Design of two-helix motifs in peptides: crystal structure of a system of linked helices of opposite chirality and a model helix–linker peptide

Background: An attempt is being made to produce two-helix bundles that are soluble in apolar media, without the use of a rigid template. The approach relies on the use of stereochemically constrained amino acids for helix construction, while a flexible linker is obtained by the use of an ε-aminocaproic acid residue (Acp). The Acp linker has appropriate NH and COOH termini to connect to the N and C termini of the helices, a flexible (CH2)5 moiety and sufficient length to make the desired assembly.Results: The conformations in crystals (determined by X-ray diffraction analyses) are described for a partial assembly consisting of a 7-residue helix with Acp (helix–Acp) and for two assemblies of 7-residue helices with Acp (helix–Acp–helix) in which the chiralities of the helices are L, L (already published) and L,D (this publication). The Acp linker is extended away from the helix in the L,L analog in a zig-zag manner, but assumes a helical conformation in the L,D analog. The two helices in the L,L and L,D analogs are displaced laterally by the linker, but in neither case has the linker folded the molecule into the desired U-conformation. Cell parameters for Boc-L-Val-L-Ala-L-Leu-Aib-L-Val-L-Ala-L-Leu-Acp-D-Val-D-Ala-D-Leu-Aib-D-Val-D-Ala-D-Leu-OMe are space group P41 with a = b = 10.094(6) Å and c = 93.383(12) Å.Conclusions: Strong hydrogen bonds (NH···O=C) between the displaced helices of one molecule and the displaced helices of a neighboring molecule, which form near the linker of each helix assembly, appear to dominate in both the L,L and L,D crystal. The (CH2)5 segment of the linker readily adopts different conformations that result in the L and D helices packing in a similar spatial motif. Greater conformational control at the linking segment or introduction of specific interhelix interactions may be necessary in order to achieve U-type folding between neighboring helices in a single molecule