Conformational Energy Calculations Research Articles

Conformational features of cepacian: the exopolysaccharide produced by clinical strains of Burkholderia cepacia

Conformational energy calculations and molecular dynamics investigations, both in water and in dimethyl sulfoxide, were carried out on the exopolysaccharide cepacian produced by the majority of the clinical strains of Burkholderia cepacia, an opportunistic pathogen causing serious lung infection in patients affected by cystic fibrosis, The investigation was aimed at defining the structural and conformational features, which might be relevant for clarification of the structure–function relationships of the polymer. The molecular dynamics calculations were carried out by Ramachandran-type energy plots of the disaccharides that constitute the polymer repeating unit. The dynamics of an oligomer composed of three repeating units were investigated in water and in Me 2SO, a non-aggregating solvent. Analysis of the time persistence of hydrogen bonds showed the presence of a large number of favourable interactions in water, which were less evident in Me 2SO. The calculations on the cepacian chain indicated that polymer conformational features in water were affected by the lateral chains, but were also largely dictated by the presence of solvent. Moreover, the large number of intra-chain hydrogen bonds in water disappeared in Me 2SO solution, increasing the average dimension of the polymer chains.

β-Ala Containing Peptides: Potentials in Design and Construction of Bioactive Peptides and Protein Secondary Structure Mimics

In recent years, there has been increasing interest in de novo design and construction of novel synthetic peptides that mimic protein secondary structures, i.e., turns, helices and sheets. The unique structural influences exerted by unsubstituted, non-coded, non-chiral beta-amino acid, i.e., beta-alanine (beta-Ala; 3- or beta- aminopropionic acid) on peptide backbone, when inserted into peptide chain comprised alpha-amino acids, offer an excellent opportunity to design and construct diverse well-defined three-dimensional structures. Our current understanding of folding-unfolding behavior of the beta-Ala residues relies primarily from an examination of conformational preferences of a large number of short cyclic- as well as acyclic beta-Ala containing peptides investigated using single crystal X-ray diffraction analysis. In addition, theoretical conformational energy calculations and different spectroscopic techniques: 1H NMR, FT-IR and CD, have also been employed although, to a lesser extent. The obtainable results tend to reveal overwhelming preferences of the beta-Ala moiety for the folded gauche (mu approximately +/-65+/-10 degrees conformation in cyclic- and for an extended trans (mu approximately +/-165+/-10 degrees) as well as gauche (mu approximately +/-65+/-10 degrees) orientations in acyclic beta-Ala containing peptides. The results also indicate that in short linear beta-Ala containing peptides, the specific influence of selective neighboring side-chain substituents e.g. linear- or cyclic symmetrically C(alpha,alpha)-disubstituted glycines and other conformational constraints, may be significant in controlling the overall folded-unfolded topographical features across the two methylene units (-CbetaH2-CalphaH2-) of the beta-Ala residue. Taking into consideration the wide occurrence of beta-Ala moiety in animal and plant kingdoms and the remarkable structural versatility of the peptides incorporating beta-Ala residue(s), together with appreciable resistance towards enzymatic degradation, hold strong promise for biophysicists and biochemists not only to design molecules that fold to mimic protein secondary structures but also to develop potent peptide analogs and peptidomimetics displaying unique pharmaceutical properties.

