Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations

Replacement of the alpha-proton of an alanine residue to generate alpha-aminoisobutyric acid (Aib) in alanine-based oligopeptides favors the formation of a 3(10) helix when the length of the oligopeptide is about four to six residues. This research was aimed at experimentally identifying the structural impact of an individual Aib residue in an alanine context of short peptides in water and Aib's influence on the conformation of nearest-neighbor residues. The amide I band profile of the IR, isotropic and anisotropic Raman, and vibrational circular dichroism (VCD) spectra of Ac-Ala-Ala-Aib-OMe, Ac-Ala-Aib-Ala-OMe, and Ac-Aib-Ala-Ala-OMe were measured and analyzed in terms of different structural models by utilizing an algorithm that exploits the excitonic coupling between amide I' modes. The conformational search was guided by the respective 1H NMR and electronic circular dichroism spectra of the respective peptides, which were also recorded. From these analyses, all peptides adopted multiple conformations. Aib predominantly sampled the right-handed and left-handed 3(10)-helix region and to a minor extent the bridge region between the polyproline (PPII) and the helical regions of the Ramachandran plot. Generally, alanine showed the anticipated PPII propensity, but its conformational equilibrium was shifted towards helical conformations in Ac-Aib-Ala-Ala-OMe, indicating that Aib can induce helical conformations of neighboring residues positioned towards the C-terminal direction of the peptide. An energy landscape exploration by molecular dynamics simulations corroborated the results of the spectroscopic studies. They also revealed the dynamics and pathways of potential conformational transitions of the corresponding Aib residues.     

Preferred 3D-structure of peptides rich in a severely conformationally restricted cyclopropane analogue of phenylalanine

Terminally blocked, homo-peptide amides of (R,R)-1-amino-2,3-diphenylcyclopropane-1-carboxylic acid (c3diPhe), a chiral member of the family of Calpha-tetrasubstituted alpha-amino acids, from the dimer to the tetramer, and diastereomeric co-oligopeptides of (R,R)- or (S,S)-c3diPhe with (S)-alanine residues to the trimer level were prepared in solution and fully characterized. The synthetic effort was extended to terminally protected co-oligopeptide esters to the hexamer, where c3diPhe residues are combined with achiral alpha-aminoisobutyric acid residues. The preferred conformations of the peptides were assessed in solution by FT-IR absorption, NMR, and CD techniques, and for seven oligomers in the crystal state (by X-ray diffraction) as well. This study clearly indicates that c3diPhe, a sterically demanding cyclopropane analogue of phenylalanine, tends to fold peptides into beta-turn and 3(10)-helix conformations. However, when c3diPhe is in combination with other chiral residues, the conformation preferred by the resulting peptides is also dictated by the chiral sequence of the amino acid building blocks. The (S,S)-enantiomer of this alpha-amino acid, unusually lacking asymmetry in the main chain, strongly favors the left-handedness of the turn/helical peptides formed.     

Conformational Studies by Dynamic NMR. 71.(1) Stereodynamics of Triisopropyl(aryl)silanes in Solution and in the Solid State

A study has been carried out of the conformations of triisopropyl(aryl)silanes (i-Pr)(3)SiAr, (Ar = phenyl, 1-naphthyl, and 2-naphthyl) both as to the orientation of the three isopropyl groups and the conformation about the silicon-aromatic bonds. The report comprises dynamic NMR studies of conformational interconversions in solution and in the solid state as well as molecular mechanics calculations. The barriers for the stereomutation processes measured in the crystalline state were found significantly higher than those in solution.     

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.     

Conformational analysis and crystal structure of {[1-(3-chloro-4-fluorobenzoyl)-4-fluoropiperidin-4yl]methyl}[(5-methylpyridin-2-yl)methyl]amine, fumaric acid salt

