Design of folded peptides

Proline Editing: A Divergent Strategy for the Synthesis of Conformationally Diverse Peptides

[reaction: see text] Strong conformational biases in peptides and proteins can be achieved with 4-substituted proline residues (cis-, trans-, or disubstituted fluoroproline or hydroxyproline). The practical, divergent synthesis of peptides containing these residues, via postsynthetic modification of a peptide containing an internal trans-hydroxyproline residue, is described. Significant differences in the conformations of the peptides Ac-TYXN-NH2 were observed, including K(trans/cis) values, which varied from 1.5 (X = cis-fluoroproline) to 7.0 (X = trans-fluoroproline).

A Meccano set approach of joining trpzip a water soluble beta-hairpin peptide with a didehydrophenylalanine containing hydrophobic helical peptide

A 16 residues long, water soluble, monomeric beta-hairpin peptide 'trpzip', stabilized by tryptophan zipper has been linked via a tetraglycyl linker to a hydrophobic didehydrophenylalnine (DeltaF) containing helical octapeptide. Circular dichroism studies of this 28 residues long peptide, 'trpzipalpha' (Ac-GEWTWDDATKTWTWTE-GGGG-DeltaFALDeltaFALDeltaFA-NH(2)) in water have revealed the presence of both the beta-hairpin and the helical conformations. This is the first instance where a DeltaF containing peptide has been found to display a helical fold in water. The fluorescence emission wavelengths of tryptophan in Ac-G-W-G-NH(2), trpzip and trpzipalpha were 341.5, 332.8 and 332.6 nm, respectively. The fluorescence quantum yield of trpzip was 2.6-fold higher than trpzipalpha suggesting that proximal interactions between the beta-hairpin and the helix caused the quenching of tryptophan fluorescence in the former by the DeltaFs in the latter. The molar ellipticity of the far UV couplet characteristic of trpzip was reduced in trpzipalpha and the CD based thermal melting temperatures at 228 nm were 62 degrees C (trpzip) and 57 degrees C (trpzipalpha). A concentration-dependent variable temperature CD study in water showed that in trpzipalpha, increasing temperature is detrimental to the beta-hairpin, but it augments the helical motif, perhaps by intermolecular oligomerization. Our results show that in water, trpzipalpha exhibits long-range interactions between two different secondary structures. In contrast to trpzip, trpzipalpha has shown a greater tendency to oligomerize in water.

Functionalized foldamers: synthesis and characterization of a glycosylated beta-peptide 314-helix conveying the TN-antigen

Herein we describe the design, synthesis, and solution structure of a novel type of conjugate composed of a naturally occurring bio-active ligand bound to an artificial peptidomimetic backbone; in this first report on such functionalized foldamers we utilized a beta-peptide as backbone and a GalNAc carbohydrate residue as ligand.

Chain-length-dependent helical motifs and self-association of beta-peptides with constrained side chains

Homo-oligomers constructed by using trans-2-aminocyclohexanecarboxylic acid monomers without protecting groups were studied. Both ab initio theory and NMR measurements showed that the tetramer tends to adopt a 10-helix motif, while the pentamer and hexamer form the known 14-helix. It was concluded that the conformationally constrained backbone is flexible enough to afford both 10-helical and 14-helical motifs, this observation in turn providing evidence of the true folding process. Self-association of the helical units was also detected, and the results of variable-temperature diffusion NMR measurements strongly suggested the presence of helical bundles in methanol solution.

@-Tides as Reporters for Molecular Associations

The 1,6-dihydro-3(2H)-pyridinone unit is an amino acid surrogate that favors the extended beta-strand conformation when incorporated in an oligopeptide ("@-tide") strand. We now report that the circular dichroism (CD) signature of the vinylogous amide in the @-unit is sensitive to conformation in organic and aqueous solvents and, therefore, is useful as a quantitative measure of @-tide association and folding processes that involve this moiety. Moreover, this method can be employed in the micromolar concentration range, which is not readily accessible using other techniques. Measurements of @-tide dimerization and beta-hairpin folding equilibria not only demonstrate the utility and generality of this approach but also provide a way to quantify amino acid side chain-side chain interactions relevant to beta-sheet stability.

@-Tide-Stabilized β-Hairpins

As minimalist versions of beta-structure, two-stranded beta-hairpins are commonly employed as platforms for assessing the interactions that stabilize beta-sheets in proteins. We have found that the presence of a 1,6-dihydro-3(2H)-pyridinone moiety (the "@-unit") as an amino acid replacement at the i - 1 or i + 4 positions relative to a beta-turn strongly stabilizes the hairpin conformation. Hybrids of this type bridge the gap between natural beta-hairpins and unnatural beta-sheets because the @-unit only replaces one residue in a peptide while stabilizing the hairpin conformation to a greater extent than a normal amino acid. In this report, we describe the synthesis of a variety of @-tide-templated hairpins and the NMR and CD characterization of their conformations in both polar and nonpolar solvents.