Crystal Structure of Alternating Ethylene−Norbornene Copolymer

Models for the crystal structure of alternating isotactic ethylene−norbornene copolymers (ENCs) are presented. Oriented fibers of ENCs samples have been obtained, and the corresponding X-ray fiber diffraction pattern has been reported. A value of the chain axis periodicity of 8.9 Å has been evaluated. A geometrical analysis and conformational energy calculations have shown that both isotactic and syndiotactic ENC chains assume nearly extended conformations having 2-fold helical s(2/1)m and glide plane tcm symmetries, respectively. Both conformations account for the experimental chain axis periodicity of 8.9 Å. The crystal structure is mainly defined by the packing of the quasi-spherical norbornene units. The barycenters of the norbornene units are arranged on a face-centered crystalline lattice, producing a short-range three-dimensional positional order. Different kinds of structural disorder are present in the structure. A short-range order in the average positioning of the norbornene rings is maintained, while disorder in the positioning of the carbon atoms of the ethylene units is present. The ethylene units may assume different positions along a and b axes of the unit cell and connect with equal probability a given norbornene unit with any of its next neighbors, producing orientational disorder of the polymer chains as well as of the spherical norbornene units. The amount and the kind of disorder depend on the microstructure of the chains and on the condition of crystallization. The structure may be described by limit disordered models of packing, in unit cells having a = b = 9.4 Å and c = 8.9 Å or a = 9.3 Å, b = 9.5 Å, and c = 8.9 Å. and statistical orthorhombic or tetragonal space groups Bmcm or I4/mmm. The partial threedimensional order, guided by the ordered positioning of the ball-like norbornene units, is obtained even though the polymers are configurationally disordered, provided that they have a regular alternation of the comonomeric units.

Chain Conformations in the Crystalline Field of Syndiotactic Vinyl Polymers Deriving from 1,3‐Diene Monomers. Analysis by Molecular Mechanics

AbstractSummary: Conformational energy calculations on the chain conformation in the crystalline field have been performed for various syndiotactic vinyl polymers deriving from 1,3‐diene monomers. Energy maps as a function of the independent torsion angles have evidenced for all the polymers minima corresponding to highly extended and to helical chains. Energy minimizations as a function of all the internal parameters for the s(2/1)2 and tcm symmetries have allowed the evaluation of the energy differences between chains having the two symmetries and the prediction of the values of the conformational parameters for each polymer. The results have been compared with the experimental data reported in the literature for some of the studied polymers.Conformational energy map of sPBD12.magnified imageConformational energy map of sPBD12.

Vanishing Polymorphism of (2E)-2-Cyano-3-[4-(Diethylamino)phenyl]prop-2-enethioamide: X-ray Structural Study and Polymorph Prediction

Synthesis and crystallization of a polar organic compound (2E)-2-cyano-3-[4-(diethylamino)phenyl]prop-2-enethioamide (CDPE) gave two new crystalline polymorphs (1 and 2) and an acetonitrile solvate (pseudopolymorph, 3) of this compound. The third crystalline polymorph of CDPE (4) was described in the literature earlier. It was found that in crystalline polymorphs 1, 2, and 4 molecules adopt three different conformations. Experimental observations show that polymorph 1 is a predominant form of the CDPE compound, while all other crystalline forms we were unable to reproduce under different conditions. Quantum ab initio calculations of relative conformational energies of molecules found in these polymorphs revealed that the conformer in polymorph 1 has significantly lower energy than conformers in polymorphs 2 and 4. This fact explains the predominant formation of polymorph 1 under different experimental conditions. The polarity of CDPE molecules and distinctions in their molecular and crystal structures make CDPE polymorphs 1, 2, and 4 a perfect model for testing of the methodology of crystal structure prediction with the Polymorph Predictor module from the Cerius2 program package. It was shown that if the starting molecular model corresponds to X-ray data and considered to be rigid it is possible to predict all three polymorphs. In contrast, usage of a flexible molecular model does not give positive results. Reasons for such differences are discussed.

Disulfide bonding arrangements in active forms of the somatomedin B domain of human vitronectin.