{[1-(3-Chloro-4-fluorobenzoyl)-4-fluoropiperidin-4yl]methyl}[(5-methylpyridin-2-yl)methyl]amine, fumaric acid salt (C(20)H(22)ClF(2)N(3)O, C(4)H(4)O(4)) (1) was synthesized and characterized by the complete (1)H, (13)C and (19)F NMR analyses. The conformation of the piperidin ring, in the solution state, was particularly studied from the coupling constants determined by recording a double-quantum filtered COSY experiment in phase-sensitive mode. (1)H NMR line-shape analysis was used, at temperatures varying between -5 and +60 degrees C, to determine the enthalpy of activation of the rotational barrier around the CN bond. Compound 1 crystallizes in the triclinic space group P1 with a=8.517(3) Angstrom, b=12.384(2) Angstrom, c=12.472(3) Angstrom, alpha=70.88(2) degrees, beta=82.04(2) degrees, gamma=83.58(2) degrees. The results strongly indicate that the solid and solution conformations are similar. Thermal stability and phases transitions were investigated by thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC). Furthermore polymorphism screening was studied from recrystallization of 1 performed in seven solvents and by slurry conversion in water. The X-ray powder diffraction (XRPD) and differential scanning calorimetry results suggested that 1 crystallizes into one crystalline form which melts at 157 degrees C (DeltaH=132 J g(-1)).     

The role of cystine knots in collagen folding and stability,part I. Conformational properties of (Pro-Hyp-Gly)5 and (Pro-(4S)-FPro-Gly)5 model trimers with an artificial cystine knot

In analogy to the cystine knots present in natural collagens, a simplified disulfide cross-link was used to analyse the conformational effects of a C-terminal artificial cystine knot on the folding of collagenous peptides consisting of solely (Pro-Hyp-Gly) repeating units. Assembly of the alpha chains into a heterotrimer by previously applied regioselective disulfide-bridging strategies failed because of the high tendency of (Pro-Hyp-Gly)(5) peptides to self-associate and form homotrimers. Only when side-chain-protected peptides were used, for example in the Hyp(tBu) form, and a new protection scheme was adopted, selective interchain-disulfide cross-linking into the heterotrimer in organic solvents was successful. This unexpected strong effect of the conformational properties on the efficiency of well-established reactions was further supported by replacing the Hyp residues with (4S)-fluoroproline, which is known to destabilise triple-helical structures. With the related [Pro-(4S)-FPro-Gly](5) peptides, assembly of the heterotrimer in aqueous solution proceeded in a satisfactory manner. Both the intermediates and the final fluorinated heterotrimer are fully unfolded in aqueous solution even at 4 degrees C. Conversely, the disulfide-crossbridged (Pro-Hyp-Gly)(5) heterotrimer forms a very stable triple helix. The observation that thermal unfolding leads to scrambling of the disulfide bridges was unexpected. Although NMR experiments support an extension of the triple helix into the cystine knot, thermolysis is not associated with the unfolding process. In fact, the unstructured fluorinated trimer undergoes an equally facile thermodegradation associated with the intrinsic tendency of unsymmetrical disulfides to disproportionate into symmetrical disulfides under favourable conditions. The experimental results obtained with the model peptides fully support the role of triple-helix nucleation and stabilisation by the artificial cystine knot as previously suggested for the natural cystine knots in collagens.     

Ring-closing metathesis of olefinic peptides: design, synthesis, and structural characterization of macrocyclic helical peptides

Heptapeptides containing residues with terminal olefin-derivatized side chains (3 and 4) have been treated with ruthenium alkylidene 1 and undergone facile ring-closing olefin metathesis (RCM) to give 21- and 23-membered macrocyclic peptides (5 and 6). The primary structures of peptides 3 and 4 were based upon a previously studied heptapeptide (2), which was shown to adopt a predominantly 3(10)-helical conformation in CDCl(3) solution and an alpha-helical conformation in the solid state. Circular dichroism, IR, and solution-phase (1)H NMR studies strongly suggested that acyclic precursors 3 and 4 and the fully saturated macrocyclic products 7 and 8 also adopted helical conformations in apolar organic solvents. Single-crystal X-ray diffraction of cyclic peptide 8 showed it to exist as a right-handed 3(10)-helix up to the fifth residue. Solution-phase NMR structures of both acyclic peptide 4 and cyclic peptide 8 in CD(2)Cl(2) indicated that the acyclic diene assumes a loosely 3(10)-helical conformation, which is considerably rigidified upon macrocyclization. The relative ease of introducing carbon-carbon bonds into peptide secondary structures by RCM and the predicted metabolic stability of these bonds renders olefin metathesis an exceptional methodology for the synthesis of rigidified peptide architectures.     