Design, folding, and activities of metal-assembled coiled coil proteins

Metal ions serve many purposes in natural proteins, from the stabilization of tertiary structure to the direction of protein folding to crucial roles in electron transfer and catalysis. There is considerable interest in creating metal binding sites in designed proteins to understand the structural role of metal ions and to design new metalloproteins with useful functions. The de novo design of metalloproteins and the role of metals in the folding of designed proteins are reviewed here, with particular focus on the design, folding, and activities of the [M(bpy-peptide)(3)](2+) structure. This maquette is constructed by the covalent attachment of 2,2'-bipyridine to the N-termini of amphiphilic peptides, and it is assembled into a folded trimeric coiled coil by the addition of a six-coordinate transition metal ion and the resulting hydrophobic collapse of the peptides. The [M(bpy-peptide)(3)](2+) structure has been employed in diverse applications, ranging from electron transfer pathway studies to the study of optimal hydrophobic packing in a virtual library to the construction of receptors and biosensors.

X-Ray crystallographic signature of supramolecular triple helix formation from a water soluble synthetic tetrapeptide

Single crystal X-ray diffraction studies on the water soluble, synthetic tetrapeptide Tyr(1)-Aib(2)-Tyr(3)-Val(4) with a non-coded amino acid residue (Aib: [small alpha]-amino isobutyric acid) reveal that the peptide adopts an "S"-shaped molecular structure which self-assembles to form a supramolecular triple helix using various non-covalent interactions including water mediated hydrogen bonds in the solid state.

Stereoselective synthesis of conformationally constrained ω-amino acid analogues from pyroglutamic acid

Bicyclic lactams derived from pyroglutamic acid provide a useful scaffold for synthesis of conformationally restricted analogues of lysine, ornithine and glutamine, as well as an Ala-Ala dipeptide analogue. Amino alcohol and carboxylic acid derivatives are accessible from a common intermediate. In this strategy, the bicyclic lactam system not only controls, but also facilitates the determination of the stereochemistry of the synthetic intermediates.

Conformational study on glycosylated asparagine-oligopeptides by NMR spectroscopy and molecular dynamics calculations

The conformational properties of the homo oligomers of increasing chain length Boc-(Asn)(n)-NHMe (n = 2, 4, 5), (GlcNAc-beta-Asn)(n)-NHMe (n = 2, 4, 5, 8) and Boc-[GlcNAc(Ac)(3)-beta-Asn](n)-NHMe (n = 2, 4, 5) were studied by using NOE experiments and molecular dynamic calculations (MD). Sequential NOEs and medium range NOEs, including (i,i+2) interactions, were detected by ROESY experiments and quantified. The calculated inter-proton distances are longer than those characteristic of beta-turn secondary structures. Owing to the large conformational motions expected for linear peptides, MD simulations were performed without NMR constraints, with explicit water and by applying different treatments of the electrostatic interactions. In agreement with the NOE results, the simulations showed, for all peptides, the presence of both folded and unfolded structures. The existence of significant populations of beta-turn structures can be excluded for all the examined compounds, but two families of structures were more often recognized. The first one with sinusoidal or S-shaped forms, and another family of large turns together with some more extended conformations. Only the glycosylated pentapeptide shows in vacuo a large amount of structures with helical shaped form. The results achieved in water and in DMSO are compared and discussed, together with the effect of the glycosylation.

Conformational studies of peptides containing cis-3-hydroxy-D-proline

Conformational analysis of peptides containing cis-3-hydroxy-d-proline (d-cis-3-Hyp) by NMR studies revealed that the 3-hydroxyl group in this amino acid plays a significant role in the overall three-dimensional structures of the peptides. When the d-cis-3-Hyp had its 3-hydroxyl group protected as the benzyl (Bn) ether, the peptide displayed a beta-hairpin structure in both CDCl(3) and DMSO-d(6). Even after the removal of the Bn group, the resulting deprotected compound retained the same structure as in the protected version in CDCl(3). However, in polar solvent DMSO-d(6), the C-terminal strand of the hydroxyl-deprotected peptide flipped to the side of the hydroxyl group, breaking the hairpin to form a pseudo beta-turn-like nine-membered ring structure involving an intramolecular hydrogen bond between LeuNH --> HypC3-OH.