The N-terminal cysteine-rich somatomedin B (SMB) domain (residues 1-44) of the human glycoprotein vitronectin contains the high-affinity binding sites for plasminogen activator inhibitor-1 (PAI-1) and the urokinase receptor (uPAR). We previously showed that the eight cysteine residues of recombinant SMB (rSMB) are organized into four disulfide bonds in a linear uncrossed pattern (Cys(5)-Cys(9), Cys(19)-Cys(21), Cys(25)-Cys(31), and Cys(32)-Cys(39)). In the present study, we use an alternative method to show that this disulfide bond arrangement remains a major preferred one in solution, and we determine the solution structure of the domain using NMR analysis. The solution structure shows that the four disulfide bonds are tightly packed in the center of the domain, replacing the traditional hydrophobic core expected for a globular protein. The few noncysteine hydrophobic side chains form a cluster on the outside of the domain, providing a distinctive binding surface for the physiological partners PAI-1 and uPAR. The hydrophobic surface consists mainly of side chains from the loop formed by the Cys(25)-Cys(31) disulfide bond, and is surrounded by conserved acidic and basic side chains, which are likely to contribute to the specificity of the intermolecular interactions of this domain. Interestingly, the overall fold of the molecule is compatible with several arrangements of the disulfide bonds. A number of different disulfide bond arrangements were able to satisfy the NMR restraints, and an extensive series of conformational energy calculations performed in explicit solvent confirmed that several disulfide bond arrangements have comparable stabilization energies. An experimental demonstration of the presence of alternative disulfide conformations in active rSMB is provided by the behavior of a mutant in which Asn(14) is replaced by Met. This mutant has the same PAI-1 binding activity as rVN1-51, but its fragmentation pattern following cyanogen bromide treatment is incompatible with the linear uncrossed disulfide arrangement. These results suggest that active forms of the SMB domain may have a number of allowed disulfide bond arrangements as long as the Cys(25)-Cys(31) disulfide bond is preserved.

RIS Models and Unperturbed Chain Properties of Polyesters Containing 1,3‐Cyclobutylene and 1,4‐Cyclohexylene Linkages

AbstractPolyesters containing 1,3‐cyclobutylene and 1,4‐cyclohexylene linkages in the main chain are investigated using conformational energy calculations. Rotational isomeric state (RIS) models are developed for poly(1,4‐cyclohexylenedimethylene terephthalate) (PCT), poly(1,4‐cyclohexylenedimethylene 2,5‐dimethylterephthalate) (DMPCT), poly(1,4‐cyclohexylenedimethylene 1,4‐cyclohexylenedicarboxylate) (PCC), and poly(2,2,4,4‐tetramethyl‐1,3‐cyclobutylene terephthalate) (CBDO). In DMPCT, the ester linkage prefers skewed conformations with respect to the phenyl group to relieve the steric strain caused by the methyl groups. The methyl groups on the cyclobutanediol moiety in CBDO restrict the rotational freedom about the oxycyclobutylene linkage. The unperturbed dimensions as described by characteristic ratio and persistence length are calculated for the trans and cis configurations of these polyesters. CBDO shows highly extended chain conformations among these polyesters indicating relative chain rigidity of the backbone. For DMPCT and PCC, in their trans configuration, the chain dimensions decrease with an increase in temperature while for their cis configurations, the chain dimensions increase with temperature, arising from basic differences in the fragment structures that control the competition of the relative populations as affected by temperature. Temperature has negligible influence on the unperturbed dimensions of both isomeric linkages of CBDO, while this is true for the trans configuration of PCT. The study shows that induction of cyclobutylene groups in the main chain results in a greater rigidity for homopolyesters than for chains with cyclohexylene groups. Structure of the repeat units of polyesters in the planar trans configuration and the schematic of the RIS models with definition of geometrical parameters.imageStructure of the repeat units of polyesters in the planar trans configuration and the schematic of the RIS models with definition of geometrical parameters.

