Pseudopeptides and beta folding: x-ray structures compared with structures in solution

Formation of a Turn like Structure in BocNH(CH2)2CON(C6H11)CONH(C6H11): An X-Ray Diffraction Study

β-Alanine is an amino acid which is important in the design of diverse peptides. Crystallographic study shows that the N-acyl adduct of β-Alanine, an ω-amino acid important in peptide design for the production of structural and functional diversities, and N,N′-dicyclohexyl urea(DCU) forms a turn like structure without any intra-molecular hydrogen bonding.

Thermodynamic and kinetic consequences of substituting glycine at different positions in a Pro-Hyp-Gly repeat collagen model peptide

A glycine occurs at every third residue in the X-Y-Gly repeat of natural collagen. Replacing Gly residues destabilizes collagen and is often associated with many diseases. We present a comprehensive study on the thermodynamic and kinetic consequences of replacing Gly residues at different sites in collagen. For this, we prepared a series of peptides that contain a single substitution of Gly with L-Ala, D-Ala, β-Ala, or sarcosine (Sar), at different positions in a host peptide (Pro-Hyp-Gly)(8) . Circular dichroism measurements showed that peptides with the mutation site near the C-terminus (C-terminal mutations) form a more stable collagen triple helix than those with the substitution near the N-terminus (N-terminal mutations), which is consistent with the known in vivo folding mechanism of collagen, from the C to the N-terminus. Thermodynamic analysis indicated that the destabilization in C-terminal mutations is due to entropic effects, while that in N-terminal mutations is mainly from enthalpic effects. The destabilization order is L-Ala < Sar < β-Ala < D-Ala substitution in both the N and C-terminal mutations, suggesting that residues with normal torsion angles are less destabilizing at either position. Moreover, Sar was shown to be a better substituent than the other three amino acids at the central site of collagen strands. Kinetic studies further demonstrated that steric strains imposed by the side chains may be the most critical factor affecting the folding rate of collagen. Our data provide valuable insights into how backbone conformation, side chains, and interstrand hydrogen bonds affect the collagen triple helix at different positions.

Structural studies of model peptides containing β-, γ- and δ-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-betaGly-NHMe (2), Piv-Pro-betaGly-OMe (3), Piv-Pro-deltaAva-OMe (4) and Boc-Pro-gammaAbu-OH (5) are described (Piv: pivaloyl; NHMe: N-methylamide; betaGly: beta-glycine; OMe: O-methyl ester; deltaAva: delta-aminovaleric acid; gammaAbu: gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-betaGly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the deltaAva residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H...O hydrogen bond.

Conformational investigation of alpha,beta-dehydropeptides. XV: N-acetyl-alpha,beta-dehydroamino acid N 'N '-dimethylamides: conformational properties from infrared and theoretical studies

The FTIR spectra were analysed in the region of the nu(s)(N-H), AI(C=O) and nu(s)(Calpha=Cbeta) bands for a series of Ac-DeltaXaa-NMe2, where DeltaXaa = DeltaAla, (Z)-DeltaAbu, (Z)-DeltaLeu, (Z)-DeltaPhe and DeltaVal, to determine a predominant solution conformation of these alpha,beta-dehydropeptide-related molecules. Measurements were taken in CCl4, DCM and MeCN solutions. In the same way, spectra of saturated analogues Ac-Xaa-NMe2, where Xaa = Ala, Abu, Leu, Phe and Val, were investigated. To help interpret the spectroscopic results, conformational maps were calculated by the B3LYP/6-31+G** method. Also, the relative energies of all conformers of the dehydro compounds in vacuo as well as in the studied solvents in addition to the theoretical IR frequencies of these conformers were calculated. For comparison, molecules of two saturated analogues, Ac-L-Ala-NMe2 and Ac-L-Phe-NMe2, were calculated in a similar way. Both unsaturated and saturated compounds, which have an aliphatic side chain, occur in CCl4 and DCM mainly as a mixture of extended conformers with the C5 H-bond and open conformers. As solvent polarity increases, participation of the open conformers also increases, and in MeCN, the model amides are almost exclusively in the open form, except Ac-DeltaAla-NMe2, which shows a small amount of the H-bonded conformer. Ac-DeltaAla-NMe2 and Ac-DeltaAbu-NMe2 have stronger C5 hydrogen bonds than those of their saturated counterparts. As the calculations indicate, the open conformation of the unsaturated amides is conformer H/F with phi, psi -44 +/- 5 degrees, 127 +/- 4 degrees. This is the second lowest in energy conformer in vacuo and in CCl4 and the lowest one in more polar solvents. The open conformation of Ac-L-Ala-NMe2 constitutes conformer C with phi, psi -101.5 degrees, 112.7 degrees. For Ac-DeltaAla-NMe2 and Ac-DeltaAbu-NMe2, FTIR also reveals the presence of a third conformer. Calculations indicate that is the semiextended conformer D with the N1-H1...N2 hydrogen bond/contact. In all solvents, Ac-L-Phe-NMe2 and Ac-(Z)-DeltaPhe-NMe2 show only the extended E and the open H/F, respectively. In both there is an amide/pi(Ph) interaction.