X-ray structure analysis of a designed oligomeric miniprotein reveals a discrete quaternary architecture

The x-ray crystal structure of an oligomeric miniprotein has been determined to a 1.2-A resolution by means of multiwavelength anomalous diffraction phasing with selenomethionine analogs that retain the biophysical characteristics of the native peptide. Peptide 1, comprising alpha and beta secondary structure elements with only 21 aa per monomer, associates as a discrete tetramer. The peptide adopts a previously uncharacterized quaternary structure in which alpha and beta components interact to form a tightly packed and well defined hydrophobic core. The structure provides insight into the origins of the unusual thermal stability of the oligomer. The miniprotein shares many characteristics of larger proteins, including cooperative folding, lack of 1-anilino-8-naphthalene sulfonate binding, and limited deuterium exchange, and possesses a buried surface area typical of native proteins.

In search of peptide-based catalysts for asymmetric organic synthesis

The discovery of short peptide sequences that function as asymmetric catalysts for a variety of reactions is documented. The evolution of the project from an exercise in rational design to an endeavor that combines combinatorial screening with various mechanism-based experiments is presented. The specific development of catalysts for enantioselective acylation, phosphorylation, conjugate addition, and Morita-Baylis-Hillman reactions is described.

Synthesis of 310-Helix-Inducing Constrained Analogues of l-Proline

A bicyclic indolizidinone carboxylic acid and a tricyclic constrained analogue of l-proline were synthesized and evaluated for their ability to induce helix formation as l-Ala tetrapeptides. Variable-temperature NMR, DMSO titration, CD spectra, and X-ray structure analyses, in conjunction with molecular modeling, confirmed the existence of 3(10)-helical motifs with di- and tetrapeptides of l-Ala.

Structure and assembly of designed beta-hairpin peptides in crystals as models for beta-sheet aggregation

De novo designed beta-hairpin peptides have generally been recalcitrant to crystallization. The crystal structures of four synthetic peptide beta-hairpins, Boc-Leu-Val-Val-DPro-Gly-Leu-Phe-Val-OMe (1), Boc-Leu-Phe-Val-DPro-Ala-Leu-Phe-Val-OMe (2), Boc-Leu-Val-Val-DPro-Aib-Leu-Val-Val-OMe (3), and Boc-Met-Leu-Phe-Val-DPro-Ala-Leu-Val-Val-Phe-OMe (4), are described. The centrally positioned DPro-Xxx segment promotes prime beta-turn formation, thereby nucleating beta-hairpin structures. In all four peptides well-defined beta-hairpins nucleated by central type II' DPro-Xxx beta-turns have been characterized by X-ray diffraction, providing a view of eight crystallographically independent hairpins. In peptides 1-3 three intramolecular cross-strand hydrogen bonds stabilized the observed beta-hairpin, with some fraying of the structures at the termini. In peptide 4, four intramolecular cross-strand hydrogen bonds stabilized the hairpin. Peptides 1-4 reveal common features of packing of beta-hairpins into crystals. Two-dimensional sheet formation mediated by intermolecular hydrogen bonds formed between antiparallel strands of adjacent molecule is a recurrent theme. The packing of two-dimensional sheets into the crystals is mediated in the third dimension by bridging solvents and interactions of projecting side chains, which are oriented on either face of the sheet. In all cases, solvation of the central DPro-Xxx peptide unit beta-turn is observed. The hairpins formed in the octapeptides are significantly buckled as compared to the larger hairpin in peptide 4, which is much flatter. The crystal structures provide insights into the possible modes of beta-sheet packing in regular crystalline arrays, which may provide a starting point for understanding beta-sandwich and cross-beta-structures in amyloid fibrils.

External Chirality-Triggered Helicity Control Promoted by Introducing a β-Ala Residue into the N-Terminus of Chiral Peptides

The noncovalent chiral domino effect (NCDE), defined as chiral interaction upon an N-terminus of a 3(10)-helical peptide, will provide a unique method for structural control of a peptide helix through the use of external chirality. On the other hand, the NCDE has not been considered to be effective for the helicity control of peptides strongly favoring a one-handed screw sense. We here aim to promote the NCDE on peptide helicity using two types of nonapeptides: H-beta-Ala-Delta(Z)Phe-Aib-Delta(Z)Phe-X-(Delta(Z)Phe-Aib)(2)-OCH(3) [Delta(Z)Phe = alpha,beta-didehydrophenylalanine, Aib = alpha-aminoisobutyric acid], where X as the single chirality is L-leucine (1) or L-phenylalanine (2). NMR, IR, and CD spectroscopy as well as energy calculation revealed that both peptides alone form a right-handed 3(10)-helix. The original CD amplitudes or signs in chloroform, irrespective of a strong screw-sense preference in the central chirality, responded sensitively to external chiral information. Namely added Boc-L-amino acid stabilized the original right-handed helix, while the corresponding d-isomer destabilized it or transformed it into a left-handed helix. These peptides were also shown to bind more favorably to an L-isomer from the racemate. Although similar helicity control was observed for analogous nonapeptides bearing an N-terminal Aib residue (Inai, Y.; et al. Biomacromolecules 2003, 4, 122), the present findings demonstrate that the N-terminal replacement by the beta-Ala residue significantly improves the previous NCDE to achieve more effective control of helicity. Semiempirical molecular orbital calculations on complexation of peptide 2 with Boc-(L or D)-Pro-OH reasonably explained the unique conformational change induced by external chirality.