Conformational characteristics of poly(ethylene phthalate)s

AbstractThe conformational characteristics, as embodied in the unperturbed mean‐square end‐to‐end distances (〈r2〉o) and the characteristic ratios of the dimensions [Cn = 〈r2〉o/(n〈l2〉] are calculated for the para, meta, and ortho isomers of poly(ethylene phthalate)s: poly(ethylene terephthalate) (PET), poly(ethylene isophthalate) (PEI), and poly(ethylene phthalate) (PEP), respectively. Although each of these isomeric and partially aromatic polyesters has identical permissible conformations available to their ethylene glycol fragments, their connections through the ester bonds to the phenyl rings are quite distinct. In addition, for the ortho isomer (PEP), the close spatial proximity of the ester groups bonded to the same phenyl ring results in an interdependence of their orientations with respect to each other and the phenyl ring to which they are attached, unlike the independent orientations of ester groups in the para and meta isomers (PET and PEI). Conformational energy calculations, dependent on the orientation of the ester groups in PEP, are used to characterize their rotational interdependence to modify the rotational isomeric state (RIS) conformational models for PET and PEI and thereby obtain an RIS model appropriate for PEP. This leads to calculated relative dimensions (〈r2〉o) of 1.0:0.70:0.37 PET:PEI:PEP and characteristic ratios [Cn = 〈r2〉o/(n〈l2〉)] of 4.13:4.67:2.49 PET:PEI:PEP. These results are discussed in an effort to obtain some understanding of the inherent static (or equilibrium) and dynamic flexibilities of the isomeric poly(ethylene phthalate)s. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1254–1260, 2002

X-ray Diffraction Analysis and Conformational Energy Computations of β-Turn and 310-Helical Peptides Based on α-Amino Acids with an Olefinic Side Chain. Implications for Ring-Closing Metathesis

We describe the X-ray diffraction structure of the terminally protected dipeptide amide Boc-Aib-L-Mag-NHBzl (Aib is α-aminoisobutyric acid and Mag is Cα-methyl, Cα-allyl-glycine) and the results of conformational energy computations on Ac-L-Mag-NHMe, Ac-Aib-L-Mag-NHMe, and Ac-L-Mag-Aib-NHMe. On the basis of these data, we performed conformational energy computations on the sequence -Aib-Xxx-(Aib)2-Xxx-Aib- (Xxx = L-Mag) to check the feasibility of ring-closing metathesis, a currently extensively investigated reaction useful to enhance peptide helicity and metabolic stability, on this 310-helix forming model hexamer with the two olefinic amino acids at the i, i+3 relative positions. Computations were extended to peptides based on olefinic residues with the side chains elongated by one (L-hMag) or two (L-hhMag) carbon atoms. A comparison was also made with peptides characterized by the related, non-Cα-methylated (Cα-trisubstituted) L-Agl (Cα-allyl-L-glycine), L-hAgl, and L-hhAgl residues. We conclude that, to achieve ring-closing metathesis with an unperturbed 310-helical conformation and a symmetrical all-hydrocarbon tether, the side-chain length for each of the two i, i+3 olefinic amino acids requires at least five carbon atoms (hhMag or hhAgl), thereby producing an 18-atom macrocycle.

Screw sense preference of non-polarL-amino acid residues second from the N-terminal position

To understand the positional effects of a single chiral residue on the helical screw sense of an achiral segment, we adopted five kinds of peptides Boc-Aib-X*-(Aib-ΔZPhe)2-Aib-OMe (Boc, t-butoxycarbonyl; Aib, α-aminoisobutyric acid; ΔZPhe, (Z)-dehydrophenylalanine; OMe, methoxy), wherein the X* residue is an L-residue of leucine (Leu), alanine (Ala), valine (Val), phenylalanine (Phe), or 1-naphthylalanine (Nap). Here the segment -(Aib-ΔZPhe)2-Aib-OMe was employed as an achiral backbone for generating two “enantiomeric” (left-handed/right-handed) helices. All of the peptides are folded into a 310-type helical conformation in chloroform, as evidenced by FT-IR and 1H NMR techniques. A CD analysis of these peptides indicates that they adopt both left-handed and right-handed helices, and that the prevailing screw sense as well as the screw sense bias depend on the type of solvent. Thus, the L-residue located at the position second from the N-terminus plays a unique role for energetically permitting both helices. These peptides also undergo a solvent-induced interconversion between both helices. The rank order of the penultimate L-residues for inducing a right-handed screw sense is Val > Leu ∼ Ala > Phe > Nap, of which the reverse order represents the tendency to promote a left-handed screw sense. The prevailing screw sense induced by the penultimate L-residue is also discussed on the basis of conformational energy calculations. In conclusion, we here have been able to express experimentally a unique screw sense preference of these non-polar L-amino acids.