An observation of non-superimposable stereogeometrical features in a non-chiral one-component β-Ala model peptide

This paper describes the chemical synthesis and crystal molecular conformation of a non-chiral beta-Ala containing model peptide Boc-beta-Ala-Acc5-OCH3. The analysis revealed the existence of two crystallographically independent molecules A and B, in the asymmetric unit. Unexpectedly, while the magnitudes of the backbone torsion angles in both molecules are remarkably similar, the signs of the corresponding torsion angles are reverse therefore, inclining us to suggest the existence of non-superimposable stereogeometrical features in a non-chiral one-component beta-Ala model system. The critical mu torsion angle around CbetaH2-CalphaH2 bond of the beta-Ala residue represents a typical gauche orientation i.e., mu = 67.7 degrees in A and mu = -61.2 degrees in B, providing the molecule an overall crescent shaped topology. The observed conformation contrasts markedly to those determined for the correlated non-chiral model peptides: Boc-beta-Ala-Acc6-OCH3 and Boc-beta-Ala-Aib-OCH3 signifying the role of stereocontrolling elements since the stereochemically constrained Calpha, alpha-disubstituted glycyl residues (e.g., Acc5, Acc6, and the prototype Aib) are known to strongly restrict the peptide backbone conformations in the 3(10)/alpha-helical-regions ( phi approximately +/-60+/-20 degrees, psi approximately +/-30+/-20 degrees) of the Ramachandran map. Unpredictably, the preferred, phi, psi torsion angles of the Acc5 residue fall outside the helical regions of the Ramachandran map and exhibit opposite-handed twists for A and B. The implications of the semi-extended conformation of the Acc5 residue in the construction of backbone-modified novel scaffolds and peptides of biological relevance are highlighted. Taken together, the results indicate that in short linear beta-Ala containing peptides specific structural changes can be induced by selective substitution of non-coded linear- or cyclic symmetrically Calpha,alpha-disubstituted glycines, reinstating the hypothesis that in addition to conformational restrictions, the chemical nature of the neighboring side-chain substituents and local environments collectively influences the stabilization of folding-unfolding behavior of the two methylene units of a beta-Ala residue.

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.

Effect of sequence on peptide geometry in 5-tert-butylprolyl type VI beta-turn mimics

The influence of sequence on turn geometry was examined by incorporating (2S,5R)-5-tert-butylproline (5-(t)BuPro) into a series of dipeptides and tetrapeptides. (2S,5R)-5-tert-Butylproline and proline were respectively introduced at the C-terminal residue of N-acetyl dipeptide N'-methylamides 1 and 2. The conformational analysis of these analogues was performed using NMR and CD spectroscopy as well as X-ray diffraction to examine the factors that control the prolyl amide (in this text, the term "prolyl amide" refers to the tertiary amide composed of the pyrrolidine nitrogen of the prolyl residue and the carbonyl of the N-terminal residue) equilibrium and stabilize type VI beta-turn conformation. The high cis-isomer population with aromatic residues N-terminal to proline was shown to result from a stacking interaction between the partial positive charged prolyl amide nitrogen and the aromatic pi-system as seen in the crystal structure of 1c. The effect of sequence on the prolyl amide equilibrium of 5-(t)BuPro-tetrapeptides (Ac-Xaa-Yaa-5-(t)BuPro-Zaa-XMe, 13 and 14) was studied by varying the amino acids at the Xaa, Yaa, and Zaa positions. High (>80%) cis-isomer populations were obtained with alkyl groups at the Xaa position, an aromatic residue at the Yaa position, and either an alanine or a lysine residue at the Zaa position of the 5-(t)BuPro-tetrapeptide methyl esters in water. Tetrapeptides Ac-Ala-Phe-5-(t)BuPro-Zaa-OMe (Zaa = Ala, Lys), 14d and 14f, with high cis-isomer content adopted type VIa beta-turn conformations as shown by their NMR and CD spectra. Although a pattern of amide proton temperature coefficient values indicative of a hairpin geometry was observed in peptides 14d and 14f, the value magnitudes did not indicate strong hydrogen bonding in water.

