Development of new potent agonists able to interact with two postulated subsites of the cholecystokinin CCK-B receptor

Summary Since the biochemical and pharmacological profile of BC 197 and BC 264, two CCK₈-derived agonists with high specificity for CCK-B receptors, suggests their potential interaction with two CCK-B receptor subsites, it appeared essential to design new series of compounds that would be able to discriminate between these two subsites. As CCK₄ is the shortest fragment of CCK which interacts selectively with CCK-B receptors, compounds derived from the C-terminal tetrapeptide domain of BC 264, Boc-Trp-(NMe)Nle-Asp-Phe-NH₂, and of the cyclic compound BC 197, were prepared. While RB 360 (N-(cycloamido)-α-Me(R)Trp-[(2S)-2-amino-9-((cycloamido)carbonyl)nonanoyl]-Asp-Phe-NH₂), like BC 197, has a CCK-B₁ profile with anxiogenic-like effects in the elevated plus-maze test, RB 400 (HOOC-CH₂-CO-Trp-(NMe)Nle-Asp-Phe-NH₂), like BC 264, seems to be a specific CCK-B₂ agonist, able to increase attention and/or memory processes in the Y-maze test.     

Studies on cyclic peptides. IV. Conformation of cyclo(Sar-Sar-Gly)2, cyclo(Sar)6 and cyclo(Sar-Gly-Gly)2 and their conformational change induced by alkali thiocyanates

Conformation of cyclo (Sar-Sar-Gly)₂, cyclo(Sar)₆, and cyclo(Sar-Gly-Gly)₂ was investigated by nmr spectroscopy. cyclo(Sar-Sar-Gly)₂, were shown to assume various conformations in dimethysulfoxide. It was attributed to the distribution of cis as well as trans Gly-Sar or Sar-Sar amide links along the peptide backbone. In particular, cyclo(Sar-Sar-Gly)₂ took five or six different conformations: one or three C₂-symmetric conformations and four or three asymmetric conformations, respectively. Three of nine NH resonance signals were ascribed to the internally hydrogen-bonded glycine residues. cyclo(Sar-Sar-Gly)₂ and cyclo(Sar)₆ showed a spectral change on the addition of alkali thiocyanates, indicating a conformational change induced by a complex formation with the alkali cations. The complex nmr spectrum due to a hybridization of different conformations changed with the salt addition into a simple nmr spectrum, suggesting a preponderence of a new, single conformation. On the basis of the spectral change, the strength for the cations binding the cyclic peptides was found to be in the order of K⁺ > Na⁺ > Rb⁺ > Cs⁺ for cyclo(Sar-Gly-Gly)₂ and K⁺ > Rb⁺ > Cs⁺ for cyclo(Sar)₆. On the other hand, cyclo(Sar-Gly-Gly)₂ in dimethylsulfoxide assumed a single C₂ conformation having two glycyl peptide protons shielded from solvent and the other two exposed to solvent. This conformation did not change with the salt addition. Finally, the conformations of several cyclic peptides containing the sarcosine residue such as cyclo(Sar)₆ cyclo(Sar-Sar-Gly)₂ cyclo(Pro-Sar-Gly)₂, and cyclo (Sar-Gly-Gly)₂ were compared. It appeared that proline and glycine residues reduced the conformational multiplicity of the cyclic peptide backbone, and the ability to bind alkali metal cations decreased in the above order.     

