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.

Abstract

ABSTRACT.Although the peptide Boc-Aibl-Ala2-Leu3-Aib4-Alas-Leu'-Aib7-Ala8-Leu9-Aib'0-OMe [with a t-butoxycarbonyl (Boc) blocking group at the amino terminus, a methyl ester (OMe) at the carboxyl terminus, and four a-aminoisobutyric (Aib) residues] has a 3-fold repeat of residues, the helix formed by the peptide backbone is irregular. The carboxyl-terminal half assumes an at-helical form with torsion angles ) and r of approximately -60°and -45°, respectively, whereas the amino-terminal half is distorted by an insertion of a water molecule between the amide nitrogen of Ala5 [N(5)] and the carbonyl oxygen of Ala2 [0(2)]. The water molecule W(1) acts as a bridge by forming hydrogen bonds N(5).W(1) (2.93 A) and W(1)---0(2) (2.86 A). The distortion of the helix exposes the carbonyl oxygens of Aib' and Aib4 to the outside environment, with the consequence that the helix assumes an amphiphilic character despite having all apolar residues. Neighboring helices in the crystal run in antiparallel directions. On one side of a helix there are only hydrophobic contacts with efficient interdigitation of leucine side chains with those from the neighboring helix. On the other side of the helix there are hydrogen bonds between protruding carbonyl oxygens and four water molecules that separate two neighboring helices. Along the helix axis the helices bind head-to-tail with a direct hydrogen bond N(2)-0(9) (3.00 A). Crystals grown from methanol/water solution are in space group P2, with a = 15.778 ± 0.004 A, b = 11.228 ± 0.002 A, c = 18.415 ± 0.003 A, = 102.10 ± 0.02ur and two formula units per cell for C49HON1003 2H2OCH3OH. The overall agreement factor R is 7.5% for 3394 reflections observed with intensities >3a(F), and the resolution is 0.90 A.Transmembrane channels formed by alamethicin and related fungal peptides are likely to arise by close association of peptide helices in bilayer membranes (1, 2). 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. In the present study, the Aib content is 40%. The initial intent was to determine the type ofhelix formed and the mode of aggregation of these helices in the crystal. The serendipitous entry of a water molecule into the helix formed by the backbone atoms has produced unanticipated insights into the hydration and aggregation behavior of helices in peptides.EXPERIMENTAL PROCEDURES Boc-(Aib-Ala-Leu)3-Aib-OMe (where Boc is t-butoxycarbonyl) was synthesized by conventional solution-phase procedures and crystals were grown from CH3OH/H20 solution in the form of thin hexagonal plates. A crystal of size 0.20 X 0.35 x 0.08 mm was sealed in a t...

Heterogeneous H-Bonding in a Foldamer Helix

“…This possibility was initially suggested by the seven crystal structures described here, in which the α residue C=O( i ) → γ residue H-N( i-1 ) H-bond distances were long, or other molecules were interpolated into these interactions. Such interpolations have occasionally been observed in proteins 21 or short conventional peptides, 22 and more recently in α/γ-peptides, 23 but the frequency of this unusual phenomenon in our structural data set stands out. HDX and DMSO titration results support the conclusion that there is an energetic differentiation between the two types of H-bond in the 12/10-helical conformation formed by the α/γ( I ) backbone.…”

Polyproline II helix is the preferred conformation for unfolded polyalanine in water

“…Strong interactions between water and small polar solutes (e.g., ions, hydrates of inorganic salts, model amides) are mainly enthalpic: See Table 1 in Avbelj et al29 Water molecules reorganize around the polar moiety with a comparatively small loss of conformational entropy 30 Water molecules isolated from the bulk and transferred into an apolar environment (e.g., a hydrophobic cavity in a protein) can gain entropy31 owing to increased liberational freedom, akin to transfer from solution to the gas phase. Finally, water molecules isolated from the bulk and transferred into a multiply hydrogen‐bonded polar environment (e.g., a 3 10 ‐helix32) would be expected to lose both rotational and translational entropy. …”

“…Finally, water molecules isolated from the bulk and transferred into a multiply hydrogen‐bonded polar environment (e.g., a 3 10 ‐helix32) would be expected to lose both rotational and translational entropy.…”

The crystal structure of Z‐(Aib)10‐OH at 0.65 Å resolution: three complete turns of 310‐helix

“…This space comprises the left‐handed and right‐handed helical region of the Ramachandran plot. Aib residues are known as strong helix formers in peptides, also in the presence of common amino acids . Helical conformation is a prerequisite for the formation of pores by self‐association of naturally occurring peptides rich in Aib‐residues (e.g.…”