A nonhelical,multiple β-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central α-aminoisobutyric acid residue

The conformational properties of the protected seven-residue C-terminal fragment the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl₃ and (CD₃)₂SO by ¹H-nmr. Evidence for a multiple β-turn conformation [type I′ at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I′ at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl₃. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline slates. A structural transition to a frayed right-handed helix is absented in (CD₃)₂SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides. © 1995 John Wiley & Sons, Inc.     

Omega amino acids in peptide design: incorporation into helices

Incorporation of easily available achiral ω-amino acid residues into an oligopeptide results in substitution of amide bonds by polymethylene units of an aliphatic chain, thereby providing a convenient strategy for constructing a peptidomimetic. The central Gly-Gly segment of the helical octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-Ome(1) has been replaced by δ-amino-valeric acid (δ-Ava) residue in the newly designed peptide Boc-Leu-Aib-Val-δ-Ava-Leu-Aib-Val-OMe(2). ¹H-nmr results clearly suggest that in the apolar solvent CDCl₃, the δ-Ava residue is accommodated into a folded helical conformation, stabilized by successive hydrogen bonds involving the NH groups of Val(3), δ-Ava(4), and Leu(5). The δ-Ava residue must adopt a gauche-gauche-trans-gauche-gauche conformation along the central polymethylene unit of the aliphatic segment, a feature seen in an energy-minimized model conformation based on nmr parameters. The absence of hydrogen bonding functionalities, however, limits the elongation of the helix. In fact, in CDCl₃, the folded conformation consists of an N-terminal helix spanning residues 1–4, followed by a Type II β-turn at residues 5 and 6, whereas in strongly solvating media like (CD₃)₂SO, the unfolding of the N-terminal helix results in β-turn conformations at Leu(1)-Aib(2). The Type II β-turn at the Leu(5)-Aib(6) segment remains intact even in (CD₃)₂SO. CD comparisons of peptides 1 and 2 reveal a “nonhelical” spectrum for 2 in 2,2,2-trifluoroethanol. © 1996 John Wiley & Sons, Inc.     

Stereochemistry of α-aminoisobutyric acid peptides in solution: Conformations of decapeptides with a central triplet of contiguous L-amino acids

The decapeptides Boc-Aib-L -Val-Aib-Aib-(L -Val)₃-Aib-L -Val-Aib-OMe and Boc-Aib-L -Leu-Aib-Aib-(L -Leu)₃-Aib-L -Leu-Aib-OMe have been studied in CDCl₃ and (CD₃)₂SO solutions by 270-MHz¹ H-nmr. In CDCl₃, the presence of eight intramolecularly hydrogen-bonded NH groups has been established, consistent with a 3₁₀-helical conformation, for both decapeptides. In (CD₃)₂SO, only seven solvent-shielded NH groups are observed, supporting either an α-helical conformation or a partially unfolded 3₁₀-helix. Ir studies provided supporting evidence for intramolecularly hydrogen-bonded structures in CHCl₃, while CD studies suggest helical conformation in both decapeptides in various solvents. CD studies also support helical folding in the C-terminal hexapeptides. The central triplet of L-amino acids appears to destabilize 3₁₀-helical conformations in polar solvents like (CD₃)₂SO.     

The solution conformations of gramicidin A and its analogs

The conformational states in dioxane and ethanol of gramicidin A and of analogs varying in chain length and amino acid sequence have been studied. Infrared, CD, and polarization of fluorescence spectra of the peptides were measured, from which dimerization constants were determined and spectral characteristics of the monomeric and dimeric states obtained. Resonance splitting of the amide I ir band has been calculated for all gramicidin A models proposed earlier. Detailed comparison of the experimental and computed spectra showed that the four dimeric gramicidin species present in solution are predominantly antiparallel double ?ππ_ld helices in equilibrium with smaller amounts of head-to-head associated π_LD helices. The gramicidin A monomer was found to be a π_LD^4.4 helix in dioxane. For each conformational form the number of residues per turn and the helical sense were determined. The relationship between the amino acid sequence and the structure and stability of the dimer in the series of gramicidin A and its analogs is discussed. The above findings are rationalized in terms of the membrane channel properties of gramicidin A, in particular the conformational rearrangements occurring during the passage of metal ions through the channel and also the differences in conformation of the antibiotic in nonpolar solutions and in the membrane.     