Conformational investigation of alpha,beta-dehydropeptides. X. Molecular and crystal structure of Ac-DeltaAla-NMe2 compared with those of Ac-L-Ala-NMe2, Ac-DL-Ala-NMe2 and other dimethylamides

A series of three homologous dimethyldiamides Ac-DeltaAla-NMe2, Ac-L-Ala-NMe2 and Ac-DL-Ala-NMe2 has been synthesized and the structures of these amides determined from single-crystal X-ray diffraction data. To learn more about the conformational preferences of compounds studied, the fully relaxed (phi-psi) conformational energy maps in vacuo (AM1) of Ac-DeltaAla-NMe2 and Ac-L-Ala-NMe2 were obtained, and the calculated minima reoptimized with the DFT/B3LYP/6-31G** method. The crystal-state results have been compared with the literature data. Ac-DeltaAla-NMe2 and other alpha,beta-dehydroamino acid dimethyldiamides, Ac-DeltaXaa-NMe2 adopt the conservative conformation of the torsion angles phi, psi = approximately -45 degrees, approximately 130 degrees, which are located in the high-energy region (region H) of Ramachandran diagram. Ac-L-Ala-NMe2 and Ac-DL-Ala-NMe2, as well as other saturated amino acid dimethylamides Ac-L/DL-Xaa-NMe2, present common peptide structures, and no conformational preferences are observed. Molecular packing of the amides analysed reveals two general hydrogen-bonded motifs. Dehydro and DL-species are paired into centrosymmetric dimers, and L-compounds form catemers. However, Ac-DeltaAla-NMe2 and Ac-DL-Ala-NMe2 constitute exceptions: their molecules also link into catemers.

Collateral existence of folded and extended conformations of the beta-Ala moiety in a model peptide

The single-crystal X-ray diffraction analysis of a nonchiral beta-Ala-containing model peptide, Boc-beta-Ala-Aib-OCH(3) 1 (beta-Ala, 3-aminopropionic acid; Aib, alpha-aminoisobutyric acid), establishes the coexistence of distinctly different backbone conformations in two crystallographically independent molecules, A and B, in the asymmetric unit. Interestingly, the central mu torsion angle around the -C(beta)-C(alpha)- bond of the conformationally flexible beta-Ala residue appears to be critical in dictating the overall distinct structural features, i.e., in molecule A it adopts a folded gauche conformation: mu = -71.0 degrees, whereas it favors an extended trans conformation, mu = 161.2 degrees, in molecule B. As expected, the stereochemically constrained Aib residue preferred an energetically favorable folded backbone conformation, the torsion angles being phi = 46.2 degrees and psi = 48.3 degrees for molecule A and phi = -43.6 degrees and psi = -45.5 degrees for molecule B, lying in the left-handed and right-handed helical regions of the Ramachandran map, respectively. Considering the signs as well as the magnitudes of the backbone torsional angles, molecule A typically folds into a pseudo type III' beta-turn-like structure while molecule B prefers an overall extended conformation. Entrapping the two dramatically distinct conformational characteristics in the crystalline state clearly suggests that the gauche and the trans effects of the beta-Ala moieties are indeed energetically accessible to a short linear peptide and receive strong experimental support. The analyses permitted us to emphasize that in addition to conformational constraints of the neighboring residue, the chemical nature of the side-chain acyclic substituents and the "local environments" collectively seem to influence the stabilization of the folding-unfolding behavior of the two methylene units (-CONH-CH(2)-CH(2)-CONH-) in 1.