Conformation of CD4-derived cyclic hexapeptides by nmr and molecular dynamics

Two cyclic hexapeptides, cyclo[Ala¹-D -Ala²-Ser³-Phe⁴-Gly⁵-Ser⁶] and cyclo[Ala¹-Gly²-Ser³-Phe⁴-Gly⁵-Ser⁶], derived from the loop portion of the C′C″ ridge of CD4, were characterized by high-resolution nmr spectroscopy and simulated annealing studies. In DMSO-d₆ both of these peptides display a single conformer on the nmr time scale with two intramolecular H-bond (1 ← 4) stabilized β-turns at positions 2–3 and 5–6. The nmr derived distance constraints were used in simulated annealing calculations to generate the solution structures. These structures adopt energetically comparable conformational substates that are not resolvable on the nmr time scale. In aqueous solution, the H-bond stabilized β-turn conformation for cyclo [Ala-D -Ala-Ser-Phe-Gly-Ser] is no longer the predominant structural form. Structures generated using molecular dynamics simulations with no experimental constraints were compared with those from nmr analysis. The correlation between these two sets of structures allows the use of molecular simulations as a predictive tool for the conformational analysis of small peptides. © 1994 John Wiley & Sons, Inc.     

Development of new potent agonists able to interact with two postulated subsites of the cholecystokinin CCK-B receptor

Since the biochemical and pharmacological profile of BC 197 and BC 264,two CCK₈-derived agonists with high specificity for CCK-Breceptors, suggests their potential interaction with two CCK-B receptorsubsites, it appeared essential to design new series of compounds that wouldbe able to discriminate between these two subsites. As CCK₄ isthe shortest fragment of CCK which interacts selectively with CCK-Breceptors, compounds derived from the C-terminal tetrapeptide domain of BC264, Boc-Trp-(NMe)Nle-Asp-Phe-NH₂, and of the cyclic compoundBC 197, were prepared. While RB 360(N-(cycloamido)--Me(R)Trp-[(2S)-2-amino-9-((cycloamido)carbonyl)nonanoyl]-Asp-Phe-NH₂), like BC 197, has a CCK-B₁ profilewith anxiogenic-like effects in the elevated plus-maze test, RB 400(HOOC-CH₂-CO-Trp-(NMe)Nle-Asp-Phe-NH₂), like BC264, seems to be a specific CCK-B₂ agonist, able to increaseattention and/or memory processes in the Y-maze test.     

Conformational analysis of polyoxyethylene-bound homo-oligo-L-glutamates in a weakly interacting medium, CDCl3

A detailed conformational analysis of polyoxyethylene-bound N-t-butyloxycarbonyl homo-oligo-L -glutamates up to the heptamer was carried out in CDCl₃ solution using high-resolution ¹H-nmr spectroscopy. Unequivocal assignments of resolved backbone NH and α-CH resonances were obtained with specifically deuterated oligomers. From nmr measurements, chemical-shift dependencies with respect to temperature and solvent, and the line-broadening effects of free radicals allowed the determination of hydrogen-bonded residues. The nmr data, along with model-building studies, suggest that seven-membered rings may exist in the N-terminal portion of these peptides. Replacement of the N-t-butyloxycarbonyl group by an acetyl or pyroglutamyl residue gave aggregated peptides, pointing to a special contribution by the Boc group to hydrogen bonding and solubility in CDCl₃.     

Conformational energy studies on N-methylated analogs of thyrotropin releasing hormone, enkephalin, and luteinizing hormone-releasing hormone

Empirical conformational energy calculations have been carried out for N-methyl derivatives of alanine and phenylalanine dipeptide models and N-methyl-substituted active analogs of three biologically active peptides, namely thyrotropin-releasing hormone (TRH), enkephalin (ENK), and luteinizing hormone-releasing hormone (LHRH). The isoenergetic contour maps and the local dipeptide minima obtained, when the peptide bond (ω) preceding the N-methylated residue is in the trans configuration show that (1) N-methylation constricts the conformational freedom of both the ith and (i + 1)th residues; (2), the lowest energy position for both residues occurs around ? = ?135° ± 5° and ψ = 75° ± 5°, and (3) the α_L conformational state is the second lowest energy state for the (i + 1)th residue, whereas for the ith residue the C₅ (extended) conformation is second lowest in energy. When the peptide bond (ω_i) is in the cis configuration the ith residue is energetically forbidden in the range ? = 0° to 180° and ψ = ?180° to +180°. Conformations of low energy for ω_i = 0° are found to be similar to those obtained for the trans peptide bond. In all the model systems (irrespective of cis or trans), the α_R conformational state is energetically very high. Significant deviations from planarity are found for the peptide bond when the amide hydrogen is replaced by a methyl group. Two low-energy conformers are found for [(N-Me)His²]TRH. These conformers differ only in the ? and ψ values at the (N-Me)His² residue. Among the different low-energy conformers found for each of the ENK analogs [D -Ala²,(N-Me)Phe⁴, Met⁵]ENK amide and [D -Ala²,(N-Me)Met⁵]ENK amide, one low-energy conformer was found to be common for both analogs with respect to the side-chain orientations. The stability of the low-energy structures is discussed in the light of the activity of other analogs. Two low-energy conformers were found for [(N-Me)Leu⁷]LHRH. These conformations differ in the types of bend around the positions 6 and 7 of LHRH. One bend type is eliminated when the active analog [D -Ala⁶,(M-Me)Leu⁷]LHRH is considered.     