Intrinsic protein-lipid interactions. Infrared spectroscopic studies of gramicidin A, bacteriorhodopsin and Ca2+-ATPase in biomembranes and reconstituted systems

Infrared spectroscopy has been applied to the study of a number of aqueous systems of model and natural biomembranes. The absorption bands arising from water and buffer solutions were eliminated by means of an infrared spectrometer data station. Spectra were examined using H₂O and ²H₂O aqueous buffer systems. Pure lecithin-water systems, and various model biomembranes containing cholesterol, gramicidin A, bacteriorhodopsin or Ca²⁺-ATPase were examined. The infrared spectra of the reconstituted biomembranes were compared with those of the corresponding natural biomembranes, i.e. the purple membrane of Halobacterium halobium and also sarcoplasmic reticulum membranes, respectively.Changes in lipid chain conformation caused by the various intrinsic molecules incorporated within the model lipid bilayer structures were monitored by studying the shifts in frequency (cm^?1) of the CH₂ symmetric and asymmetric absorption bands arising from the lipid chains. The effect of gramicidin A and also the intrinsic proteins, as indicated by the shift of band frequencies, are quite different from that of cholesterol at temperatures above the main lipid transition temperature t_c. Cholesterol causes a reduction in gauche isomers which increases with concentration of cholesterol within the lipid bilayer. Whilst gramicidin A and the intrinsic proteins at low concentration cause a reduction of gauche isomers, at higher concentrations of these molecules, however, there is little difference in gauche isomer content when the intrinsic molecule is present compared with that of the fluid lipid alone. These results are considered and compared with previously published studies using deuterium nuclear magnetic resonance spectroscopy on similar model biomembrane systems. Below the lipid t_c value, all the intrinsic molecules produce an increase in gauche isomers presumably by disturbing the lipid chain packing in the crystalline lipid arrangement.Information about the polypeptide structure within gramicidin A. the reconstituted proteins and also the proteins in the natural biomembranes was obtained by examining the region of the infrared spectrum between 1600 and 1700 cm^?1 associated with the amide I and amide II bands. An examination of the infrared band frequencies of the different systems in this region leads to the conclusions: (1) that gramicidin A within a phospholipid bilayer structure probably has a single helix rather than a double helix structure; (2) that there are differences in band widths of the reconstituted Ca²⁺-ATPase and bacteriorhodopsin compared with the spectra of the corresponding sarcoplasmic reticulum and purple membrane; (3) different membrane proteins adopt different conformations as evinced by a comparison of the spectra of the sarcoplasmic reticulum and purple membrane; (4) the polypeptide arrangement in the purple membrane is mainly helical but the abnormal frequency of the amide I band suggests that some distortion of the helix occurs: and (5) the sarcoplasmic reticulum membrane contains unordered as well as α-helix polypeptide arrangements.     

Vibrational analysis of nucleic acids. IV. normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Raman and ir spectra are reported for diethyl phosphate [(CH₃CH₂O)₂PO^-₂] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH¹³₃CH₂O)₂PO^-₂] and deuterium substituents on methyl and methylene carbons [(CH₃CD₂O)₂PO^-₂, (CD₃CH₂O)₂PO^-₂ (CD₃CD₂O)₂PO^-₂]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O^-₂)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G^* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group. © 1996 John Wiley & Sons, Inc.     

Conformations of model compounds of proteins. I. Acetylglycine N-methylamide

Infrared spectra in the region 4000–60 cm^?1 have been measured for acetylglycine N-methylamide and its deuterium homologs, CD₃CONHCH₂CONHCH₃, CH₃-CONHCD₂CONHCH₃, CH₂CONHCH₂CONHCD₃, and CH₃CONDCH₂CONDCH₃. Normal frequencies have also been calculated for these molecules with various conformations. The spectra show that this compound has two crystalline modifications, form A and form B. The frequencies and their isotope shifts show that the molecular conformation (Ψ, ?) of form B is near (0, 120) and that of form A near (180, 120). The short-range factors determining the conformation of peptide backbone having glycine residues are discussed.     

Solid state and solution conformations of a helical peptide with a central gly-gly segment