Stabilization of a novel beta-turn-like motif by nonconventional intramolecular hydrogen-bonding interactions in a model peptide incorporating beta-alanine

The chemical synthesis and x-ray crystal structure analysis of a model peptide incorporating a conformationally adaptable unsubstituted beta-Ala residue: Boc-beta-Ala-Acc6-OCH3 (C16H28N2O5, molecular weight = 328.41; 1) has been described. The peptide crystallized in the space group P2(1)2(1)2(1) a = 8.537 (3), b = 8.872 (10), c = 25.327 (8), alpha = beta = gamma = 90.0 degrees, Z = 4. An attractive feature of the crystal structure analysis of 1 is an accommodation of a significantly folded beta-Ala residue in a short linear peptide. The overall peptide conformation is typically folded into a beta-turn-like motif. The stabilization of the peptide backbone conformation by nonconventional C-H...O weak intramolecular hydrogen-bonding interactions, involving the ester terminal carbon atom and the ethereal oxygen of the Boc group, has been evoked. The conformational constraint that seems most apparent is the phi, psi value of the highly constrained hydrophobic Acc6 ring that may play a key role in inducing or sustaining the observed pseudo type III or III' beta-turn structure. The resulting 12-membered hydrogen bonding ring motif in 1 is distinctly different from the one found in classical beta-turn structures, stabilized by a conventional strong C=O...H-N intramolecular hydrogen bond, comprised of alpha-amino acids. The potential of the conformationally adaptable beta-Ala residue to occupy i + 1 position (left corner) of the folded beta-turn-like structure and to design and construct novel secondary structural features have been emphasized.

Secondary structure formation in N-substituted peptides

A systematic conformational analysis on several model peptides with N-substituted amino acids was performed on the basis of ab initio MO theory at the HF/6-31G* and HF/3-21G levels with inclusion of solvation effects to study the influence of N-substitution on the formation of typically secondary structural elements, e.g. beta sheets, helices and turns. The conformational flexibility of some structures was examined by means of molecular dynamics simulations in the gas phase and in solution. The results show a restriction of the conformational flexibility of the peptide chain after introduction of an N-substituted amino acid. N-substitution makes beta sheet formation more difficult. Several consecutive N-substituted amino acids in a sequence lead to conformers different from those found on the energy hypersurface of the corresponding N-unsubstituted peptides. There is a strong tendency to form periodically helical conformations, e.g. the polyglycine II or the alpha helix, which can be extended over several N-substituted amino acid residues. As long as 1<--4 hydrogen bond formation remains possible, the major types of beta turns can be formed with a distinct preference for the betaII and betaVIa turns. The betaI turn in particular is considerably destabilized.

An exploration of the effects of constraints on the phosphorylation of synthetic protein tyrosine kinase peptide substrates

We synthesized by classical solution methods three conformational constrained analogues of EDNEYTA, a heptapeptide sequence that represents the common major autophosphorylation site of the protein tyrosine kinases (PTKs) of the Src family. The correlation between the different structural properties induced by the modifications of the native sequence and the propensity of the peptides to act as PTK substrates was examined. The kinetic data obtained indicate that the introduction of the tyrosine-analogue constraints Tic(OH) and MeTyr, which block the ring flexibility, completely prevents the phosphorylation catalysed by the kinases Lyn and Fgr. On the other hand PTKIIB/p38syk can phosphorylate the two derivatives albeit with an efficiency lower than that found with the native sequence. A third derivative contained side chain to side chain cyclization. This analogue, in which the freedom of the phenolic moiety is not altered, can be phosphorylated by all the PTKs tested with kinetic constants comparable to the parent peptide.

Solution conformation of tuftsin

Conformation of chemically synthesized tetrapeptide tuftsin, an important immunomodulator, with the sequence Thr-Lys-Pro-Arg-OH has been studied in aqueous solution as well as in a number of organic solvents viz. trifluoroethanol (TFE), methanol and dioxane by circular dichroism (CD) spectroscopy which reveals preferential occurrence of mixture of random coil and beta-turns, that has already been predicted as bioactive conformation of this peptide.

Peptides and peptoids--a quantum chemical structure comparison

Peptoids represent a very interesting structure alternative to peptides. Based on ab initio MO theory employing the 6-31G* and 3-21G basis sets and considering correlation energy, a systematic structure comparison between the basic structure units of peptoids and peptides is performed. The calculations show three minimum conformations denoted as C7 beta, alpha D, and alpha that do not correspond to conformers on the peptide potential energy hypersurface. The possibility of cis peptide bonds in the peptoids was examined. The solvent influence on the structure was estimated by means of various quantum chemical continuum models.

Crystal structures of peptides and modified peptides

The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.