Solution conformation study of substance P methyl ester and [Nle10]-neurokinin A (4–10) by nmr spectroscopy

High-resolution proton spectra at 500 MHz of two tachykinin peptides, substance P methyl ester (SPOMe) and [Nle¹⁰]-neurokinin A (4–10), have been obtained in dimethylsulfoxide (DMSO), and for SPOMe, also in 2, 2, 2-trifluoroethanol (TFE)/water mixtures. Complete chemical shift assignments for these peptides were made based on two-dimensional (2D) nmr techniques, correlated spectroscopy and total COSY. J coupling measurement and nuclear Overhauser effect spectroscopy (NOESY) were then used to determine the conformation of these peptides in the various solvents. Based on the J coupling, NOE correlations, and temperature coefficients of the NH resonances, it is concluded that these two peptides exist in DMSO at room temperature as a mixture of conformers that are primarily extended. For SPOMe in TFE/water with high TFE content, however, helical structures are found to be present, and they become quite clear at temperatures between 270 and 280 K. The variation of the ¹³C chemical shifts of the C_α (the secondary shift) with TFE contents corroborates this conclusion. The NOE and C_α shifts show that the main helical region for SPOMe lies between ⁴P and ⁹G. The C-terminus segment L? M? NH₂ is found to be quite flexible, which appears to be quite common for neurokinin-1 selective peptides. © 1993 John Wiley & Sons, Inc.     

Conformational changes due to vicinal glycosylation: The branched α-l-Rhap(1–2)[β-d-Galp(1–3)]-β-d-Glc1-OMe trisaccharide compared with its parent disaccharides*

Conformations of the α-l -Rhap(1-2)-β-d -Glc1-OMe and β-d -Galp(1-3)-β-d -Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d₆ solution by ¹H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417–432, 1998     

Measurement of long-range2 13C-1H coupling constants of 95% uniformly 13C-labeled polysaccharide from streptococcus mitis J22

The coaggregation of Streptococcus mitis strain J22 in the early stages of dental plaque formation has been shown to result from interaction of cell wall polysaccharides with lectins on the surface of other oral bacterial species. This bacterium was grown in a medium containing ¹³C as the sole carbon source. We have isolated the lectin receptor polysaccharide from this strain with full enrichment in ¹³C and have determined a number of two-bond and three-bond ¹³C-¹H coupling constants from measurements of the offsets in two-dimensional homonuclear nmr spectra [exclusive correlated spectroscopy (E-COSY) method]. A scheme for reliable extraction of these coupling constants from homonuclear Hartmann-Hahn and nuclear Overhauser effect spectroscopy spectra is tested in model compounds. We interpret the three-bond coupling across the glycosidic linkage in terms of dihedral angles in order to provide conformational information to supplement molecular modeling and nuclear Overhauser effect data. We show that the E-COSY method works well even for coupling constants smaller than the nmr line width and that a number of the ³J_CH across the glycosidic linkage are in the range of 1–2 Hz, which is much smaller than many previously reported values. © 1994 John Wiley & Sons, Inc.     