Conformational preferences and self-template macrocyclization of squaramide-based foldable modules

Secondary squaramides have considerable potential as hydrogen bond donors and acceptors. In CHCl(3) both, anti- and syn-squaramide rotamers are observed by NMR. The energetic barrier for anti/syn mutual interconversion determined by complete band shape analysis is approximately 63 kJ mol(-1). As in proline derivatives, a low rotational barrier is crucial for the design of foldable modules. In this paper, folding based on the low rotational barrier of squaramides is driven by donor atoms (N or O) located in the gamma position of an alkyl chain of a secondary squaramide. We demonstrate that the resulting minimal module exists as a folded conformer through the formation of a nine-membered ring stabilized by intramolecular hydrogen bonding. Molecular mechanics calculations and NMR studies support the existence of these folded conformers. The intramolecularly hydrogen bonded conformers are clearly visible even in CHCl(3)-EtOH mixtures. Folding occurs even in pure ethanol. As an indirect test, we studied the effectiveness of macrocyclization reactions in pure ethanol that require an effective templating effect to take place. The high yields obtained support the dominant role of a folded conformer even in this solvent.

Effect of Side Chains on Turns and Helices in Peptides of β3-Aminoxy Acids

We have investigated, using NMR, IR, and CD spectroscopy and X-ray crystallography, the conformational properties of peptides 1-10 of beta(3)-aminoxy acids (NH(2)OCHRCH(2)COOH) having different side chains on the beta carbon atom (e.g., R = Me, Et, COOBn, CH(2)CH(2)CH=CH(2), i-Bu, i-Pr). The beta N-O turns and beta N-O helices that involve a nine-membered-ring intramolecular hydrogen bond between NH(i)(+2) and CO(i), which have been found previously in peptides of beta(2,2)-aminoxy acids (NH(2)OCH(2)CMe(2)COOH), are also present in those beta(3)-aminoxy peptides. X-ray crystal structures and NMR spectral analysis reveal that, in the beta N-O turns and beta N-O helices induced by beta(3)-aminoxy acids, the N-O bond could be either anti or gauche to the C(alpha)-C(beta) bond depending on the size of the side chain; in contrast, only the anti conformation was found in beta(2,2)-aminoxy peptides. Both diamide 1 and triamide 9 exist in different conformations in solution and in the solid state: parallel sheet structures in the solid state and predominantly beta N-O turn and beta N-O helix conformations in nonpolar solvents. Theoretical studies on a series of model diamides rationalize very well the experimentally observed conformational features of these beta(3)-aminoxy peptides.

Metal ion-binding ability of tetrapeptides containing alpha-aminoisobutyric acid

alpha-Aminoisobutyric acid (Aib), one of the Calpha,alpha-disubstituted glycines, is a sterically hindered amino acid that acts as a conformational constraint in peptides. However, studies for the application of the ability of Aib to control conformation are quite few. The paper focuses on the molecular recognition ability of acyclic oligopeptides containing Aib. Liquid-liquid extraction of nine kinds of metal ions from aqueous layers to nonpolar organic layers with acyclic tetrapeptides, X-Trp-Xaa2-Gly-Xaa4-NH-Ar (X = H or C6H5CH2OCO (Z), Xaa2 = Aib or Gly, Xaa4 = Leu or Ala, Ar = phenyl or 3,5-dimethylphenyl) was examined using picrate as the anion of ion pairs. The extraction behaviour of the metal ions with the tetrapeptides was investigated in the pH range from 3 to 9. In the case of basic pH regions, Cu(II) and Ag(I) were effectively extracted with Trp-Aib-Gly-Leu-NH-Ar. Pd(II) was specifically extracted with Trp-Aib-Gly-Leu-NH-Ar in acidic pH regions. The extraction percent (%E) of the peptide host, which has a 3,5-dimethylphenyl group, was even larger than that of the host, which has a phenyl group. Moreover, Pd(II) was extracted with a peptide host which has Leu and a 3,5-dimethylphenyl group in the absence of picrate as the anion of ion pairs. The free alpha-amino group, the turn conformation and the hydrophobicity of peptide molecules were important factors for the extraction of the metals.