Preferred 3D‐Structure of Peptides Rich in a Severely Conformationally Restricted Cyclopropane Analogue of Phenylalanine

Terminally blocked, homo‐peptide amides of (R,R)‐1‐amino‐2,3‐diphenylcyclopropane‐1‐carboxylic acid (c₃diPhe), a chiral member of the family of C^α‐tetrasubstituted α‐amino acids, from the dimer to the tetramer, and diastereomeric co‐oligopeptides of (R,R)‐ or (S,S)‐c₃diPhe with (S)‐alanine residues to the trimer level were prepared in solution and fully characterized. The synthetic effort was extended to terminally protected co‐oligopeptide esters to the hexamer, where c₃diPhe residues are combined with achiral α‐aminoisobutyric acid residues. The preferred conformations of the peptides were assessed in solution by FT‐IR absorption, NMR, and CD techniques, and for seven oligomers in the crystal state (by X‐ray diffraction) as well. This study clearly indicates that c₃diPhe, a sterically demanding cyclopropane analogue of phenylalanine, tends to fold peptides into β‐turn and 3₁₀‐helix conformations. However, when c₃diPhe is in combination with other chiral residues, the conformation preferred by the resulting peptides is also dictated by the chiral sequence of the amino acid building blocks. The (S,S)‐enantiomer of this α‐amino acid, unusually lacking asymmetry in the main chain, strongly favors the left‐handedness of the turn/helical peptides formed.     

Synthesis of [L-Ala-1]RA-VII, [D-Ala-2]RA-VII,and [D-Ala-4]RA-VII by epimerization of RA-VII,an antitumor bicyclic hexapeptide from Rubia plants,through oxazoles

Three epimers of a natural cyclic hexapeptide RA-VII were prepared via formation of oxazoles from thioamides or thioimidates of RA-VII followed by hydrolysis. They are the epimers at l-Ala-1, d-Ala-2, and d-Ala-4, respectively. The one having l-Ala-1 adopted trans-cis-trans-trans-trans-trans (t-c-t-t-t-t) amide configurations in the crystal, a type-VI beta-turn for residues 1-4 stabilized by one intramolecular hydrogen bond between Ala-4 NH and l-Ala-1 C = O, and in CDCl(3) existed as a mixture of six conformers, of which the major conformer was very similar to that in the crystal, but quite different from that of RA-VII in solution. The second epimer, having d-Ala-2 had in the crystalline state t-t-t-t-c-t amide configurations, a gamma-turn at Tyr-3 stabilized by two intramolecular hydrogen bonds between d-Ala-2 NH and Ala-4 C = O and between Ala-4 NH and d-Ala-2 C = O, and existed in CDCl(3) as a single conformer, the structure of which was very similar to its crystal structure, and to the crystal structure of peptide 25 except for the backbone and the side chains at residues 1 and 2. The third epimer, having d-Ala-4 had t-c-t-t-c-t amide configurations in the crystal, a type-VI beta-turn for residues 1-4 as observed in the first epimer, and in CDCl(3) existed in three conformers, of which the major one was similar to that in the crystal but different from that of RA-VII in solution. The three epimers showed very weak cytotoxicity on P-388 leukemia cells, which may be because of their conformational differences from the active conformation of RA-VII.     

The Distinct Conformational Landscapes of 4S-Substituted Prolines That Promote an endo Ring Pucker

4-Substitution on proline directly impacts protein main chain conformational preferences. The structural effects of N-acyl substitution and of 4-substitution were examined by NMR spectroscopy and X-ray crystallography on minimal molecules with a proline 4S-nitrobenzoate. The effects of N-acyl substitution on conformation were attenuated in the 4S-nitrobenzoate context, due to the minimal role of the n→π* interaction in stabilizing extended conformations. By X-ray crystallography, an extended conformation was observed for most molecules. The formyl derivative adopted a δ conformation that is observed at the i+2 position of β-turns. Computational analysis indicated that the structures observed crystallographically represent the inherent conformational preferences of 4S-substituted prolines with electron-withdrawing 4-position substituents. The divergent conformational preferences of 4R- and 4S-substituted prolines suggest their wider structure-specific application in molecular design. In particular, the proline endo ring pucker favored by 4S-substituted prolines uniquely promotes the δ conformation [(ϕ, ψ) ≈(−80°, 0°)] found in β-turns. In contrast to other acyl capping groups, the pivaloyl group strongly promoted trans amide bond and polyproline II helix conformation, with a close n→π* interaction in the crystalline state, despite the endo ring pucker, suggesting its special capabilities in promoting compact conformations in ϕ due to its strongly electron-donating character.     