Nmr studies of the molecular conformations in the linear oligopeptides H-(L-Ala)n-L-Pro-OH

The molecular conformations of the linear oligopeptides H-(L -Ala)_n-L -Pro-OH, with n = 1,2 and 3, have been investigated. ¹³C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)_n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from ¹H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.     

Conformational interconversions in peptide β-turns: Discrimination between enantiomeric conformations by chiral perturbation

The crystal structure of the model tripeptide Boc-Aib-Gly-Leu-OMe ( 1 ) reveals two independent molecules in the asymmetric unit that adopt “enantiomeric” type I and type I′ β-turn conformations with the Aib and Gly residues occupying the corner (i + 1 and i + 2) positions. ¹³C cross polarization and magic angle sample spinning spectra in the solid state also support the coexistence of two conformational species. ¹³C-nmr in CDCl₃ establishes the presence of a single species or rapid exchange between conformations. 400 MHz ¹H-nmr provides evidence for conformational exchange involving a major and minor species, with β-turn conformations supported by the low solvent exposure of Leu(3) NH and the observation of N_iH ↔ N_i+1H nuclear Overhauser effects. CD bands in the region 190–230 nm are positive, supporting a major population of type I′ β-turns. The isomeric peptide, Boc-Gly-Leu-Aib-OMe ( 2 ), adopts an “open” type II′ β-turn conformation in crystals. Solid state and solution nmr support population of a single conformational species. Chiral perturbation introduced outside the folded region of peptides may provide a means of modulating screw sense in achiral sequences. © 1998 John Wiley & Sons, Inc. Biopoly 45: 191–202, 1998     

Conformational analysis of the type II and type III collagen α-1 chain N-telopeptides by 1H-NMR spectroscopy and restrained molecular mechanics calculations

The type II and type III collagen α-1 chain N-telopeptides are a nonadecamer with the sequence pEMAGGFDEKAGGAQLGVMQ-NH₂ and a tetradecamer with the sequence pEYEAYDVKSGVAGG-NH₂, respectively. Their conformations have been studied in CD₃OH/H₂O (60/40) solution by means of two-dimensional proton nmr spectroscopy. Based on double quantum filtered correlation spectroscopy, total correlation spectroscopy, rotating frame nuclear Overhauser enhancement (ROE) spectroscopy, and nuclear Over-hauser enhancement (NOE) spectroscopy experiments, all resonances were assigned and the conformational properties were analyzed in terms of vicinal NH-H_α coupling constants, sequential and medium-range NOEs (ROEs), and amide proton temperature coefficients. The NOE distance constraints as well as dihedral constraints based on the vicinal NH-H_α coupling constants were used as input parameters for restrained molecular mechanics, consisting of restrained molecular dynamics and restrained energy minimization calculations. The type II N-telopeptide's conformation is dominated by a fused βγ-turn between Phe⁶ and Ala¹⁰, stabilized by three hydrogen bonds and a salt bridge between the side-chain end groups of Glu⁸ and Lys⁹. The first 5 amino acids are extended with a much higher degree of conformational freedom. The 2 Gly residues following the turns were found to be highly flexible (hinge-like), leaving the spatial position of the second half of the molecule relative to the fused βγ-turn undefined. In the type III telopeptide, a series of sequential NH(i)-NH(i + 1) ROEs were observed between the amino acids Tyr² and Ser⁹, indicating that a fraction of the conformational space is helical. However, the absence of medium-range ROEs and the lack of regularity of the effects associated with α-helices suggest the presence of a nascent rather than a complete helix. © 1993 John Wiley & Sons, Inc.     

Studies on cyclic peptides. III. The specific interaction of cyclic peptides with benzene and an application of the solvent-induced Nmr shift to the conformational analysis of cyclo-(Pro-Sar-Gly).