De Novo Design and Characterization of a Helical Hairpin Eicosapeptide

De novo design of supersecondary structures is expected to provide useful molecular frameworks for the incorporation of functional sites as in proteins. A 21 residue long, dehydrophenylalanine-containing peptide has been de novo designed and its crystal structure determined. The apolar peptide folds into a helical hairpin supersecondary structure with two right-handed helices, connected by a tetraglycine linker. The helices of the hairpin interact with each other through a combination of C-H.O and N-H.O hydrogen bonds. The folding of the apolar peptide has been realized without the help of either metal ions or disulphide bonds. A remarkable feature of the peptide is the unanticipated occurrence of an anion binding motif in the linker region, strikingly similar in conformation and function to the "nest" motif seen in several proteins. The observation supports the view for the possible emergence of rudimentary functions over short sequence stretches in the early peptides under prebiotic conditions.

Conformational properties of hybrid peptides containing alpha- and omega-amino acids*

This review briefly surveys the conformational properties of guest omega-amino acid residues when incorporated into host alpha-peptide sequences. The results presented focus primarily on the use of beta- and gamma-residues in alphaomega sequences. The insertion of additional methylene groups into peptide backbones enhances the range of accessible conformations, introducing additional torsional variables. A nomenclature system, which permits ready comparisons between alpha-peptides and hybrid sequences, is defined. Crystal structure determination of hybrid peptides, which adopt helical and beta-hairpin conformations permits the characterization of backbone conformational parameters for beta- and gamma-residues inserted into regular alpha-polypeptide structures. Substituted beta- and gamma-residues are more limited in the range of accessible conformation than their unsubstituted counterparts. The achiral beta,beta-disubstituted gamma-amino acid, gabapentin, is an example of a stereochemically constrained residue in which the torsion angles about the Cbeta-Cgamma (theta1) and Calpha-Cbeta (theta2) bonds are restricted to the gauche conformation. Hybrid sequences permit the design of novel hydrogen bonded rings in peptide structures.

Substituent Effects on Pyrid-2-yl Ureas toward Intramolecular Hydrogen Bonding and Cytosine Complexation

Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d(7) at -70 degrees C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K(i) around 1-2. However, the K(i) value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 +/- 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d(7) with binding constants K(B) ranging from 30 to 1700 M(-1). Electron withdrawing substituents, such as the 4-O(2)NC(6)H(4)- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.

Expected and unexpected results from combined β-hairpin design elements

A model beta-hairpin dodecapeptide [EFGWVpGKWTIK] was designed by including a favorable D-ProGly Type II' beta-turn sequence and a Trp-zip interaction, while also incorporating a beta-strand unfavorable glycine residue in the N-terminal strand. This peptide is highly folded and monomeric in aqueous solution as determined by combined analysis with circular dichroism and 1H NMR spectroscopy. A peptide representing the folded conformation of the model beta-hairpin [cyclic(EFGWVpGKWTIKpG)] and a linear peptide representing the unfolded conformation [EFGWVPGKWTIK] yield unexpected relative deviations between the CD and 1H NMR spectroscopic results that are attributed to variations in the packing interactions of the aromatic side chains. Mutational analysis of the model beta-hairpin indicates that the Trp-zip interaction favors folding and stability relative to an alternate hydrophobic cluster between Trp and Tyr residues [EFGYVpGKWTIK]. The significance of select diagonal interactions in the model beta-hairpin was tested by rearranging the cross-strand hydrophobic interactions to provide a folded peptide [EWFGIpGKTYWK] displaying evidence of an unusual backbone conformation at the hydrophobic cluster. This unusual conformation does not appear to be a result of the glycine residue in the beta-strand, as replacement with a serine results in a peptide [EWFSIpGKTYWK] with a similar and seemingly characteristic CD spectrum. However, an alternate arrangement of hydrophobic residues with a Trp-zip interaction in a similar position to the parent beta-hairpin [EGFWVpGKWITK] results in a folded beta-hairpin conformation. The differences between side chain packing of these peptides precludes meaningful thermodynamic analysis and illustrates the caution necessary when interpreting beta-hairpin folding thermodynamics that are driven, at least in part, by aromatic cross strand interactions.

