide corresponds closely to that of an antiparallel alpha-pleated sheet, and likely constitutes the first example of a structure of this kind for which a characterization at the atomic level has been achieved. A molecular dynamics study has shown that the molecular conformation of the tripeptide in the crystalline state is determined primarily by intermolecular interactions.

Conformational characteristics of alternating stereo-co-oligopeptides of D- and L-norleucine: influence of an N-methyl group.

The conformational behavior of members of the series Boc-(L-Nle)m-(D-Nle-L-Nle)(n-m)/2-OMe (m = 0 or 1; n = total number of residues) with n < or = to 12, and of analogs of comparable chain length having a NMe-group on the (n - 3)th residue has been investigated. The study has shown that D,L-alternating oligonorleucines behave very differently from stereo-co-oligopeptides of D-alloisoleucine and L-isoleucine, D- and L-valine, or D- and L-leucine. In particular, it has been found that oligonorleucines do not form beta-helices as do the other oligopeptides. Instead, they form aggregates (very likely of the alpha-pleated sheet type), which are insoluble in common organic solvents even at moderate chain lengths. In marked contrast with this behavior, N-methylated analogs such as those studied, with n from 9 to 15, cannot generate very stable aggregates owing to the N-methyl group, and they prefer to form beta-helices. These beta-helices have been found by solution 1H NMR techniques to be almost exclusively of the types beta 4.4 (single-stranded with about 4.4 residues per turn) and decreases increases beta 5.6 (double-stranded, antiparallel, with about 5.6 residues per turn).

Conformationally constrained D,L-alternating oligopeptides.

The possibility of selectively reducing the number of beta-helical structures theoretically possible for a D,L-alternating peptide by using a N-methyl group as conformational constraint is considered. Some 1H-nmr data regarding Boc(L-Nle-D-Nle)3-L-Nle-D-MeNle-L-Nle-D-Nle-L-Nle-OMe (I), its formyl analogue (II), and the pentadecapeptide Boc(D-Leu-L-Leu)5-D-MeLeu-(L-Leu-D-Leu)2-OMe (III) are presented. It is shown that these alternating stereocooligopeptides with a N-methyl group in the (n - 3) (I and II) or (n - 4) position (III) differ drastically in their behavior from the corresponding nonmethylated compounds. In chloroform, I and II form predominantly -- beta 7.2-helices and III forms almost exclusively -- beta 5.6 or -- beta 7.2-helices. The helices are in every case those having the maximum possible number of interchain H bonds.

Regularly alternating L,D-peptides. I. The double-stranded left-handed antiparallel beta-helix in the structure of Boc-(L-Val-D-Val)4-OMe.

The structure of Boc-(L-Val-D-Val)4-OMe has been determined by x-ray single-crystal diffraction analysis. The octapeptide crystallizes in the trigonal system, space group P3(2)21 with a = b = 12.760 A, c = 63.190 A and Z = 6. The independent unit is represented by one octapeptide chain. The structure has been solved by direct methods and it was anisotropically refined by least-squares procedures to a final R value of 0.08 for the 3018 "observed" reflections. One molecule of water was also located in the unit cell. Two octapeptide chains, related by a crystallographic binary axis, wind up around each other giving rise to a double-stranded left-handed antiparallel increases decreases beta 5.6-helix. The dimer, stabilized by 14 interstrand N--H....O = C hydrogen bonds, can be regarded as a cylinder with an hydrophilic inner core represented by the peptide units and an hydrophobic exterior of isopropyl groups. The inner diameter of the cylinder is 5.1 A.

Regularly alternating L,D-peptides. II. The double-stranded right-handed antiparallel beta-helix in the structure of t-Boc-(L-Phe-D-Phe)4-OMe.

The crystal structure of Boc-(L-Phe-D-Phe)4-OMe has been determined by x-ray diffraction analysis. The peptide crystallizes in the triclinic system, space group P1 with a = 15.290 A, b = 15.163 A, c = 19.789 A, alpha = 102.49 degrees, beta = 96.59 degrees, gamma = 74.22 degrees, and Z = 2. The structure has been solved by coupling of the molecular replacement technique and expansion by tangent formula refinement of the set of known phases. Several cycles of Fourier calculations and least-squares refinement led to the location of 194 atoms of the two independent octapeptide chains and few molecules of cocrystallized solvent (chloroform, water, and methanol). The isotropic refinement converged to R = 0.13 for the 3077 "observed" reflections. The two independent octapeptide molecule form a dimer in the solid state: the two chains are associated by interstrand hydrogen bonds (12 of the type N-H ... O = C) with the formation of a double-stranded antiparallel right-handed -- beta 5.6-helix. These double helices can be represented as a cylinder with a hydrophilic inner core represented by the peptide units and an hydrophobic exterior constituted by the aromatic moieties. The dimensions of the cylinder are equal to those observed for Boc-(L-Val-D-Val)4-OMe. In the solid state the dimers pack with each other in an hexagonal fashion with the formation of layers; between the layers, solvent molecules fill empty spaces.

Regularly alternating L,D-peptides. III. Hexacyclic peptides from valine or phenylalanine.

In the present paper we describe the single-crystal x-ray analyses of two cyclic hexapeptides containing an equal number of alternating L,D-residues as putative analogues of the metal binding compounds, enniatin and beauvericine. Both the molecules of c(L-Val-D-Val)3 and C(L-Phe-D-Phe)3 retain in the solid state the center of symmetry and crystallize with six and eight trifluoroacetic acid molecules, respectively. The peptides are strongly hydrogen bonded to the solvent molecules. We estimate, on the basis of the molecular geometry and spatial arrangement of the peptide carbonyl groups and in comparison with other metal binding cyclic peptides, the ability of these molecules to interact with metal ions as 1:1 complexes.