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Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C-12 hydrogen bonded turns which may be considered as backbone expanded analogues of C-10 beta-turns) found in alpha alpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alpha gamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C-gamma-C-beta (theta(1)) and C-beta-C-alpha (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C-12 turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C-12 hydrogen bonded structures which are energetically feasible in alpha gamma and gamma alpha sequences.

Gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn) is an achiral, conformationally constrained gamma amino acid residue. A survey of available crystal structures of Gpn peptides reveals that the torsion angles about the C-gamma-C-beta (theta(1)) and C-beta-C-alpha(theta(2)) bonds are overwhelmingly limited to gauche, gauche (g(+)g(+)/g(-)g(-)) conformations. The Gpn residue forms C-7 and C-9 hydrogen bonds in which the donor and acceptor atoms come from the flanking peptide units. In combination with alpha amino acid residues alpha gamma and gamma alpha segments can adopt C-12 hydrogen bonded structures. The conformational choices available to the Gpn residue have been probed using energy calculations, adopting a grid search strategy. Ramachandran phi-psi maps have been constructed for fixed values of theta(1) and theta(2), corresponding to the gauche and trans conformations. The sterically allowed and energetically favorable regions of conformational space have been defined and experimental observations compared. C-7 and C-9 hydrogen bonded conformational families have been identified using a grid search approach in which theta(1) and theta(2) values are varied over a range of +/- 10 degrees about ideal values at 1 degrees intervals. The theoretical analysis together with experimental observations for 59 Gpn residues from 35 crystal structures permits definition of the limited range of conformational possibilities at this gamma amino acid residue. .

The author has brought to our attention the following revision for Table II of the article listed above, published in Biopolymers 2008, 90(2):138–150. See the revised table shown on the following page.

The conformational preferences of the 3,3-disubstituted \beta-amino acid residue, 1-aminocyclohexaneacetic acid $(\beta^{3,3}Ac_6c)$ have been investigated by determining the crystal structures of the parent amino acid, the hydrochloride derivative, 10 protected derivatives and di and tripeptides. The symmetrical cyclohexyl substituent at the \beta-position restricts the values of the torsion angles \phi $(N-C^{\beta})$ and \theta $(C^{\beta}-C^ {\alpha})$ to approximately gauche values $(\pm60^o)$. Relatively few intramolecularly hydrogen bonded conformations are observed. In the dipeptide $Boc-\beta^{3,3}Ac_6c-\beta^{3,3}$ $Ac_6c-NHMe$ a $C_6$ hydrogen bond is observed. In Piv-Pro-$\beta^{3,3}Ac_6c-NHMe$ a $C_{11}$ hydrogen bonded hybrid \alpha \beta turn is characterized. In a majority of cases the amino group occupies the axial position in the cyclohexane ring. The conformations observed are compared with crystallographically observed structures for other \beta-residues, including $b^{2,2}Ac_6c$.

The insertion of the higher homologues of the \alpha-amino acids, specifically \beta, \gamma, and \delta residues, into a peptide sequences results in hybrid structures with novel hydrogen-bonding possibilities.[1] Research in this area of hybrid polypeptides has been stimulated by the observation of novel helical structures in \beta oligopeptides in which the hydrogen-bond polarities are reversed. For example, the 12 helix $(2.5_{12}$ or $2.5_1-P)$ in a $(\beta)_n$ sequence maintains the same directionality $(C=O(i)^{...}NH(i+3))$ as the canonical $3_{10}$ helixin an $(\alpha)_n$ sequence[2] and may be formally considered as an expanded version of the latter. By contrast, the 14 helix $(3_{14}$ or $3_1-M)$ in a $(\beta)_n$ sequence possesses a reversed hydrogen-bond polarity $(NH(i)^{...}C=O(i+2))$.[3] Initial crystallographic results with hybrid \alpha\beta and \alpha\gamma sequences suggest that the expanded analogues of the $3_{10}$ helix, namely, the $C_{11}$ $(\alpha\beta)$ and $C_{12}$ $(\alpha\gamma)$ helices, can indeed be observed in short peptides.[4] Calculations suggest that helices with alternating hydrogen-bond polarities may indeed be stable structures in hybrid sequences.[1c,d] In this Communication, we report the $C_{12}/C_{10}$ mixed hydrogen-bonding pattern in the crystal structure of the tetrapeptide Boc-Leu-Gpn-Leu-Aib-OMe (1; Boc: tertbutoxycarbonyl; Gpn: 1-(aminomethyl)cyclohexaneacetic acid (gabapentin); Aib: aminoisobutyric acid), which was serendipitously obtained during the synthesis of longer hybrid sequences. This novel helical conformation can be generalized as an $(\alpha\gamma)_n$ sequence. The sequence contains the stereochemically constrained \gamma residue gabapentin, which is an achiral \beta,\beta-disubstituted \gamma-amino acid. The presence of gem-dialkyl substituents on the $C\beta$ atom limits the torsion angles about the $C{\gamma}-C{\beta}$ $(\theta_1)$ and $C{\beta}-C{\alpha}$ $(\theta_2)$ bonds to approximately $\pm 60^o$.[5]