Novel model peptide for Atx1-like metallochaperones

The novel cyclodecapeptide c(GMTCSGCSRP) is able to bind soft metals with a selectivity for Hg(2+) and Cu(+) over Pb(2+), Cd(2+) and Zn(2+), and is demonstrated to be an excellent structural model of the binding loop of the copper metallochaperone Atx1 in its apo and mercury loaded forms.

Stage-specific profiling of Plasmodium falciparum proteases using an internally quenched multispecificity protease substrate

Novel internally quenched fluorescence peptide substrates containing sequence specific sites for cleavage by multiple proteases were designed and synthesized. The 28 and 29 residue peptides contain an N-terminal fluorescence acceptor group, 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL), and a C-terminal fluorescence donor group, 5-(2-aminoethylamino)naphthalene-1-sulfonic acid (EDANS). Efficient energy transfer between the donor and acceptor groups flanking the peptide sequence was achieved by incorporation of a central DPro-Gly segment, which serves as a conformation nucleating site, inducing hairpin formation. This multispecificity protease substrate was used to profile the proteolytic activities in the malarial parasite Plasmodium falciparum in a stage dependent manner using a combination of fluorescence and MALDI mass spectrometry. Cysteine protease activity was shown to be dominating at neutral pH, whereas aspartic protease activity contributed predominantly to the proteolytic repertoire at acidic pH. Maximum proteolysis was observed at the trophozoite stage followed by the schizonts and the rings.

Crystal structure of a hydrophobic 19-residue peptide helix containing three centrally located D amino acids

The design of the synthetic 19-residue peptide Boc-Leu-Aib-Val-Ala-Leu5-Aib-Val-D-Ala-d-Leu-Leu10-Val-Phe-Val-Aib-D-Val15-Leu-Phe-Val-Val-OMe (Aib, alpha-aminoisobutyric acid; OMe, methyl ester) was intended to produce a crystalline peptide with independent helical and hairpin domains. The design was partially based on an octapeptide with the same sequence as residues 11-18 above, which was shown to fold into a beta-hairpin in the crystal. However, the crystal structure of the present peptide provided a surprising result. The conformation is the longest characterized right-handed alpha-helix, with as many as three internal d residues in the sequence. The completely helical structure was also unexpected, because beta-branched residues such as Val have a low propensity for helix formation in proteins. The helical peptides in the present structure assemble to form hydrophobic channels that accommodate five toluene molecules per peptide along the length of the channel. The structural results illustrate the similarity in energetics between helical and beta-hairpin conformations for peptides containing Aib residues. The crystallographic parameters for C107H179N19O22.3H2O.2.5 toluenes are: space group C2, a = 34.679(3) A, b = 12.866(1) A, c = 31.915(3) A, beta = 96.511(8) degrees, V = 14,148 A3, Z = 4, dcalc = 1.099 g/cm3, and agreement factor R1 = 10.2%.

Probing the Role of the C−H···O Hydrogen Bond Stabilized Polypeptide Chain Reversal at the C-terminus of Designed Peptide Helices. Structural Characterization of Three Decapeptides

The structural characterization in crystals of three designed decapeptides containing a double d-segment at the C-terminus is described. The crystal structures of the peptides Boc-Leu-Aib-Val-Xxx-Leu-Aib-Val-(D)Ala-(D)Leu-Aib-OMe, (Xxx = Gly 2, (D)Ala 3, Aib 4) have been determined and compared with those reported earlier for peptide 1 (Xxx = Ala) and the all l analogue Boc-Leu-Aib-Val-Ala-Leu-Aib-Val-Ala-Leu-Aib-OMe, which yielded a perfect right-handed alpha-helical structure. Peptides 1 and 2 reveal a right-handed helical segment spanning residues 1 to 7, ending in a Schellman motif with (D)Ala(8) functioning as the terminating residue. Polypeptide chain reversal occurs at residue 9, a novel feature that appears to be the consequence of a C-H.O hydrogen bond between residue 4 C(alpha)H and residue 9 CO groups. The structures of peptides 3 and 4, which lack the pro R hydrogen at the C(alpha) atom of residue 4, are dramatically different. Peptide 3 adopts a right-handed helical conformation over the 1 to 7 segment. Residues 8 and 9 adopt alpha(L) conformations forming a C-terminus type I' beta-turn, corresponding to an incipient left-handed twist of the polypeptide chain. In peptide 4, helix termination occurs at Aib(6), with residues 6 to 9 forming a left-handed helix, resulting in a structure that accommodates direct fusion of two helical segments of opposite twist. Peptides 3 and 4 provide examples of chiral residues occurring in the less favored sense of helical twist; (D)Ala(4) in peptide 3 adopts an alpha(R) conformation, while (L)Val(7) in 4 adopts an alpha(L) conformation. The structural comparison of the decapeptides reported here provides evidence for the role of specific C-H.O hydrogen bonds in stabilizing chain reversals at helix termini, which may be relevant in aligning contiguous helical and strand segments in polypeptide structures.