The influence of amino acids with contrasting conformational tendencies on the stereochemistry of oligopeptides has been investigated using an octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-OMe, which contains two helix-promoting Aib residues and a central helix-destabilizing Gly-Gly segment. Single crystal x-ray diffraction studies reveal that a 3 ₁₀-helix is formed up to the penultimate Aib residue, at which point there is a helix reversal in the backbone, reminiscent of a C-terminal 6 → I hydrogen bond. The curious feature in the crystal is the solvation of the possible 6 → 1 bond by a CH₃OH molecule, where the OH is inserted between O(3) and N(8) and participates in hydrogen bonds with both. The cell parameters are as follows: space group P2₁2₁2₁, a = 10.649(4) Å, b = 15.694(5) Å, c = 30.181(8) Å, R = 6.7% for 3427 data (| F₀| > 3σF) observed to 0.9 Å. Nuclear magnetic resonance studies in CDCl₃ using NH group solvent accessibility and nuclear Overhauser effects as probes are consistent with a 3 ₁₀-helical conformation. In contrast, in (CD₃)₂SO, unfolding of the central segment results in a multiple β-turn structure, with β-turn conformations populated at residues 1–2, 3–4, and 6–7. CD studies in methanol-2,2,2-trifluoroethanol (TFE) mixtures also provide evidence for a solvent-dependent structural transition. Helical conformations are populated in TFE, while type II β-turn structures are favored in methanol. © 1996 John Wiley & Sons, Inc.     

VCD Robustness of the Amide‐I and Amide‐II Vibrational Modes of Small Peptide Models

The rotational strengths and the robustness values of amide‐I and amide‐II vibrational modes of For(AA)_nNHMe (where AA is Val, Asn, Asp, or Cys, n = 1–5 for Val and Asn; n = 1 for Asp and Cys) model peptides with α‐helix and β‐sheet backbone conformations were computed by density functional methods. The robustness results verify empirical rules drawn from experiments and from computed rotational strengths linking amide‐I and amide‐II patterns in the vibrational circular dichroism (VCD) spectra of peptides with their backbone structures. For peptides with at least three residues (n ≥ 3) these characteristic patterns from coupled amide vibrational modes have robust signatures. For shorter peptide models many vibrational modes are nonrobust, and the robust modes can be dependent on the residues or on their side chain conformations in addition to backbone conformations. These robust VCD bands, however, provide information for the detailed structural analysis of these smaller systems. Chirality 27:625–634, 2015 © 2015 Wiley Periodicals, Inc.     

Structure in solution of biscyclo(dipeptide) restricted by CSSC gauche effect

Biscyclo(Cys-Sar) [I] and biscyclo(Cys-Pro) [II] were prepared by the extension of amino acid moieties from cystine. Compound I equilibrates between two rotamers around the CSSC bond of the cystine residue in methanol, showing dual negative CD transitions (CS-SC) at 270 and 255 nm, and dual S-S vibrations at 507 and 539 cm^?1 in Raman spectra. In contrast, a conformation of P-helix type is suggested in CH₃CN, which shows a distinct negative CD at 270 nm and only one Raman band at 507 cm^?1 for the S-S bond. Compound II rotates freely in dimethylsulfoxide (Me₂SO) but takes a relatively stable conformer of P-helix type in methanol, chloroform/Me₂SO (9:1), and chloroform/trifluoroacetic acid (9:1). The conformation in chloroform is retained even on addition of trifluoroacetic acid. A more complete conformation of compound II in water was determined from the negative CD of S-S transition and ¹H-nmr spectra of the Cys-β-CH₂ protons.     

Life in Its Uniqueness Remains Difficult to Define in Scientific Terms

Abstract

The crystal structure of the dehydro octapeptide Boc-Val-ΔPhe-Phe-Ala-Leu-Ala-ΔPhe-Leu-OH has been determined to atomic resolution by X-ray crystallographic methods. The crystals grown by slow evaporation of peptide solution in methanol/water are orthorhombic, space group P2₁2₁2₁. The unit cell parameters are a= 8.404 (3), b= 25.598(2) and c = 27.946(3) Å, Z=4. The agreement factor is R= 7.58% for 3636 reflections having (IF₀I) ≥ 3σ (IF₀I). The peptide molecule is characterised by a 3₁₀-helix at the N-terminus and a π-turn at the C-terminus. This conformation is exactly similar to the helix termination features observed in proteins. The π-turn conformation observed in the octapeptide is in good agreement with the conformational features of π-turns seen in some proteins. The α_L-position in the π-turn of the octapeptide is occupied by ΔPhe⁷, which shows that even bulky residues can be accommodated in this position of the π-turns. In proteins, it is generally seen that aL- position is occupied by glycine residue. No intermolecular head-to-tail hydrogen bonds are observed in solid state structure of the octapeptide. A water molecule located in the unit cell of the peptide molecule is mainly used to hold the peptide molecule together in the crystal. The conformation observed for the octapeptide might be useful to understand the helix termination and chain reversal in proteins and to construct helix terminators for denovo protein design.     