L29M] substitution in the interface of subunit-subunit interactions enhances Escherichia coli RecA protein properties important for its recombinogenic activity

Genetic analysis of RecA protein chimeras and their ancestors, RecAEc (from Escherichia coli) and RecAPa (Pseudomonas aeruginosa) had allowed us to place these proteins with respect to their recombinogenic activities in the following order: RecAPa > RecAX21 > RecAX20=RecAEc. While RecAX20 differs from RecAEc in five amino acid residues with two substitutions ([S25A] and [I26V]) at the interface of subunit interactions in the RecA polymer, RecAX20 and RecAX21 differ only by a single substitution [L29M] present at the interface. Here, we present an analysis of the biochemical properties considered important for the recombinogenic activity of all four RecA proteins. While RecAX20 was very similar to RecAEc by all activities analysed, RecAX21 differed from RecAEc in several respects. These differences included an increased affinity for double-stranded DNA, a more active displacement of SSB protein from single-stranded DNA (ssDNA), a decreased end-dependent RecAX21 protein dissociation from a presynaptic complex, and a greater accumulation of intermediate products relative to the final product in the strand-exchange reaction. RecAPa was more tolerant than RecAX21 only to the end-dependent RecA protein dissociation. In addition, RecAPa was more resistant to temperature and salt concentrations in its ability to form a presynaptic RecAPa∷ATP∷ssDNA filament. Calculations of conformational energy revealed that the [L29M] substitution in RecAX21 polymer caused an increase in its flexibility. This led us to conclude that even a small change in the flexibility of the RecA presynaptic complex could profoundly affect its recombinogenic properties.

Conformation of the tripeptide Cbz-Pro-Leu-Trp-OBzl(CF3)2 deduced from two-dimensional 1H-NMR and conformational energy calculations is related to its affinity for NK1-receptor.

Chemical modifications of dual NK1/NK2 ligand Cbz-Gly-Leu-Trp-OBzl(CF3)2 (1) enabled us to create a high NK1 selective ligand Cbz-Pro-Leu-Trp-OBzl(CF3)2 (2). A determination of the conformational behavior of tripeptide 2 in solution is described. The 1D and 2D 1H-NMR techniques (COSY and ROESY) were used to assign resonances. Observed interproton distance restraints were considered to characterize conformational behavior. Spectral data indicate that tripeptide 2 presents a rigidified structure in DMSO stabilized by H-bond in two gamma-turns. Agreement with experimental data was obtained by averaging the 1H-NMR parameters over several combinations of low-energy conformations.

Solid-state conformations of oligopeptides possessing an -(Aib-ΔZPhe)2- segment†

An X-ray crystallographic analysis was carried out for Boc-(Aib-ΔZPhe)2-Aib-OMe 1 and Boc-L-Pro-(Aib-ΔZPhe)2-Aib-OMe 2 (Aib = α-aminoisobutyric acid; ΔZPhe = α,β-dehydrophenylalanine; Boc = tert-butoxycarbonyl; OMe = methoxy) to provide detailed conformational data for oligopeptides possessing an -(Aib-ΔZPhe)2- segment. Both peptides adopted a typical 310-helical conformation characterized by = 52.8°, = 29.3°, and = −173.8° for the average values of the four residues of the -(Aib-ΔZPhe)2- segment in peptide 1, and = 54°, = 27°, and = −175° for those in peptide 2. The preference for a 310-helix in the -(Aib-ΔZPhe)2- segment is ascribed to the presence of Aib and ΔZPhe residues being strong inducers for the formation of a 310-helix. In peptide 2, the N-terminal L-Pro residue adopted a semiextended conformation, leading to a left-handed screw sense for the following achiral segment. This result was also supported by conformational energy calculation, in which the L-Pro residue leading to a left-handed 310-helical segment prefers a semiextended conformation rather than a right-handed helical conformation.

Influence of lysine content and pH on the stability of alanine-based copolypeptides.