The interaction between cyclic peptides [cyclo-(Sar₄), cyclo-(Pro-Sar-Gly)₂, cyclo-(Sar-Sar), and cyclo-(Sar-Gly)] with benzene has been investigated by nmr spectroscopy. The experiment with cyclo-(Sar₄) showed that benzene interacted preferentially with the trans peptide bond in a similar manner to the dimethylformamide–benzene interaction. The solvent-induced nmr shift was then applied to the conformational analysis of cyclo-(Pro-Sar-Gly)₂ with the aid of the molecular model. The major conformation was proved to possess the C₂ symmetry with internally hydrogen-bonded glycine residues, in which all peptide bonds were trans. The interaction of cyclo-(Sar-Sar) and cyclo-(Sar-Gly) with benzene was also studied. The association constant was 0.115-kg solution per mole of cyclo-(Sar-Sar) and 0.089-kg solution per mole of cyclo-(Sar-Gly) in chloroform.     

Nmr and molecular dynamics study of four carbocyclic muramyl dipeptide analogues

We have performed a conformational analysis of the carbocyclic muramyl dipeptide analogues (1′R, 2′R)- and (1′S, 2′S)-N-[2-(2′-acetamidocyclohexyIoxy)acetyl]-L Ala-D -iGln (-D -Glu) utilizing ¹H-nmr spectroscopy and nuclear Overhauser effect restrained molecular dynamics. Intramolecular H bonding for all four diastereoisomers is suggested by the Ala-NH temperature coefficients. Distance restraints were obtained by NOE spectroscopy and rotating frame NOE spectroscopy experiments. Structures with low potential energy and high agreement with NOE data were sought by restrained molecular dynamics. The ring configuration was found to induce conformational preferences. The β-like turn characterized by the intramolecular C₁₀ H-bond Ala-NH-acetamido-CO is preferred with the (1′S, 2′S), but appears to be less stable with (1′R, 2′R), diastereoisomers. Calculations show the double β-turn proposed for muramyl dipeptide [S. Fermandjian, B. Perly, M. Level, and P. Lefrancier (1987) Carbohydrate Research, Vol. 162, pp. 23–32] to have higher potential energy. © 1993 John Wiley & Sons, Inc.     

Two-dimensional 1H-NMR investigation of the water conformation of the atrial natriuretic factor (ANF 101-126)

The complete sequential assignment of the ¹H-nmr resonance frequencies of the active fragment of the rat atrial natriuretic factor (ANF 101–126) has been performed. Two-dimensional nmr techniques have been employed, including phase-sensitive nuclear Overhauser spectroscopy (NOESY), relayed coherence transfer spectroscopy (RELAY), and J-correlated spectroscopy (COSY). Experiments were performed both in D₂0 and H₂0 solutions at different pH values. With few exceptions, resonance frequencies were practically pH independent. NOESY spectra were recorded using both 300- and 500-ms mixing times, and no long-range connectivities were observed, leading to the conclusion that ANF 101–126 has no defined secondary nor tertiary structure in water in the pH range used (2.73–5.21).     

The impact of β‐azido(or 1‐piperidinyl)methylamino acids in position 2 or 3 on biological activity and conformation of dermorphin analogues

The synthesis of new dermorphin analogues is described. The (R)‐alanine or phenylalanine residues of natural dermorphin were substituted by the corresponding α‐methyl‐β‐azidoalanine or α‐benzyl‐β‐azido(1‐piperidinyl)alanine residues. The potency and selectivity of the new analogues were evaluated by a competitive receptor binding assay in rat brain using [³H]DAMGO (a μ ligand) and [³H]DELT (a δ ligand). The most active analogue in this series, Tyr‐(R)‐Ala‐(R)‐α‐benzyl‐β‐azidoAla‐Gly‐Tyr‐Pro‐Ser‐NH₂ and its epimer were analysed by ¹H and ¹³C NMR spectroscopy and restrained molecular dynamics simulations. The dominant conformation of the investigated peptides depended on the absolute configuration around C^α in the α‐benzyl‐β‐azidoAla residue in position 3. The (R) configuration led to the formation of a type I β‐turn, whilst switching to the (S) configuration gave rise to an inverse β‐turn of type I′, followed by the formation of a very short β‐sheet. The selectivity of Tyr‐(R)‐Ala‐(R) and (S)‐α‐benzyl‐β‐azidoAla‐Gly‐Tyr‐Pro‐Ser‐NH₂ was shown to be very similar; nevertheless, the two analogues exhibited different conformational preferences. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.     