Unfolding of an α-helix in peptide crystals by solvation: Conformational fragility in a heptapeptide

The structure of the peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe has been determined in crystals obtained from a dimethylsulfoxide–isopropanol mixture. Crystal parameters are as follows: C₃₈H₆₉N₇O₁₀ · H₂O · 2C₃H₇OH, space group P2₁, a = 10.350 (2) Å, b = 26.084 (4) Å, c = 10.395(2) Å, β = 96.87(12), Z = 2, R = 8.7% for 2686 reflections observed > 3.0 σ (F). A single 5 → 1 hydrogen bond is observed at the N-terminus, while two 4 → 1 hydrogen bonds characteristic of a 3₁₀-helix are seen in the central segment. The C-terminus residues, Ala(6) and Leu(7) are expended, while Val(5) is considerably distorted from a helical conformation. Two isopropanol molecules make hydrogen bonds to the C-terminal segment, while a water molecule interacts with the N-terminus. The structure is in contrast to that obtained for the same peptide in crystals from methanol-water [ I. L. Karle, J. L. Flippen-Anderson, K. Uma, and P. Balaram (1990) Proteins: Structure, Function and Genetics, Vol. 7, pp. 62–73] in which two independent molecules reveal an almost perfect α-helix and a helix penetrated by a water molecule. A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding. The fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDC1₃ and (CD₃)₂SO. A helical conformation is supported in the apolar solvent CDCl₃, whereas almost complete unfolding is observed in the strongly solvating medium (CD₃)₂SO. © 1993 John Wiley & Sons, Inc.     

Structural Polymorphism of Gramicidin A Channels: Ion Conductivity and Spectral Studies

The relation between the various spatial structures of the gramicidin A channels and their ionic conductance has been studied. For this aim, various conformations of the peptide were pre-formed in liposomal bilayer and after subsequent fusion of liposomes with planar lipid bilayer the measured channel conductance was correlated with gramicidin structures established in liposomes. To form the single-stranded π6.3π 6.3 helix the peptide and lipid were co-dissolved in TFE prior to liposome preparation. THF and other solvents were used to form parallel (↑ ↑ π π) and antiparallel (↑ ↓ π π) double helices. Conformation of gramicidin in liposomes made by various phosphatidylcholines was monitored by CD spectroscopy, and computer analysis of the spectra obtained was performed. After fusion of gramicidin containing liposomes with planar bilayer membranes from asolectin, the histograms of single-channel conductance were obtained. The histograms had one or three distinct peaks depending on the liposome preparation. Assignment of the structure of the channel to conductance levels was made by correlation of CD data with conductance histograms. The channel-forming analogue, des(Trp-Leu)₂-gramicidin A, has been studied by the same protocol. The channel conductances of gramicidin A and the shortened analogue increase in the following order: ↑ ↓ π π 2 ↑ ↑ π π < π 6.3π6.3. Single-channels formed by double helices have higher dispersity of conductance than the π6.3π6.3 helical channel. Lifetimes of the double helical and the π6.3π6.3 helical channels are very close to each other. The data obtained were compared with theoretically predicted properties of double helices [1].     

Raman study of crystalline peptides containing beta turns

The Raman spectra of crystalline H-ProLeuGlyNH₂ which has a type II β turn, crystalline S-benzylCysProLeuGlyNH₂ which has a type I β-turn, and crystalline gramicidin S which has two β turns and β-sheet structure in its conformation, were investigated. The amide I and amide III bands of the peptides with β turns were generally different from those which are diagnostic for α-helix and β-sheet conformations. The patterns of the amide I and amide III bands, when examined together, indicate that Raman spectra can provide diagnostic evidence for β-turn structure in peptides.     

Type II β-turn conformation of pivaloyl-L-prolyl-α-aminoisobutyryl-N-methylamide: Theoretical,spectroscopic, and X-ray studies

Pivaloyl-L -Pro-Aib-N-methylamide has been shown to possess one intramolecular hydrogen bond in (CD₃)₂SO solution, by ¹H-nmr methods, suggesting the existence of β-turns, with Pro-Aib as the corner residues. Theoretical conformational analysis suggests that Type II β-turn conformations are about 2 kcal mol^?1 more stable than Type III structures. A crystallographic study has established the Type II β-turn in the solid state. The molecule crystallizes in the space group P2₁ with a = 5.865 Å, b = 11.421 Å, c = 12.966 Å, β = 97.55°, and Z = 2. The structure has been refined to a final R value of 0.061. The Type II β-turn conformation is stabilized by an intramolecular 4 → 1 hydrogen bond between the methylamide NH and the pivaloyl CO group. The conformational angles are ?_Pro = ?57.8°, ψ_Pro = 139.3°, ?_Aib = 61.4°, and ψ_Aib = 25.1°. The Type II β-turn conformation for Pro-Aib in this peptide is compared with the Type III structures observed for the same segment in larger peptides.     