To account for the relative contributions of lysine and alanine residues to the stability of alpha-helices of copolymers of these two residues, conformational energy calculations were carried out for several hexadecapeptides at several pHs. All the calculations considered explicitly the coupling between the conformation of the molecule and the ionization equilibria as a function of pH. The total free energy function used in these calculations included terms that account for the solvation free energy and free energy of ionization. These terms were evaluated by means of a fast multigrid boundary element method. Reasonable agreement with experimental values was obtained for the helix contents and vicinal coupling constants ((3)J(HNalpha)). The helix contents were found to depend strongly on the lysine content, in agreement with recent experimental results of Williams et al. (Journal of the American Chemical Society, 1998, Vol. 120, pp. 11033-11043) In the lowest energy conformation computed for a hexadecapeptide containing 3 lysine residues at pH 6, the lysine side chains are preferentially hydrated; this decreases the hydration of the backbone CO and NH groups, thereby forcing the latter to form hydrogen bonds with each other in the helical conformation. The lowest energy conformation computed for a hexadecapeptide containing 6 lysine residues at pH 6 shows a close proximity between the NH3(+) groups of the lysine side chains, a feature that was previously observed in calculations of short alanine-based oligopeptides. The calculation on a blocked 16-mer of alanine shows a 7% helix content based on the Boltzmann averaged vicinal coupling constants computed from the dihedral angles phi, consistent with previous experimental evidence on triblock copolymers containing a central block of alanines, and with earlier theoretical calculations.

Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution).

The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.

Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides.

We have carried out conformational energy calculations on alanine-based copolymers with the sequence Ac-AAAAAXAAAA-NH(2) in water, where X stands for lysine or glutamine, to identify the underlying source of stability of alanine-based polypeptides containing charged or highly soluble polar residues in the absence of charge-charge interactions. The results indicate that ionizable or neutral polar residues introduced into the sequence to make them soluble sequester the water away from the CO and NH groups of the backbone, thereby enabling them to form internal hydrogen bonds. This solvation effect dictates the conformational preference and, hence, modifies the conformational propensity of alanine residues. Even though we carried out simulations for specific amino acid sequences, our results provide an understanding of some of the basic principles that govern the process of folding of these short sequences independently of the kind of residues introduced to make them soluble. In addition, we have investigated through simulations the effect of the bulk dielectric constant on the conformational preferences of these peptides. Extensive conformational Monte Carlo searches on terminally blocked 10-mer and 16-mer homopolymers of alanine in the absence of salt were carried out assuming values for the dielectric constant of the solvent epsilon of 80, 40, and 2. Our simulations show a clear tendency of these oligopeptides to augment the alpha-helix content as the bulk dielectric constant of the solvent is lowered. This behavior is due mainly to a loss of exposure of the CO and NH groups to the aqueous solvent. Experimental evidence indicates that the helical propensity of the amino acids in water shows a dramatic increase on addition of certain alcohols, such us trifluoroethanol. Our results provide a possible explanation of the mechanism by which alcohol/water mixtures affect the free energy of helical alanine oligopeptides relative to nonhelical ones.

Azomethine sulfone macromers with thermotropic liquid crystalline behavior

New azomethine sulfone macromers containing benzylideneaniline mesogens were prepared by the conventional methods available in the literature by condensing the sulfone aldehyde monomer with aromatic diamines (DA1–DA5) using N, N-dimethylformamide as solvent. The macromers (M1–M5) were confirmed by IR, 1H-NMR, and elemental analyses, and were characterized by thermogravimetric analysis and X-ray diffraction. Their thermotropic liquid crystalline behavior was studied using polarization light microscopy, thermo-optical analysis, and differential scanning calorimetry. A nematic texture was observed for macromers M1–M3 containing the two benzylideneaniline mesogens either connected by etheric (M1), methylenic links (M2), or directly coupled (M3). Conformational energy and mesogenic index (MI) calculations were performed and used to explain the TLC behavior of the macromers studied.