Crystal structure of achiral nonapeptide Boc-(Aib-?zPhe)4-Aib-OMe at atomic resolution: Evidence for a 310-helix

An x-ray crystallographic analysis was carried out for Boc-(Aib-DeltaZPhe)4-Aib-OMe (1: Boc = t-butoxycarbonyl; Aib = alpha-aminoisobutyric acid; DeltaZPhe = Z-alpha,beta-didehydrophenylalanine) to provide the precise conformational parameters of the octapeptide segment -(Aib-DeltaZPhe)4-. Peptide 1 adopted a typical 3(10)-helical conformation characterized by <phi> = +/-55.8 degrees (50 degrees -65 degrees), <psi> = +/-26.7 degrees (15 degrees -45 degrees), and <omega> = +/-179.5 degrees (168 degrees -188 degrees) for the average values of the -(Aib-DeltaZPhe)4- segment (the range of the eight values). The 3(10)-helix contains 3.1 residues per turn, being close to the "perfect 3(10)-helix" characterized by 3.0 residues per turn. NMR and Fourier transform infrared (FTIR) spectroscopy revealed that the 3(10)-helical conformation at the atomic resolution is essentially maintained in solution. Energy minimization of peptide 1 by semiempirical molecular orbital calculation converged to a 3(10)-helical conformation similar to the x-ray crystallographic 3(10)-helix. The preference for a 3(10)-helix in the -(Aib-DeltaZPhe)4- segment is ascribed to strong inducers of the 3(10)-helix inherent in Aib and DeltaZPhe residues-in particular, the Aib residues tend to stabilize a 3(10)-helix more effectively. Therefore, the -(Aib-DeltaZPhe)4- segment is useful to rationally design an optically inactive 3(10)-helical backbone, which will be of great importance to provide novel insights into noncovalent and covalent chiral interactions of a helical peptide with a chiral molecule.

α-γHybrid Peptides that Contain the Conformationally Constrained Gabapentin Residue: Characterization of Mimetics of Chain Reversals

The crystal structures of four dipeptides that contain the stereochemically constrained gamma-amino acid residue gabapentin (1-(aminomethyl)cyclohexaneacetic acid Gpn) are described. The molecular conformation of Piv-Pro-Gpn-OH (1), reveals a beta-turn mimetic conformation, stabilized by a ten atom C[bond]H...O hydrogen bond between the Piv CO group and the pro S hydrogen of the Gpn CH(2)[bond]CO group. The peptides Boc-Gly-Gpn-OH (2), Boc-Aib-Gpn-OH (3), and Boc-Aib-Gpn-OMe (4) form compact, folded structures, in which a distinct reversal of polypeptide chain direction is observed. In all cases, the Gpn residue adopts a gauche,gauche (g,g) conformation about the C(gamma)[bond]C(beta) (theta(1)) and C(beta)[bond]C(alpha) (theta(2)) bonds. Two distinct Gpn conformational families are observed. In peptides 1 and 3, the average backbone torsion angle values for the Gpn residue are phi=98 degrees, theta(1)=-62 degrees, theta(2)=-73 degrees, and psi=79 degrees, while in peptide 2 and 4 the average values are phi=-103 degrees, theta(1)=-46 degrees, theta(2)=-49 degrees, and psi=-92 degrees. In the case of 1 and 3, an intramolecular nine-membered O[bond]H...O hydrogen bond is formed between the C[double bond]O of the preceding residue and the terminal carboxylic acid OH group. All four alpha-gamma dipeptide sequences yield compact folded backbone conformations; this suggests that the Gpn residue may be employed successfully in the design of novel folded structures.

Stereocontrolled Synthesis of ψ[CH(CF3)NH]Gly-Peptides

[reaction: see text] A novel class of peptidomimetics having a stereogenic [CH(CF(3))NH] replacement for a [CONH] peptide bond has been synthesized. The new compounds have been obtained in a stereocontrolled fashion using a kinetically controlled aza-Michael addition of chiral alpha-amino acid esters to trans-3,3,3-trifluoro-1-nitropropene. The stereoselectivity is strongly influenced by the solvent, the base, its stoichiometry, and the R side-chain. Diastereomeric ratios higher than 11:1 were achieved using H-Val-OtBu.HCl in toluene with 1.1 equiv of DIPEA.

