The N‐Terminal Nonapeptide of Cephaibols A and C: A Naturally Occurring Example of Mismatched Helical Screw‐Sense Control

The N‐terminal nonapeptide domain of the fungal nonribosomal peptide antibiotics cephaibol A and cephaibol C (AcPheAib₄LeuIvaGly‐ Aib) is reported to adopt a right‐handed helical conformation in the crystalline state. However, this conformation is at odds with the left‐handed helicity observed in solution in related synthetic oligomers capped with Ac‐L ‐PheAib₄ fragments. We report the synthesis of four diastereoisomers of the cephaibol N‐terminal nonapeptide, and show by NMR and CD spectroscopy that the peptide containing the chiral amino acids Phe and Leu in the naturally occurring relative configuration exists in solution as an interconverting mixture of helical screw‐sense conformers. In contrast, the nonapeptide containing the unnatural relative configuration at Phe and Leu adopts a single, stable helical screw‐sense, which is left handed when the N‐terminal Phe residue is L and right‐handed when the N‐terminal Phe residue is D .     

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,conformation and cytotoxicity of new,branched polymeric polypeptides containing hydrophobic amino acid or arginine moiety

In this paper we report on the synthesis and solution conformation of a new set of structurally related polycationic branched chain polypeptides (poly[Lys(X _i -dl-Ala _m )]) with hydrophobic (Ile, Nle, Val) or cationic (Arg) amino acids at the N-terminal end of the side chains as well as their cytotoxic effect on murine bone marrow derived macrophages. Solution conformation of the polypeptides was studied with circular dichroism spectroscopy under different conditions (pH, ionic strength). The results of these comparative studies indicate that a) polypeptides could adopt an ordered (mainly helical) conformation at physiological pH and salt concentration (pH 7.4, 0.2 M NaCl); b) the nature of side chain terminal amino acid (X) could determine under which conditions the ordered structure was formed. Thus, the solution conformation of branched polypeptides could be modulated by the selection of amino acid X under physiological conditions. All polypeptides with hydrophobic amino acid at the terminal position were essentially non-toxic on macrophages, whereas the polypeptide with terminal Arg proved to be markedly cytotoxic.

     

Crystal Structures of the Potassium and Silver Salts of Nitroform

The solid state structures of three nitroformate (NF) salts were determined using single crystal X‐ray crystallography. The NF anion was found to be a non‐planar moiety which adopts either the commonly observed C_2v conformation or distorted propeller conformation (D₃) in the case of the silver salts, or, a C₂ conformation in the case of the potassium salt. This latter C₂ conformation has been uniquely observed for potassium nitroformate. All structures exhibit cation‐anion interactions that influence the structure of the anion. The ¹³C and ¹⁴N NMR spectra of the NF anion show broad singlets, which indicates the equivalence of the nitro groups in solution within the NMR time‐scale. In addition, the vibrational and mass spectra of potassium nitroformate and silver nitroformate monohydrate were recorded. Furthermore, the gaseous decomposition products of potassium nitroformate at 25 °C were detected using IR spectroscopy and mass spectrometry.     

Conformational analysis of a secondary hydroxamic acid in aqueous solution by NOE spectroscopy

Hydroxamic acids are metal‐binding compounds used by micro‐organisms and possess applications in medicine and industry. Hydroxamic acids favor two conformations, E and Z; metal binding is limited to the Z conformation. The Z conformation may be identifiable by NOE spectroscopy, but analysis is complicated by the potential for long‐range coupling as well as for relayed NOEs due to conformational switching. In this report, we re‐examine the reported conformational preference of N‐methyl acetohydroxamic acid (NMHA) in D₂O using NOE spectroscopy. We find that the favored conformation of NMHA in aqueous solution is the E conformation, contrary to an earlier report. NOE build‐up curves are proposed as a valuable tool to probe conformational behavior in similar systems. Copyright © 2013 John Wiley & Sons, Ltd.     

