Parallel packing of alpha-helices in crystals of the zervamicin IIA analog Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.2H2O.

Abstract

An apolar synthetic analog of the first 10 residues at the NH2-terminal end of zervamicin HA crystallizes in the triclinic space group P1 with cell dimensions a = 10. Ac-Trp-Ile-Gln-Aib-Ile-Thr-Aib-Leu-Aib-Hyp- 15-Gln-Aib-Hyp-Aib-Pro-Phe-ol.(Hyp is 4-hydroxyproline; Phe-ol is phenylalaninol.) The decapeptide whose structure is reported in this paper is the apolar analog of the first 10 residues in which Gln-3, Thr-6, and Hyp-10 have been replaced with Ala, Val, and Pro, respectively; the NH2 terminus has been blocked with t-butoxycarbonyl (Boc) rather than acetyl; and the COOH terminus has been esterified with methanol:Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe.EXPERIMENTAL PROCEDURE Boc-Trp-Ile-Ala-Aib-Ile-Val-Aib-Leu-Aib-Pro-OMe was synthesized by conventional solution-phase procedures, and crystals were grown from dimethyl sulfoxide/H20 in the form of triangular prisms. X-ray diffraction data were measured from a crystal that was 0.10 mm thick and 0.30 mm on each side of the triangular face. The crystal was sealed in a capillary with a small amount of mother liquor. The data were collected with a four-circle automated diffractometer using Cu Ka radiation and a graphite monochromator (A = 1.54178 A). The 0-20 scan technique was used with a 2.00 scan, 15'/min scan rate, and 2ma,,x = 1150, for a total of 5294 independent reflections and 4378 reflections with intensities >3a(F) to a resolution of 0.91 A. Three reflections monitored after every 60 measurements remained constant within 3% during the data collection. Lorentz, polarization, and absorption corrections were applied to the data. The structure was solved by direct phase determination using the random-tangent formula procedure in the SHELXTL computer programt. Initially, the positions of 36 atoms, mainly in the backbone, were found. The positions of the remainder of the C, N, and 0 atoms were found by means of partial structure development. Eight of the nine H atoms on amide groups were found in difference maps after partial least-squares refinement, and subsequently their coordinates and isotropic thermal factors were refined by least-squares. Hydrogen atoms for the two water molecules were not found. Although peaks for many other H atoms also were found in difference maps, idealized calculated positions were used for all the H atoms on C atoms. Least-squares refinement with anisotropic thermal factors for the C, N, and 0 atoms; isotropic thermal factors for eight amide H atoms; and 88 H atoms on C atoms kept fixed in idealized positions yielded an agreement factor of R = 5.61% for the 4378 reflections measured >3a(F). Fractional coordinates for the C, N, and o atoms and the amide H atoms are listed in Table 1

Facile transition between 310‐ and α‐helix: Structures of 8‐, 9‐, and 10‐residue peptides containing the ‐(Leu‐Aib‐Ala)2‐Phe‐Aib‐fragment

“…The largest difference between the backbones in B and C occurs with a greater helix distortion in B than C helix at the penultimate residue where 4 = -150" and -96", respectively. In helices ending with an Aib residue, there often are helix distortions or reversals at the penultimate residue (see, for example, Karle et al, 1986Karle et al, , 1990a, and these appear to be independent of helix length. If residues 9 and 10 are omitted, the average values for 4 and $ in B, -60.2' and -26.7", respectively, are quite similar to those in C.…”

Aqueous channels within apolar peptide aggregates: solvated helix of the alpha-aminoisobutyric acid (Aib)-containing peptide Boc-(Aib-Ala-Leu)3-Aib-OMe.2H2O.CH3OH in crystals.

“…The expectation was that Boc-(Aib-Ala-Leu)3-Aib-OMe would form an a-helix, or perhaps a mixed 310-helix/a-helix, like other apolar deca-and undecapeptides that contain several Aib residues (5,12). The fortuitous insertion of a water molecule into the helix of the present peptide gives rise to a stable, static model of solvation of a helix backbone.…”

“…The bulky side groups of Leu3 and Leu6, as well as the tert-butyl moiety of the Boc blocking group, are directed toward one side of the helix. On the other side, where the water molecule W(1) resides, there are only the Aib and Ala residues and, due to the bend in the helix axis, the CH3 groups of these residues are directed away from the area of W (1) There is a reversal in the sign of the value for Aib'0, which is not unusual for a terminal Aib residue (4,5).…”

“…The role of specific side chains in promoting helix association is being studied by means of synthetic analogues., It has been observed that a-aminoisobutyric (Aib) residues, common components of membrane-active peptides, promote the formation of 310-helices in short peptides (3,4), and in longer peptides (>7 residues) if they comprise one-half or more of the peptide (ref. 5 and references therein). An a-helix has been favored in longer peptides when the Aib residues constitute one-third of the total.…”

Conformation of a 16-residue zervamicin IIA analog peptide containing three different structural features: 3(10)-helix, alpha-helix, and beta-bend ribbon.

“…The crystal structure of the decapeptide fragment composed of residues 1-10 has been published (3). A helical conformation (for residues 9-16) containing three p-bend reversals (for Prol'-Ala", Aib12-Prol3, and Aib14- ribbon was proposed for the conformation of Z-(Aib-Pro)4-OMe (Z, benzyloxycarbonyl) in solution (4,5).…”