Ghrelin: a step forward in the understanding of somatotroph cell function and growth regulation.

the releaseof growth hormone (GH) from pituitary cells, althoughtheir potency was rather weak (1). Further studiesbased on conformational energy calculations in con-junction with peptide chemistry modifications andbiological activity testing, led in 1984 to the develop-ment of several more potent peptides, including growthhormone-releasing peptide-6 (GHRP-6) (2). This hexa-peptide was shown to be a potent releaser of GH both

Synthesis of delta(E)Phe-containing tripeptide via photoisomerization and its conformation in solution.

A new synthetic route to (E)-beta-phenyl-alpha,beta-dehydroalanine (delta(E)Phe)-containing peptide was presented via photochemical isomerization of the corresponding (Z)-beta-phenyl-alpha,beta-dehydroalanine (delta(Z)Phe)-containing peptide. By applying this method to Boc-Ala-delta(Z)Phe-Val-OMe (Z-I: Boc, t-butoxycarbonyl; OMe, methoxy), Boc-Ala-delta(E)Phe-Val-OMe (E-I) was obtained. The identification of peptide E-I was evidenced by 1H-nmr, 13C-nmr, and uv absorption spectroscopy, elemental analysis, and hydrogenation. The conformation of peptide E-I in CDCl3 was investigated by 1H-nmr spectroscopy (solvent dependence of NH chemical shift and difference nuclear Overhauser effect). Interestingly, peptide E-I differed from peptide Z-I in the hydrogen-bonding mode. Namely, for peptide Z-I, only Val NH participates in intramolecular hydrogen bonding, which leads to a type II beta-turn conformation supported by hydrogen bonding between CO(Boc) and NH(Val). On the other hand, for peptide E-I, two NHs, delta(E)Phe NH and Val NH, participate in intramolecular hydrogen bonding. In both peptides, a remarkable NOE (approximately 11-13%) was observed for Ala C(alpha) H-deltaPhe NH pair. Based on the nmr data and conformational energy calculation, it should be concluded that peptide E-I takes two consecutive gamma-turn conformations supported by hydrogen bonding between CO(Boc) and NH(delta(E)Phe), and between CO(Ala) and NH(Val) as its plausible conformation.

Effect of lengthening of peptide backbone by insertion of chiral beta-homo amino acid residues: conformational behavior of linear peptides containing alternating L-leucine and beta-homo L-leucine residues.

The synthesis and the solution behavior of the linear peptides containing a beta-homo (beta-H) leucine residue-Boc-Leu-beta-HLeu-Leu-OMe, Boc-beta-HLeu-Leu-beta-HLeu-Leu-OMe, and Boc-Leu-beta-HLeu-Leu-beta-HLeu-Leu-OMe-as well as the solid structure of the tripeptide, are reported. The conformational behavior of the peptides was investigated in solution by two-dimensional nmr. Our data support the existence in solution with different families of conformers in rapid interchange. The crystals of the tripeptide are orthorhombic, space group P2(1)2(1)2, with a = 15.829(1) A, b = 29.659(1) A, c = 6.563(1) A, and Z = 4. The structure has been solved by direct methods and refined to final R1 and wR2 indexes of 0.0530 and 0.1436 for 2420 reflections with I > 2sigma(I). In the solid state, the tripeptide does not present intramolecular H bonds, and the peptide backbone of the two leucine residues adopts a quasi-extended conformation. For the beta-HLeu residue, the backbone conformation is specified by the torsion angles straight phi(2) = -120.9(4) degrees, mu(2) = 56.7(4) degrees, psi(3) = -133.2(4) degrees. The side chains of the three residues assume the same conformation (g(-), g(-), trans), and all peptide bonds, except the urethane group at the N-terminus, are in the trans conformation. Preliminary conformational energy calculations carried out on the Ac-NH-beta-HAla-NHMe underline that the conformations with mu angle equal to 180 degrees and 60 degrees assume lower energy with respect to the others. In addition, we found a larger conformational freedom for the psi angle with respect to the straight phi angle.