Determination of the Absolute Configuration of Pentacoordinate Chiral Phosphorus Compounds in Solution by Using Vibrational Circular Dichroism Spectroscopy and Density Functional Theory

Vibrational circular dichroism (VCD) spectroscopic measurements and density functional theory (DFT) calculations have been used to obtain the absolute structural information about four sets of diastereomers of pentacoordinate spirophosphoranes derived separately from l‐ (or d‐ ) valine and l‐ (or d‐ ) leucine for the first time. Each compound contains three stereogenic centers: one at the phosphorus center and two at the amino acid ligands. Extensive conformational searches for the compounds have been carried out and their vibrational absorption (VA) and VCD spectra have been simulated at the B3LYP/6‐311++G** level. Although both VA and VCD spectra are highly sensitive to the structural variation of the apical axis, that is, the O? P? O or N? P? O arrangement, the rotamers generated by the aliphatic amino side chains show little effect on both. The dominant experimental VCD features in the 1100–1500 cm^?1 region were found to be controlled by the chirality at the phosphorus center, whereas those at the C?O stretching region are determined by the chirality of the amino acid ligands. The good agreement between the experimental VA and VCD spectra in CDCl₃ solution and the simulated ones allows us to assign the absolute configurations of these pentacoordinate phosphorus compounds with high confidence. This study shows that the VCD spectroscopy complemented with DFT calculations is a powerful and reliable method for determining the absolute configurations and dominating conformers of synthetic phosphorus coordination complexes in solution.     

Thiazole‐Based γ‐Building Blocks as Reverse‐Turn Mimetic to Design a Gramicidin S Analogue: Conformational and Biological Evaluation

This paper describes the ability of a new class of heterocyclic γ‐amino acids named ATCs (4‐amino(methyl)‐1,3‐thiazole‐5‐carboxylic acids) to induce turns when included in a tetrapeptide template. Both hybrid Ac‐Val‐(R or S)‐ATC‐Ile‐Ala‐NH₂ sequences were synthesized and their conformations were studied by circular dichroism, NMR spectroscopy, MD simulations, and DFT calculations. It was demonstrated that the ATCs induced highly stable C₉ pseudocycles in both compounds promoting a twist turn and a reverse turn conformation depending on their absolute configurations. As a proof of concept, a bioactive analogue of gramicidin S was successfully designed using an ATC building block as a turn inducer. The NMR solution structure of the analogue adopted an antiparallel β‐pleated sheet conformation similar to that of the natural compound. The hybrid α,γ‐cyclopeptide exhibited significant reduced haemotoxicity compared to gramicidin S, while maintaining strong antibacterial activity.     

Conformational Study of Heteropentapeptides Containing an α‐Ethylated α,α‐Disubstituted Amino Acid: (S)‐Butylethylglycine (=2‐Amino‐2‐ethylhexanoic Acid) within a Sequence of Dimethylglycine (=2‐Aminoisobutyric Acid) Residues

Heteropentapeptides containing the α‐ethylated α,α‐disubstituted amino acid (S)‐butylethylglycine and four dimethylglycine residues, i.e., CF₃CO‐[(S)‐Beg]‐(Aib)₄‐OEt ( 4 ) and CF₃CO‐(Aib)₂‐[(S)‐Beg]‐(Aib)₂‐OEt ( 7 ), were synthesized by conventional solution methods. In the solid state, the preferred conformation of 4 was shown to be both a right‐handed (P) and a left‐handed (M) 3₁₀‐helical structure, and that of 7 was a right‐handed (P) 3₁₀‐helical structure. IR, CD, and ¹H‐NMR spectra revealed that the dominant conformation of both 4 and 7 in solution was the 3₁₀‐helical structure. These conformations were also supported by molecular‐mechanics calculations.     

Comparison of the Electronic and Vibrational Optical Activity of a Europium(III) Complex

The geometry and the electronic structure of chiral lanthanide(III) complexes are traditionally probed by electronic methods, such as circularly polarised luminescence (CPL) and electronic circular dichroism (ECD) spectroscopy. The vibrational phenomena are much weaker. In the present study, however, significant enhancements of vibrational circular dichroism (VCD) and Raman optical activity (ROA) spectral intensities were observed during the formation of a chiral bipyridine–Eu^III complex. The ten‐fold enhancement of the vibrational absorption and VCD intensities was explained by a charge‐transfer process and the dominant effect of the nitrate ion on the spectra. A much larger enhancement of the ROA and Raman intensities and a hundred‐fold increase of the circular intensity difference (CID) ratio were explained by the resonance of the λ=532 nm laser light with the ⁷F₀ → ⁵D₀ transitions. This phenomenon is combined with a chirality transfer, and mixing of the Raman and luminescence effects involving low‐energy ⁷F states of europium. The results thus indicate that the vibrational optical activity (VOA) may be a very sensitive tool for chirality detection and probing of the electronic structure of Eu^III and other coordination compounds.     