Effect of side chains on turns and helices in peptides of beta3-aminoxy acids

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

The conformation of cyclo(-D-Pro-Ala4-) as a model for cyclic pentapeptides of the DL4 type

The conformation of the cyclic pentapeptide cyclo(-D-Pro-Ala(4)-) in solution and in the solid state was reinvestigated using modern NMR techniques. To allow unequivocal characterization of hydrogen bonds, relaxation behavior, and intramolecular distances, differently labeled isotopomers were synthesized. The NMR results, supported by extensive MD simulations, demonstrate unambiguously that the preferred conformation previously described by us, but recently questioned, is indeed correct. The validation of the conformational preferences of this cyclic peptide is important given that this system is a template for several bioactive compounds and for controlled "spatial screening" for the search of bioactive conformations.     

Multiple Stimuli-Responsive Conformational Exchanges of Biphen[3]arene Macrocycle

Conformational exchanges of synthetic macrocyclic acceptors are rather fast, which is rarely studied in the absence of guests. Here, we report multiple stimuli-responsive conformational exchanges between two preexisting conformations of 2,2′,4,4′-tetramethoxyl biphen[3]arene (MeBP3) macrocycle. Structures of these two conformations are both observed in solid state, and characterized by ¹H NMR, ¹³C NMR and 2D NMR in solution. In particular, conformational exchanges can respond to solvents, temperatures, guest binding and acid/base addition. The current system may have a role to play in the construction of molecular switches and other stimuli-responsive systems.     

Vibrational spectra and structure of 4-cyano-4′-pentalkoxybiphenyl in different physical states

The polymorphism, conformation mobility and structure of 4-cyano-4′-pentalkoxybiphenyl (5OCB) in different physical states are studied by IR spectroscopy. The spectra were measured in the frequency range 400–4000 cm⁻¹ at temperatures from 300 to 350 K. The IR spectra of 5OCB are modeled using the concept of conformational mobility of these molecules. An analysis of the experimental and theoretical spectra reveals absorption bands whose spectroscopic parameters are sensitive to variations of temperature (experiment) and conformation (theory); a relationship between these changes is established. It is concluded that the polymorphism of 5OCB is of conformation type. In the solid crystalline state, 5OCB molecules have conformations with a planar biphenyl fragment; the angle of orientation of the plane of the carbon framework of the alkyl radical relative to the biphenyl fragment decreases as the temperature increases from 35° in the solid crystalline state to 10° in the liquid crystalline and isotropic liquid states. In both of these states the biphenyl fragment becomes nonplanar. The angle between the phenyl rings is up to 30°. Saratov State University. Institute of Physics, Ukrainian Academy of Sciences. Samarkand State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 1, pp. 55–60, January–February, 1998. This work was supported by RFFR grant No. 97-03-32175a.     

Structure,tautomerism, and transformations of β-(3-nitro-2-pyridyl)- and β-(3-nitro-4-pyridyl)pyruvic acid esters

It was shown by means of IR, UV, and PMR spectra that -(3-nitro-2-pyridyl)pyruvic acid esters are practically completely enolized in the crystal state and in solution; ethyl -(3-nitro-4-pyridyl)pyruvate has an enol structure in the crystalline state and in pyridine solution but exists as a mixture of keto and enol forms in low-polarity solvents.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 389–393, March, 1974.     