Characterization of a type of β‐bend ribbon spiral generated by the repeating (Xaa–Yaa–Aib–Pro) motif: The solution structure of harzianin HC IX,a 14‐residue peptaibol forming voltage‐dependent ion channels

The three‐dimensional solution structure of harzianin HC IX, a peptaibol antibiotic isolated from the fungus Trichoderma harzianum, was determined using CD, homonuclear, and heteronuclear two‐dimensional nmr spectroscopy combined with molecular modeling. This 14‐residue peptide, Ac Aib¹ Asn² Leu³ Aib⁴ Pro⁵ Ala⁶ Ile⁷ Aib⁸ Pro⁹ Iva¹⁰ Leu¹¹ Aib¹² Pro¹³ Leuol¹⁴ (Aib, α‐aminoisobutyric acid; Iva, isovaline; Leuol, leucinol), is a main representative of a short‐sequence peptaibol class characterized by an acetylated N‐terminus, a C‐terminal amino alcohol, and the presence of three Aib‐L ‐Pro motifs at positions 4–5, 8–9, and 12–13, separated by two dipeptide units. In spite of a lower number of residues, compared to the 18/20‐residue peptaibols such as alamethicin, harzianin HC IX exhibits remarkable membrane‐perturbing properties. It interacts with phospholipid bilayers, increasing their permeability and forming voltage‐gated ion channels through a mechanism slightly differing from that proposed for alamethicin. Sequence‐specific ¹H‐ and ¹³C‐nmr assignments and conformational nmr parameters (³J_NHCαH coupling constants, quantitative nuclear Overhauser enhancement data, temperature coefficients of amide and carbonyl groups, NH–ND exchange rates) were obtained in methanol solution. Sixty structures were calculated based on 98 interproton distance restraints and 6 Φ dihedral angle restraints, using high temperature restrained molecular dynamics and energy minimization. Thirty‐seven out of the sixty generated structures were consistent with the nmr data and were convergent. The peptide backbone consists in a ribbon of overlapping β‐turns twisted into a continuous spiral from Asn² to Leuol¹⁴ and forming a 26 Å long helix‐like structure. This structure is slightly amphipathic, with the three Aib–Pro motifs aligned on the less hydrophobic face of the spiral where the Asn² side chain is also present, while the more hydrophobic bulky side chains of leucines, isoleucine, isovaline, and leucinol are located on the concave side. The repetitive (Xaa–Yaa–Aib–Pro) tetrapeptide subunit, making up the peptide sequence, is characterized by four sets of (Φ,Ψ) torsional angles, with the following mean values: Φ_i = −90°, Ψ_i = −27°; Φ_i+1 = −98°, Ψ_i+1 = −17°; Φ_i+2 = −49°, Ψ_i+2 = −50°; Φ_i+3 = −78°, Ψ_i+3 = +3°. We term this particular structure, specifically occurring in the case of (Xaa–Yaa–Aib–Pro)_n sequences, the (Xaa–Yaa–Aib–Pro)‐β‐bend ribbon spiral. It is stabilized by 4 → 1 intramolecular hydrogen bonds and differs from both the canonical 3₁₀‐helix made of a succession of type III β‐turns and from the β‐bend ribbon spiral that has been described in the case of (Aib–Pro)n peptide segments. © 1999 John Wiley & Sons, Inc. Biopoly 50: 71–85, 1999     