The Effect of Backbone‐Heteroatom Substitution on the Folding of Peptides – A Single Fluorine Substituent Prevents a β‐Heptapeptide from Folding into a 314‐Helix (NMR Analysis)

The β‐heptapeptides H‐βhVal‐βhAla‐βhLeu‐βhAla(X_n)‐βhVal‐βhAla‐βhLeu‐OH 3 – 7 with central 3‐amino‐2‐fluoro‐, 3‐amino‐2,2‐difluoro‐, or 3‐amino‐2‐hydroxybutanoic acid residues (βhAla(X_n)) of like and unlike configuration were subjected to a detailed NMR analysis in MeOH solution. For the geminal difluoro and for the F‐ and OH‐substituted derivatives of u‐configuration (see 5, 4 , and 7 , resp.), 14‐helices were found, i.e., with axial disposition of the hetero atoms on the helix. The two compounds containing the central l‐configured β‐amino acid moieties (see 3 and 6 ) are not helical over the full lengths of the chains; they have ‘quasi‐helical’ termini and a central turn consisting of a ten‐membered H‐bonded ring (Fig. 2, d and e). Quantum‐mechanical calculations with l‐ and u‐AcNH‐CHMe‐CHF‐CONH₂ confirm the observed preference for a conformation with antiperiplanar arrangement of the F? C and the C?O bond. The calculated energy difference between the observed ‘non‐helical’ geometry of this moiety and a hypothetical helical one is 6.4 kcal/mol (Fig. 3).     

Tri‐n‐butyltin binding to a low‐affinity site decreases the F1FO‐ATPase sensitivity to oligomycin in mussel mitochondria

In mussel digestive gland mitochondria the environmental pollutant tri‐n‐butyltin (TBT), other than strongly inhibiting ATPase activity at <1.0 μ m , at ≥1.0 μ m concentration was previously found to desensitize F₁F_O‐ATPase to the antibiotic oligomycin. While F₁F_O‐ATPase inhibition is widely known as one of the main mitochondrial damages caused by TBT, the enzyme's desensitization to oligomycin was quite unexpected. The possible mechanisms involved are here stepwise approached, aiming at enlightening the molecular mechanism(s) of TBT toxicity and the still poorly investigated oligomycin interaction with F_O. The findings strongly suggest that the oligomycin desensitization directly stems from the covalent binding of TBT to monothiols of the F₁F_O‐ATPase. This binding implies sulfur oxidation, irrespective of the possible formation of radical species in mitochondria, a mechanism which does not seem to be involved here. It is hypothesized that TBT interacts with the enzyme complex in at least two sites distinguished by different affinities: TBT binding to the high‐affinity site would lead to ATPase inhibition, while TBT binding to monothiols in the low‐affinity site could mirror the decrease in F₁F_O‐ATPase oligomycin sensitivity at ≥1.0 μ m TBT. Experiments carried out on inside‐out submitochondrial particles hint that TBT binding destabilizes the oligomycin‐blocked F_O conformation, allowing proton flux recovery within F_O, without uncoupling the catalytic function from proton channeling. Copyright © 2012 John Wiley & Sons, Ltd.     

Synthesis and Conformational Characterisation of Hexameric β‐Peptide Foldamers by Using Double POAC Spin Labelling and cw‐EPR

A selected set of terminally protected β‐hexapeptides, each containing two nitroxide‐based (3R,4R)‐4‐amino‐1‐oxyl‐2,2,5,5‐tetramethylpyrrolidine‐3‐carboxylic acid (POAC) residues combined with four (1S,2S)‐2‐aminocyclopentane‐1‐carboxylic acid (ACPC) residues, was synthesised by using solution methods and was fully characterised. The two POAC residues are separated in the sequences by different numbers of intervening ACPC residues. The conformational features of the doubly spin‐labelled β‐hexapeptides were examined in chloroform by FTIR absorption and continuous‐wave electron paramagnetic resonance spectroscopic techniques. In particular, the biradical exchange coupling (J) between two POAC residues within each peptide indicates unambiguously that the secondary structure overwhelmingly adopted is the 12‐helix. Taken together, these results support the view that POAC is an excellent β‐amino acid for exploring this type of helical conformation in doubly labelled β‐peptides.     