Systematic evaluation of the conformational properties of aliphatic omega-methoxy methyl esters

[structure: see text] A systematic conformational study of omega-methoxy methyl esters, CH(3)O-(CH2)n-COO-CH3 with n = 3 and 4, has been performed using quantum mechanical calculations at the MP2 level. Calculations have been carried out in both gas phase and chloroform solution, a polarizable continuum solvation model being used to represent the latter. Results have been compared with those recently obtained for the analogues omega-hydroxy acids, HO-(CH2)n-COOH with n = 3 and 4. The compounds with n = 3 clearly favor coiled conformations, the population expected for extended and semiextended conformations being very low. However, for compounds with n = 4 the minimum energy extended and semiextended structures become considerably more stable. The overall results indicate that the conformational preferences of the central aliphatic segment of omega-methoxy methyl esters and omega-hydroxy acids are not influenced by the formation of intramolecular O-H...O hydrogen bonds.     

Reorganization of poly(ethylene terephthalate) structures and conformations to alter properties

The solid‐state morphologies, structures, and chain conformations of poly (ethylene terephthalate) (PET) have been reorganized/altered from those normally produced by solution and melt processing. This has been achieved by two distinct methods: (1) formation of a crystalline inclusion compound (IC) between guest PET and host γ‐cylodextrin (γ‐CD), followed by removal of the host γ‐CD and coalescence of the guest PET (c‐PET) and (2) rapid precipitation of PET from a warm trifluoracetic acid solution into a large excess of rapidly stirred acetone (p‐PET). Our prior observations (FTIR, NMR, DSC, X‐ray) demonstrated that c‐PET processed in this manner has a morphology, structure, and non‐crystalline chain conformations that are quite distinct from those of as‐received PET (asr‐PET). Where possible to compare, here we find that c‐ and p‐PETs behave very similarly, but very distinctly from asr‐PET. The reorganized c‐ and p‐PETs were found to be repeatedly rapidly crystallizable from the melt with a high level of crystallinity, and in their non‐crystalline regions to have tightly packed chains predominantly adopting highly extended kink conformations, which evidence no glass‐transition behavior. What is most unusual and somewhat puzzling is that their contrasting structures, morphologies, conformations, and thermal responses were observed to be independent of melt annealing, and persisted even after holding both samples above T_m for extended periods (hours). p‐PET, which can be produced in larger quantities than c‐PET, was utilized to measure additional macroscopic properties, such as melt viscosities, densities, and the stress‐strain and thermal shrinkage of melt‐pressed films, for comparison to those of asr‐PET. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 735–746, 2007     

Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study.

In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5-Leu-(Aib)2-OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)s-Leu-(Aib)2-OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide. I. This leads to a significant difference in 3 [symbol: see text] (HN, HC alpha) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton-proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpreting molecular properties in the solution state by using X-ray crystallographic data.     

Beta-hairpin folding by a model amyloid peptide in solution and at an interface

The development of specific agents against amyloidoses requires an understanding of the conformational distribution of fibrillogenic peptides at a microscopic level. Here, I present molecular dynamics simulations of the model amyloid peptide LSFD with sequence LSFDNSGAITIG-NH2 in explicit water and at a water/vapor interface for a total time scale of approximately 1.8 micros. An extended structure was used as initial peptide configuration. At approximately 290 K, solvated LSFD was kinetically trapped in diverse misfolded beta-sheet/coil conformations. At 350 K, in contrast, the same type II' beta-hairpin in equilibrium with less ordered but also U-shaped conformations was observed for the core residues DNSGAITI in solution and at the interface in multiple independent simulations. The most stable structural unit of the beta-hairpin was the two residue turn (GA). The core residues exhibited a well-defined folded state in which the beta-hairpin was stabilized by a hydrogen bond between the side chain of Asn-385 and the main chain carbonyl group of Gly-387. My results suggest that beta-sheet conformations indicated from previous Fourier-transform infrared spectroscopy measurements immediately after preparation of the peptide solution may not arise from protofilaments as speculated by others but are a property of LSFD monomers. In addition, combined with previous results from X-ray scattering, my findings suggest that interfacial aggregation of LSFD implies a transition from U-shaped to extended peptide conformations. This work including the first simulations of reversible beta-hairpin folding at an interface is an essential step toward a microscopic understanding of interfacial peptide folding and self-assembly. Knowledge of the main conformation of the peptide core may facilitate the design of possible inhibitors of LSFD aggregation as a test ground for future computational therapeutic strategies against amyloid diseases.