Crystal structure analysis of a beta-turn mimic in hydrazino peptides

The crystal structures of four hydrazino peptides (Piv-Pro-h(N alpha-Bzl)Gly-NHiPr 1, Piv-Pro-hAla-NHiPr 2, Moc-hPro-NHiPr 3, and Boc-hPro-Gly-N(OH)Me 4) deriving from the hydrazino analogues of glycine (hGly), L-alanine (hAla) or L-proline (hPro) have been solved. They reveal a common folded structure of the alpha-hydrazino acid residue characterized by a bifurcated hydrogen bond closing an eight-membered cycle. This folded structure is topologically similar to the beta II'-turn in peptides, and the CO-NH-N hydrazide link can be considered as a good turn-inducer in peptide analogues.

Solid state and solution structure of Boc-L-Ala-delta Phe-delta Phe-NHMe: a dehydropeptide showing propensity for 3(10)-helices of both screw senses

The crystal and molecular structure of the peptide Boc-L-Ala-delta Phe-delta Phe-NHMe, containing two consecutive dehydro-phenylalanine (delta Phe) residues, has been solved by x-ray diffraction. Two independent molecules, X and Y, are present in the crystallographic unit. Their conformation corresponds approximately to an incipient 3(10)-helix stabilized by two intramolecular hydrogen bonds. The (phi, psi) torsion angles, however, have negative and positive signs in the two molecules X and Y, respectively. Therefore, in spite of the presence of an amino acid residue of the L configuration, the two helical molecules have opposite screw senses, even though the right-handed helix is less distorted than the left-handed one in correspondence of the L-Ala residue. The CD spectra in various solvents exhibit exciton bands originating from dipole-dipole interaction between the delta Phe side chains. Addition of DMSO to the chloroform solution produces, as a first step, a strong increasing of the CD bands, which are then progressively canceled by increasing DMSO concentration. The nmr data parallel the behavior observed in the CD spectra. In CDCl3 solution, the temperature coefficients of the NH resonances are consistent with the involvement of the last two amide protons of the sequence in intramolecular hydrogen bonds, but only negligibly small nuclear Overhauser effects (NOE) are observed. Addition of 5% DMSO-d6 allows the observation of diagnostic NOEs. CD and nmr data indicate that the solid state structure is retained in solution, and are consistent with the presence of right-handed and left-handed conformers, with a prevalence of the more stable right-handed one.

Crystal structures of two cyclic pseudopentapeptides containing psi[CH2S] and psi[CH2SO] backbone surrogates

The solid state conformations of cyclo [Gly-Pro psi[CH2S] Gly-D-Phe-Pro] and cyclo [Gly-Pro psi[CH2-(S)-SO]Gly-D-Phe-Pro] have been characterized by X-ray diffraction analysis. Crystals of the sulfide trihydrate are orthorhombic, P2(1)2(1)2(1), with a = 10.156(3) A, b = 11.704(3) A, c = 21.913(4) A, and Z = 4. Crystals of the sulfoxide are monoclinic, P2(1) with a = 10.662(1) A, b = 8.552(3) A, c = 12.947(2) A, beta = 94.28(2), and Z = 2. Unlike their all-amide parent, which adopts an all-trans backbone conformation and a type II beta-turn encompassing Gly-Pro-Gly-D-Phe, both of these peptides contain a cis Gly1-Pro2 bond and form a novel turn structure, i.e., a type II' beta-turn consisting of Gly-D-Phe-Pro-Gly. The turn structure in each of these peptides is stabilized by an intramolecular H bond between the carbonyl oxygen of Gly1 and the amide proton of D-Phe4. In the cyclic sulfoxide, the sulfinyl group is not involved in H bonding despite its strong potential as a hydrogen-bond acceptor. The crystal structure made it possible to establish the absolute configuration of the sulfinyl group in this peptide. The two crystal structures also helped identify a type II' beta-turn in the DMSO-d6 solution conformers of these peptides.

Peptide mimetics as enzyme inhibitors: use of free energy perturbation calculations to evaluate isosteric replacement for amide bonds in a potent HIV protease inhibitor

We present the application of free energy perturbation theory/molecular dynamics to predict the consequence of replacing each of the seven peptide bonds in the potent HIV protease inhibitor JG365: ACE (acetyl)-Ser-Leu-Asn-HEA (hydroxyethylamine analog of Phe-Pro)-Ile-Val-NME (N-methyl) by ethylene or fluoroethylene isosteres. Replacing two of these bonds may well lead to significantly tighter binding; replacing two others is predicted to significantly diminish the binding affinity. Also, for three of the peptide bonds fluoroethylene replacements could lead to increased binding of free energies of the inhibitors. Our results should be considered as predictive since there are, as yet, no experimental results on such peptide replacements as enzyme inhibitors.