The conformational properties of foldamers generated from \alpha\gamma hybrid peptide sequences have been probed in the model sequence Boc-Aib-Gpn-Aib-Gpn-NHMe. The choice of R-aminoisobutyryl (Aib) and gabapentin (Gpn) residues greatly restricts sterically accessible conformational space. This model sequence was anticipated to be a short segment of the \alpha\gamma $C_{12}$ helix, stabilized by three successive $4\rightarrow 1$ hydrogen bonds, corresponding to a backbone-expanded analogue of the \alpha polypeptide $3_{10}$-helix. Unexpectedly, three distinct crystalline polymorphs were characterized in the solid state by X-ray diffraction. In one form, two successive $C_{12}$ hydrogen bonds were obtained at the N-terminus, while a novel $C_{17}$ hydrogenbonded \gamma\alpha\gamma turn was observed at the C-terminus. In the other two polymorphs, isolated $C_9$ and $C_7$ hydrogen-bonded turns were observed at Gpn (2) and Gpn (4). Isolated $C_{12}$ and $C_9$ turns were also crystallographically established in the peptides Boc-Aib-Gpn-Aib-OMe and Boc-Gpn-Aib-NHMe, respectively. Selective line broadening of NH resonances and the observation of medium range $NH(i) \leftrightarrow NH(i+2)$ NOEs established the presence of conformational heterogeneity for the tetrapeptide in $CDCl_3$ solution. The NMR results are consistent with the limited population of the continuous $C_{12}$ helix conformation. Lengthening of the $(\alpha\gamma)_n$ sequences in the nonapeptides Boc-Aib-Gpn-Aib-Gpn-Aib-Gpn- Aib-Gpn-Xxx (Xxx) Aib, Leu) resulted in the observation of all of the sequential NOEs characteristic of an \alpha\gamma $C_{12}$ helix. These results establish that conformational fragility is manifested in short hybrid \alpha\gamma sequences despite the choice of conformationally constrained residues, while stable helices are formed on chain extension.

The stereochemically constrained gamma amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid, Gpn) has been incorporated into a host alpha-peptide sequence. The structure of a hybrid alpha gamma alpha alpha gamma alpha peptide, Boc-Leu-Gpn-Aib-Leu-Gpn-Aib-OMe in crystals reveals a continuous helical conformation stabilized by three intramolecular 4\rightarrow 1 C{12} hydrogen bonds across the alpha gamma/gamma alpha segments and one C-10 hydrogen bond across the central alpha alpha segment. This conformation corresponds to an expanded analog of the canonical all-alpha polypeptide 3(10)-helix, with insertion of two additional backbone atoms at each gamma residue. Solvent dependence of NH chemical shifts in CDCl3 solution are consistent with conformation in which the NH groups of Aib (3), Leu (4), Gpn (5), and Aib (6) are hydrogen bonded, a feature observed in the solid state. The nonsequential NOEs between Gpn (2) NH - Leu (4) NH and Gpn (2) NH Gpn (5) NH support the presence of additional conformations in solution. Temperature-dependent line broadening of NH resonances confirms the occurrence of rapid exchange between multiple conformations at room temperature. Two conformational models which rationalize the observed nonsequential NOEs tire presented, both of which contain three hydrogen bonds and ore consistent with the known stereochemical preferences of the Gpn residue.