The Propensity of α‐Aminoisobutyric Acid (=2‐Methylalanine; Aib) to Induce Helical Secondary Structure in an α‐Heptapeptide: A Computational Study

We present a molecular‐dynamics simulation study of an α‐heptapeptide containing an α‐aminoisobutyric acid (=2‐methylalanine; Aib) residue, Val¹‐Ala²‐Leu³‐Aib⁴‐Ile⁵‐Met⁶‐Phe⁷, and a quantum‐mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 3₁₀/α‐helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L ‐Ala, D ‐Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L ‐Ala and D ‐Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C₇ and 3₁₀‐helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α‐helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib‐containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.     

α‐Aminoxy Oligopeptides: Synthesis,Secondary Structure,and Cytotoxicity of a New Class of Anticancer Foldamers

α‐Aminoxy peptides are peptidomimetic foldamers with high proteolytic and conformational stability. To gain an improved synthetic access to α‐aminoxy oligopeptides we used a straightforward combination of solution‐ and solid‐phase‐supported methods and obtained oligomers that showed a remarkable anticancer activity against a panel of cancer cell lines. We solved the first X‐ray crystal structure of an α‐aminoxy peptide with multiple turns around the helical axis. The crystal structure revealed a right‐handed 2₈‐helical conformation with precisely two residues per turn and a helical pitch of 5.8 Å. By 2D ROESY experiments, molecular dynamics simulations, and CD spectroscopy we were able to identify the 2₈‐helix as the predominant conformation in organic solvents. In aqueous solution, the α‐aminoxy peptides exist in the 2₈‐helical conformation at acidic pH, but exhibit remarkable changes in the secondary structure with increasing pH. The most cytotoxic α‐aminoxy peptides have an increased propensity to take up a 2₈‐helical conformation in the presence of a model membrane. This indicates a correlation between the 2₈‐helical conformation and the membranolytic activity observed in mode of action studies, thereby providing novel insights in the folding properties and the biological activity of α‐aminoxy peptides.     

NMR Solution Structure of Phospholamban

Phospholamban (PLN), an amphipathic intrinsic membrane protein of 52 amino acids, is the modulator of the Ca²⁺ pump of cardiac, slow‐twitch, and smooth‐muscle sarcoplasmic reticulum. In response to β‐adrenergic stimulation, it becomes phosphorylated at Ser¹⁶ and/or Thr¹⁷, and dissociates from the pump, which, in turn, achieves its full activity. Here we present the three‐dimensional structure of chemically synthesized, monomeric PLN in an organic solvent. Monomerization (PLN normally forms homopentamers) was obtained by replacing Cys⁴¹ with phenylalanine (Phe=F), a modification that did not affect biological activity. The structure was determined by high‐resolution NMR in CHCl₃/MeOH of the unphosphorylated state of [F⁴¹]PLN (C41F). Of the hydrophilic cytoplasmic parts IA (Met¹ to Pro²¹) and IB (Gln²² to Asn³⁰) and the membrane‐spanning hydrophobic domain II (Leu³¹ to Leu⁵²) of PLN, domain IA, which contains the two phosphorylation sites Ser¹⁶ and Thr¹⁷, and domain II have been suggested to be helical and connected through the less‐structured hinge‐region IB. In the structural study presented here, [F⁴¹]PLN is composed of two α‐helical regions connected by a β‐turn (type III). The residues of the β‐turn (type III) are Thr¹⁷, Ile¹⁸, Glu¹⁹, and Met²⁰, the first being one of the two phosphorylation sites (Ser¹⁶ and Thr¹⁷). The hinge region is located at the C‐terminal end of domain IA, and domain IB is part of a second helix. The two α‐helices comprising amino acids 4 – 16 and 21 – 49 are well‐defined (the root‐mean‐square deviations for the backbone atoms, calculated for a family of the structures, are 0.58 and 0.92 Å, resp.). Pro²¹ is at the beginning of the C‐terminal helix and in the trans conformation.     

Dibutyltin-3-hydroxyflavone bromide: A fluorescent inhibitor of F1F0-ATPase

Dibutyltin-3-hydroxyflavone bromide [Bu₂SnBr-(of)] is a fluorescent inhibitor (excitation max, 395 nm; emission max., 450 nm) of mitochondrial F₁F₀–ATPase which does not inhibit F₁–ATPase. Bu₂SnBr(of) binding to mitochondria and submitochondrial particles results in a 10-fold fluorescence enhancement which correlates with the amount of F₁F₀–ATPase in the inner membrane. Enhancement is not affected by respiratory-chain substrates, ATP, uncoupling agents, ionophores or respiratory-chain inhibitors. It is reversed by tributyltin chloride (Bu₃SnCl), indicating competition for a common triorganotin-binding site on the F₀ segment of F₁F₀–ATPase. Enhancement is not reversed by dialkyltins, monoalkyltins, tributyl-lead acetate, efrapeptin or oligomycin. Bu₂SnBr(of) is thus a new class of fluorescent probe of the F₀ segment of F₁F₀–ATPase which titrates F₀.     