Solution structure of peptides containing two dehydro-phenylalanine residues: a CD investigation

The peptides Ac-delta Phe-Ala-delta Phe-NH-Me (1), Ac-delta Phe-Val-delta Phe-NH-Me (2), Ac-delta Phe-Gly-delta Phe-Ala-OMe (3), and Boc-Ala-delta Phe-Gly-delta Phe-Ala-OMe (4), containing two dehydro-phenylalanine (delta Phe) residues, were synthesized and the solution structure investigated in various solvents. The nmr and CD measurements indicate that all the dehydropeptides examined adopt 3(10)-helical conformations in solution. The tripeptides 1 and 2 exhibited an intense negative CD exciton couplet, which was assigned to the right-handed screw sense, while the tetrapeptide 3 displayed a CD couplet having opposite sign, which was assigned to the left-handed helical sense. In the pentapeptide 4 the sense of the helix was found to vary with solvent and temperature, as demonstrated by the sign reversal of the CD spectrum. The right-handed sense dominates in hexafluoro-2-propanol, whereas a left-handed helix prevails in chloroform, acetonitrile and methanol. A crucial role for this behavior is likely to be played by the two alanine residues positioned respectively at the head and tail of the sequence, which favor conformations having opposite screw senses.

Alpha-beta-dehydro-amino acid residues in the design of peptide structures. Molecular and crystal structures of two folded dehydro peptides

The molecular and crystal structures of two N alpha-protected tripeptide amides, containing in the central position the alpha-beta-dehydro-amino acid residue delta Phe (Z-configurational isomer), were determined by X-ray diffraction. While Z-Gly-delta Phez-L-Pro-NH2 is characterized in the crystal state by the presence of a type I beta-bend conformation (at the delta Phez-L-Pro sequence), Z-D-Ala-delta Phez-Gly-NH2 is folded into two consecutive beta-bends (type II' followed by type I), at the D-Ala-delta Phez and delta Phez-Gly sequences, respectively. In both cases the achiral delta Phez residue adopts a set of phi, psi angles typical of the right-handed helical conformation. The delta Phe residue may be exploited to design aromatic peptides with preferred secondary structures.

Conformationally restricted peptides through short-range cyclizations

The various types of conformationally restricted peptides obtained by short-range cyclizations, from residue i to residue i + 1, are presented. Relevant examples of N in equilibrium C alpha, C' in equilibrium C alpha, N in equilibrium C', C alpha in equilibrium C alpha, C' in equilibrium C', and N in equilibrium N cyclizations are reported and the pertinent literature listed. In the discussion emphasis is place on the conformational consequences for peptides from the incorporation of such ring structures.

Conformational perturbations in retro-analogs of the tBuCO-Ala-Gly-NHiPr dipeptide. Crystal structure of the retro-dipeptide with a reversed Ala-Gly amide bond

The three retro-analogs of the tBuCO-Ala-Gly-NHiPr dipeptide, in which each amide bond had been successively reversed, were studied in solution by 1H-n.m.r. and i.r. spectroscopy with reference to the conformational properties of their parent dipeptide. Reversal of the Ala-Gly amide bond proved to perturb the folding tendency of the backbone less than the inversion of either of the terminal amide bonds. The crystal structure of the retro-peptide containing a reversed Ala-Gly amide bond was also solved by X-ray diffraction and constitutes the first available data for this retro-peptide series. In contrast to the beta II-folded structure of the parent dipeptide, the retro-peptide molecule adopts an open conformation in the crystal.

X-ray crystallography of peptides: the contributions of the Italian laboratories

The review article summarizes the most relevant solid state structural and conformational results obtained in the laboratories involved in Italy in the studies of synthetic and natural peptides by x-ray diffraction analyses. Some of the topics will include research studies carried out in other European countries, whereas in other cases studies carried out in Italy will be included in other review articles included in this volume. The review deals with peptides containing symmetrically achiral and unsymmetrically chiral C alpha,alpha-dialkylated glycine residues, peptides containing beta-alanine residues, alpha,beta-dehydroamino acid residues, and aminosuccinyl residues, peptides containing the thioamide surrogate, heterochiral peptides and several bioactive peptides systems with the proposed relationships between function and structure.