The conformation of linear gramicidin is sequence dependent

A comparative monolayer and infrared study of analogues of gramicidin A containing either tyrosines or naphthylalanines instead of tryptophans indicates that the nature of the aromatic residues influences the favoured conformation of the peptides. Polar residues favour the single stranded _DL helix while non polar residues favour the double stranded helix. For partly tryptophan to naphthylalanine substituted analogues the positions of the substitutions orientate the favored conformation. The nature of these substitutions may also modify the peptide-lipid interactions. Correspondence to: F. Heitz Chemical structures of the gramicidin A analogues mentioned in this paper. The differences from gramicidin A are underlined. GM^–: GT:     

Stereochemistry of alpha-aminoisobutyric acid peptides in solution: helical conformations of protected decapeptides with repeating Aib-L-Ala and Aib-L-Val sequences

The decapeptides Boc-(Aib-L -Ala)₅-OMe and Boc-(Aib-L -Val)₅-OMe have been studied by 270-MHz ¹H-nmr in CDCl₃ and (CD₃)₂SO solutions. Intramolecular hydrogen-bonded NH groups have been delineated using the temperature and solvent dependence of the NH chemical shifts and differential broadening of the NH resonances, induced by addition of a nitroxide radical. Both peptides have eight solvent-shielded NH groups, suggesting that 3₁₀-helical conformations are maintained in the two solvents. In alternating Aib-X sequences, the Aib residues appear to play a dominant role in determining the preferred conformations, overriding the intrinsic stereochemical preferences of the X residues.     

Nuclear magnetic resonance study of ring conformations of cyclic tetradepsipeptide AM-toxins and related peptides

Cyclic tetradepsipeptides, AM-toxin I and II, are the host-specific phytotoxins of Alternaria mali. In order to elucidate conformation-toxicity relationships, we analyzed the 270-MHz proton nmr spectra of AM-toxins and hydrogenated analogs, (D -Ala²)AM-toxin I (toxic) and (L -Ala²)AM-toxin I (not toxic), in (C²H₃)₂SO. These cyclic tetradepsipeptides do not contain N-substituted amino acid residues, and all the peptide and ester groups have been found to be transoid. Two conformers with very unequal populations have been found for AM-toxin I and II; the C^β?C^α? C?O conformations of the Dha² residues are nonplanar S-trans in the major conformer and nonplanar S-cis in the minor conformer. Only one ring conformation has been found for each of (L -Ala²) and (D -Ala²)AM-toxin I. (L -Ala²)AM-toxin I takes a C₄-type ring conformation; all the C?O groups and C^α-H bonds are oriented to the same side of the ring. (D -Ala²)AM-toxin I takes a new ring conformation; the side chain and C?O group of the L -Amp¹ residue are oriented to the same side of the ring. This new conformation is also found for the major conformers of AM-toxin I and II and thus appears to be required for the toxicity. The ring conformations of Tyr(OCH₃)¹-bearing analog tetradepsipeptides have been found to be much the same as those of Amp¹-bearing depsipeptides. Furthermore, on the basis of the two distinct conformations of (D -Ala²) and (L -Ala²)AM-toxin I, an empirical rule is proposed for the stable ring conformations of cyclic tetra-D ,L -peptides, not containing N-substituted amino acid residues.     

Etude,par spectroscopie infra-rouge,de la conformation de quelques composés peptidiques modèles

Some experimental data are given on the infrared spectra between 3300 and 3500 cm^?1 of dilute solutions in carbon tetrachloride of three types of model compounds: CH_3?CONH-CH(R₁)-CONH(R₂), (I); CH₃-CON(CH₃)-CH(R₁)-CONH(R₂), (II) and CH₃-CONH-CH(R₁)-CON(R₂)₂, (III). In studying the N-H stretching bands, it was found that there are two types of intramolecular hydrogen bonds in these molecules; these result in two different cyclized conformations, C₅ and C₇, which contain respectively, five and seven atoms in the ring. By using model substances I, II, and III, in which the nitrogen atoms are unequally substituted, it is possible to identify the N-H stretching bands which are to be ascribed to the N-H oscillators included in the two different chelated conformations. It is found also that the stretching frequency of a free N-H oscillator depends upon the substituent on the nitrogen atom. Thus, it is possible to observe, with some of the model compounds I, four different absorption bands located at 3340, 3420, 3440, and 3460 cm^?1. The first two are ascribed to the N-H oscillators included in the H? bonds which lock the C₇ and C₅ conformations; the last two correspond to free N-H which differ with the substituent on the nitrogen atom.