The \beta turn segment in designed peptide hairpins has been expanded by the insertion of \beta-, \gamma- and \delta amino acids at the i+2 position. The model octapeptides Boc-Leu-Phe-Val-$^D$Pro-$Ac_6c$-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-$^D$Pro-$\beta^3$-$Ac_6c$-Leu-Phe-Val-OMe (2),and Boc-Leu-Phe-Val-$^D$Pro-Gpn-Leu-Phe-Val-OMe (3) have been shown to adopt \beta hairpin conformations in methanol by the observation of key diagnostic nuclear Overhauser effects. Boc-Leu-Val-Val-$^D$dPro-\delta-Ava-Leu-Val-Val-OMe (4) adopts a \beta hairpin conformation in crystals; this is stabilized by three cross-strand hydrogen bonds as demonstrated by X-ray diffraction. The canonical $C_{10}$ turn in an \alpha–\alpha segment is expanded to $C_{11}$, $C_{12}$,and $C_{13}$ turns in \alpha–\beta, \alpha–\gamma, and \alpha–\delta segments,respectively. The crystal structures of Piv-$^L$Pro-$\beta^3$-$Ac_6c$-NHMe (5) and Boc-$Ac_6c$-Gpn-$Ac_6c$-OMe (6) reveal intramolecularly hydrogen-bonded $C_{11}$ and $C_{12}$ conformations, respectively. Computer modeling of octapeptide sequences that contain centrally positioned hybrid-turn segments, by using turn parameters derived from the structures of peptides 5 and 6,establishes the stereochemical acceptability of the \beta hairpins in the cases of peptides 2 and 3. Accommodation of $\omega$-amino acids into the turn segments is achieved by the adoption of gauche conformations around the backbone $C - C$ bonds.

The insertion of additional atoms into \alpha -polypeptide backbones by the introduction of \beta, \gamma, and higher \omega amino acid residues expands the range of polypeptide secondary structures.[1] Two new helices, the $2.5_{1}_{2} ((P)-2.5_1)$ helix and the $3_{1}_{4} ((M)-3_{1})$ helix, were first identified in studies of oligopeptides.

A pentapeptide, $Boc-Leu-Ac_8c-Ala-Leu-Ac_8c-OMe 1$, an octapeptide, $Boc-Leu-Ac_8c-Ala-Leu-Ac_8c-Ala-Leu-Ac_8c-OMe 2$ and a tripeptide, $Boc-Aib-Ac_8c-Aib-OMe 3$ containing the 1-aminocyclooctane-1-carboxylic acid residue $(Ac_8c)$ were synthesized and conformationally characterized by x-ray diffraction studies in the crystal state. Peptides 1 and 2 were also studied by NMR in $CDCl_3$ solution. Peptide 1 adopts a purely $3_{10}-helical$ conformation in crystals, stabilized by three intramolecular 1 \longleftarrow 4 hydrogen bonds. Peptide 2 in crystals is largely $3_{10}-helical$ with distortion in the backbone at the N-terminus by the insertion of a water molecule between $Ac_8c$ (2) CO and Ala (6) NH groups. Peptide 3 forms a $C_{10}-ring$ structure, i.e. a type III (III) \beta - turn conformation stabilized by an intramolecular 1 \longleftarrow 4 hydrogen bond. Five cyclooctane rings assume boat-chair conformations, whereas the sixth $[Ac_8c(8) in 2]$ is appreciably distorted, resembling a chiral intermediate in the pseudorotational pathway from the boat-chair to the twisted boat-chair conformation. Internal bond angles of the cyclooctane rings are appreciably distorted from the tetrahedral value, a characteristic feature of the cyclooctane ring. Peptide 1 crystallized in the space group $P2_12_12_1$ with a = 11.900(4) A, b = 18.728(6) A, c = 20.471(3) A and Z = 4. The final $R_1$ and $wR_2$ values are 0.0753 and 0.2107, respectively, for 3901 observed reflections $[F_o \geq \sigma 3(F_o)]$. Peptide 2 crystallized in space group $P2_1$ with a = 12.961(5) A, b = 17.710(10) A, c = 15.101(7) A, = 108.45(4)A and Z = 2. The final $R_1$ and $wR_2$ values are 0.0906 and 0.1832, respectively, for 2743 observed reflections $[F_o \geq \sigma 3(F_o)]$. $^1H-NMR$ studies on both the peptides strongly suggest the persistence of $3_{10}-helical$ conformations in solution. Peptide 3 crystallized in the space group $P2_1/n$, with a = 10.018(1) A, b = 20.725(1) A, c = 12.915(1) A and Z = 4. The final $R_1$ and $wR_2$ values are 0.0411 and 0.1105, respectively, for 3634 observed reflections $[F_o \geq \sigma 4(F_o)]$.