Dual Catalyst Control in the Amino Acid-Peptide-Catalyzed Enantioselective Baylis−Hillman Reaction

[reaction: see text] Nucleophile-loaded peptides and proline have been found to function synergistically as cocatalysts for the asymmetric ketone-based Baylis-Hillman reaction. Although neither compound is effective independently in terms of rate or enantioselectivity, their combination leads to catalysis where enantioselectivities up to 81% have been observed.

Side-chain control of beta-peptide secondary structures

As one of the most important families of non-natural polymers with the propensity to form well-defined secondary structures, the beta-peptides are attracting increasing attention. The compounds incorporating beta-amino acid residues have found various applications in medicinal chemistry and biochemistry. The conformational pool of beta-peptides comprises several periodic folded conformations, which can be classified as helices, and nonpolar and polar strands. The latter two are prone to form pleated sheets. The numerous studies that have been performed on the side-chain dependence of the stability of the folded structures allow certain conclusions concerning the principles of design of the beta-peptide foldamers. The folding propensity is influenced by local torsional, side-chain to backbone and long-range side-chain interactions. Although beta-peptide foldamers are sensitive to solvent, the systematic choice of the side-chain pattern and spatiality allows the design of the desired specific secondary structure. The application of beta-peptide foldamers may open up new directions in the synthesis of highly organized artificial tertiary structures with biochemical functions.

Asymmetric synthesis of substituted 1-aminocyclopropane-1-carboxylic acids via diketopiperazine methodology

Diketopiperazinespirocyclopropane 12 is prepared in > 98% d.e. via the conjugate addition of a phosphorus ylide to (6S)-N,N'-bis(p-methoxybenzyl)-3-methylenepiperazine-2,5-dione 2. Deprotection and hydrolysis of adduct 12 and subsequent peptide coupling demonstrate the applicability of this methodology to the asymmetric synthesis of 1-aminocyclopropane-1-carboxylic acids for incorporation into novel peptides. A model for the high level of diastereofacial selectivity observed in the cyclopropanation reaction is presented. A highly selective asymmetric approach (> 98% d.e.) to (S)-[2,2-(2)H2]-1-aminocyclopropane-1-carboxylic acid 29 is also reported via a deuterated sulfur ylide addition to acceptor 2.

N-benzhydryl-glycolamide: the first protecting group in peptide synthesis with a strong conformational bias

We have synthesized and examined the preferred conformation of a set of N-benzhydryl-glycolamide esters from N(alpha)-protected (or N(alpha)-blocked) alpha-amino acids. Experiments were performed in CDCl(3) solution by Fourier transform infrared absorption and (1)H-NMR techniques, and in the crystalline state by x-ray diffraction. The results of our analysis strongly support the view that this type of N(alpha)-acylated alpha-aminoacyl esters has a marked tendency to fold into a beta-turn conformation, the nature of which is dictated by the structural propensity of the amino acid constituent at the i+1 position.

Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues

Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.

Conformational investigation of alpha, beta-dehydropeptides. XI. Molecular and crystal structure of Ac-(Z)-deltaPhe-NMe2 as compared to those of related molecules

A series of three homologous dimethyldiamides Ac-(Z)-deltaPhe-NMe2, Ac-L-Phe-NMe2 and Ac-DL-Phe-NMe2 have been synthesized and their structures determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of the compounds studied, the fully relaxed phi, psi conformational energy maps on the free molecules of Ac-deltaAla-NMe2 and Ac-(Z)-deltaPhe-NMe2 were obtained with the HF/3-21G method and the calculated minima re-optimized with the DFT/B3LYP/6-31G** method. The crystal state results have been compared with the literature data. The studied dimethyldiamide Ac-deltaXaa-NMe2 combines the double bond in positions alpha, beta and the C-terminal tertiary amide within one molecule. As the representative probe with deltaXaa = deltaAla, (Z)-deltaLeu and (Z)-deltaPhe shows, in the solid state they adopt the conservative conformation with phi, psi approximately -45 degrees, approximately 130 degrees and with a non-planar tertiary amide bond, whatever the packing forces are. This conformation is located on the Ramachandran map in region H/F, which is of high-energy for common amino acids, but not so readily accessible to them. The free molecule calculations on Ac-deltaAla-NMe2 and Ac-(Z)-deltaPhe-NMe2 reveal that, in spite of dissimilar overall conformational profiles of these molecules, this structure is one of their low-energy conformers and for Ac-(Z)-deltaPhe-NMe2 it constitutes the global minimum. So, the theoretical results corroborate those experimental results proving that this structure is robust enough to avoid conformational distortion due to packing forces. In contrast to Ac-deltaXaa-NMe2, the saturated Ac-L/DL-Xaa-NMe2 shows the constancy of the associative patterns but do not prefer any molecular structure in the solid state.