Terminal effect of chiral residue on helical screw sense in achiral peptides

To understand the terminal effect of chiral residue for determining a helical screw sense, we adopted five kinds of peptides I – V containing N‐ and/or C‐terminal chiral Leu residue(s): Boc–L ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( I ), Boc–(Aib–ΔPhe)₂–L ‐Leu–OMe ( II ), Boc–L ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( III ), Boc–D ‐Leu–(Aib–ΔPhe)₂–L ‐Leu–OMe ( IV ), and Boc–D ‐Leu–(Aib–ΔPhe)₂–Aib–OMe ( V ). The segment –(Aib–ΔPhe)₂– was used for a backbone composed of two “enantiomeric” (left‐/right‐handed) helices. Actually, this could be confirmed by ¹H‐nmr [nuclear Overhauser effect (NOE) and solvent accessibility of NH resonances] and CD spectroscopy on Boc–(Aib–ΔPhe)₂–Aib–OMe, which took a left‐/right‐handed 3₁₀‐helix. Peptides I – V were also found to take 3₁₀‐type helical conformations in CDCl₃, from difference NOE measurement and solvent accessibility of NH resonances. Chloroform, acetonitrile, methanol, and tetrahydrofuran were used for CD measurement. The CD spectra of peptides I – III in all solvents showed marked exciton couplets with a positive peak at longer wavelengths, indicating that their main chains prefer a left‐handed screw sense over a right‐handed one. Peptide V in all solvents showed exciton couplets with a negative peak at longer wavelengths, indicating it prefers a right‐handed screw sense. Peptide IV in chloroform showed a nonsplit type CD pattern having only a small negative signal around 280 nm, meaning that left‐ and right‐handed helices should exist with almost the same content. In the other solvents, peptide IV showed exciton couplets with a negative peak at longer wavelengths, corresponding to a right‐handed screw sense. From conformational energy calculation and the above ¹H‐nmr studies, an N‐ or C‐terminal L ‐Leu residue in the lowest energy left‐handed 3₁₀‐helical conformation was found to take an irregular conformation that deviates from a left‐handed helix. The positional effect of the L ‐residue on helical screw sense was discussed based on CD data of peptides I – V and of Boc–(L ‐Leu–ΔPhe)_n–L ‐Leu–OMe (n = 2 and 3). © 1999 John Wiley & Sons, Inc. Biopoly 49: 551–564, 1999     

Sequential resonance assignment of the 500-MHz nmr spectrum of d-(CG)6 and its structure under low-salt conditions

Two-dimensional (2D) nmr methods (correlated spectroscopy, nuclear Overhauser enhancement spectroscopy, and relayed correlated spectroscopy) have been used to obtain resonance assignment of the nonexchangeable base and sugar protons of a double-helical DNA segment, d-(CG)₆ in D₂O solutions under conditions of low ionic strength. Detailed information about the glycosidic torsion angle, sugar geometry, stacking patterns of the bases, and the overall solution structure of the dodecanucleotide has been obtained from the relative intensities of cross-peaks in the 2D spectra. The molecule shows general features of B-DNA under the experimental conditions employed. However, in spite of the repeating base sequence, there are subtle and detectable variations in the structure along the double helix. The terminal residues show considerable conformational flexibility.     

β-Alanine containing cyclic peptides with predetermined turned structure. V

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and solution structural characterization by nmr spectroscopy, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo-(Pro-Phe-β-Ala-Phe-Phe-β-Ala). The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylenechloride solution using N, N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P2₁ from methanol/ethyl acetate. The molecule adopts in the solid state a conformation characterized by cis β-Ala⁶-Pro¹ peptide bond. The α-amino acid residues are at the corner positions of turned structures. The Pro¹-Phe² segment is incorporated in a pseudo type I β-turn, while Phe⁴-Phe⁵ is in a typical type I β-turn. Assignment of all ¹H and ¹³C resonances was achieved by homo- and heteronuclear two-dimensional techniques in dimethylsulfoxide (DMSO) solutions. The conformational analysis was based on inter-proton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. Restrained molecular dynamic simulation in vacuo was also performed to built refined molecular models. The molecule is present in DMSO solution as two slowly interconverting conformers, characterized by a cis-tran isomerism around the β-Ala⁶-Pro¹ peptide bond. This work confirms our expectations on the low propensity of β-alanyl residues to be positioned at the corners of turned structure. © 1994 John Wiley & Sons, Inc.