Characterization by FTIR spectroscopy of the oligoribonucleotide duplexes r(A-U)6 and r(A-U)8

Fourier transform infrared spectroscopy has been used to characterize the helical conformation of double stranded oligoribonucleotides r(A-U)₆ and r(A-U)₈ in solution. As expected the oligoribonucleotides are found to adopt in solution an A family type conformation. The simultaneous study of a series of duplexes containing A, T or U bases combined either with riboses or deoxyriboses allows us to propose a set of infrared marker bands allowing to distinguish between C2′ endo/anti and C3′ endo/anti conformers of dA, dT, rA and rU nucleosides in nucleic acids.     

Host–guest‐like thi­amine–anion complexation in thia­minium bis­(tetra­fluoro­borate)

In the title compound, 3‐[(4‐amino‐2‐methyl‐5‐pyrimidin‐1‐io)methyl]‐5‐(2‐hydroxy­ethyl)‐4‐methyl­thia­zolium(2+) bis(tetra­fluoro­borate), C₁₂H₁₈N₄OS²⁺·2BF₄^?, the divalent thia­mine cation (in the F conformation) is associated with BF₄^? anions via two characteristic bridging interactions between the thia­zolium and pyrimidinium rings, i.e. C—H?BF₄^??pyrimidinium and N—H?BF₄^??thia­zolium interactions. Thi­amine mol­ecules are linked by N—H?O hydrogen bonds to form a helical chain structure.     

Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity

Certain Arctic and Antarctic ectotherm species have developed strategies for survival under low temperature conditions that, among others, consist of antifreeze glycopeptides (AFGP). AFGP form a class of biological antifreeze agents that exhibit the ability to inhibit ice growth in vitro and in vivo and, hence, enable life at temperatures below the freezing point. AFGP usually consist of a varying number of (Ala‐Ala‐Thr)_n units (n=4–55) with the disaccharide β‐D ‐galactosyl‐(1→3)‐α‐N‐acetyl‐D ‐galactosamine glycosidically attached to every threonine side chain hydroxyl group. AFGP have been shown to adopt polyproline II helical conformation. Although this pattern is highly conserved among different species, microheterogeneity concerning the amino acid composition usually occurs; for example, alanine is occasionally replaced by proline in smaller AFGP. The influence of minor and major sequence mutations on conformation and antifreeze activity of AFGP analogues was investigated by replacement of alanine by proline and glycosylated threonine by glycosylated hydroxyproline. The target compounds were prepared by using microwave‐enhanced solid phase peptide synthesis. Furthermore, artificial analogues were obtained by copper‐catalyzed azide–alkyne cycloaddition (CuAAC): propargyl glycosides were treated with polyproline helix II‐forming peptides comprising (Pro‐Azp‐Pro)_n units (n=2–4) that contained 4‐azidoproline (Azp). The conformations of all analogues were examined by circular dichroism (CD). In addition, microphysical analysis was performed to provide information on their inhibitory effect on ice recrystallization.     

A 310-helix single turn enforced by crosslinking of lysines with 1,1′-ferrocenedicarboxylic acid

Prior work has shown that covalently linking the side chains of amino acids in the i and i+3 and i and i+4 positions in a peptide will enforce a helical conformation. In this work the ability of an organometallic entity to enforce a helical conformation in a peptide was explored. The tetrapeptide Boc-Lys-Ala-Val-Lys-NHCH₃ was prepared, then reacted with 1,1′-ferrocenedicarboxylic acid chloride. Reaction of the lysine side chain amines with the diacid chloride resulted in a metallacyclicpeptide (1) in which the two lysines are crosslinked via the ferrocene. The solution conformation of the metallacyclicpeptide (1) was studied using CD and NMR spectroscopy. The NMR methods employed were Karplus analysis of coupling constants, chemical shift changes of NH protons and ROESY data. The results show that the metallacyclicpeptide (1) adopts a single turn of the 3₁₀-helix conformation.