Cis-trans Equilibrium Research Articles

Generation and Application of All Possible Conformations of Cyclic Tryptophan within and beyond Post-translational Modification.

Isoprenylation of the indole C3-position of tryptophan accompanied by cyclization (c-Trp) is one of the most attractive post-translational modifications because of C-C bond formation and drastic conformational alteration. As the modification generates two stereoisomers of the 6/5/5-fused ring system and consequently, a mixture of four possible conformations as considered in proline, it is expected to influence the biological activity in Bacillus quorum sensing pheromone ComX containing the c-Trp residue. In this study, the simultaneous control of the amide cis-trans equilibrium and pyrrolidine ring puckering was achieved by utilizing an N-carbamoylated and α-methylated 6/5/5-fused ring system. Furthermore, the conformationally defined tripeptides containing the c-Trp residue were utilized to examine the relationship between the biological activity and the conformation of the ComX pheromone. Several mimics showed high bioactivity, and more biologically active ComX mimics were created to reinforce the CH-π interaction of the c-Trp and the adjacent aromatic residue.

Conformation features and interaction of pyrrolidinium-based ionic liquids immobilized with silicon dioxide: Infrared spectroscopy

Ionic liquids (ILs) based on pyrrolidinium cation, 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide (BMPyrrTFSI) and 1-butyl-1-methylpirrolidinium dicyanamide (BMPyrrN(CN)2), were incorporated into the silica matrix (SiO2, particle size about 80 nm) by a simple mixing procedure. Semitransparent phase-stable ionogels with an IL content of more than 90 wt% have been obtained and studied by FTIR spectroscopy. The analysis of microscopic mechanisms of interaction, in particular, hydrogen bonding, was carried out using the procedure of fitting the characteristic bands of pure and confined ILs. The observed changes in the position and intensity of some characteristic frequencies were interpreted in terms of the interaction of SiO2 with IL. Under confined condition, the cis–trans equilibrium of both the TFSI− anion and BMPyrr+ cation changes in favor of the trans population due to the predominant interaction of cis conformers with silica walls. This data for confined BMPyrr-based ionic liquids were obtained in our study for the first time and will be useful for designing of a new nanostructured hybrid materials with promising properties.

Hydrophilic meso-substituted cyanine dyes in solution and in complexes with serum albumins: spectral properties and molecular docking study

The absorption and fluorescence spectral properties of three meso-substituted hydrophilic thiacarbocyanine dyes were studied in solutions and in noncovalent complexes with human and bovine serum albumins (HSA and BSA, respectively). The presence of alkyl substituents at the meso-position of the polymethine chain of the dyes determines the occurrence of a cis–trans equilibrium. Dyes form aggregates in aqueous media; the effect of electrolyte (NaCl) on aggregation has been studied. The interaction of the dyes with albumins leads to the decomposition of the aggregates and is accompanied by a shift in the isomeric equilibrium. Complexation with HSA leads to accumulation of dye monomers in the trans-form. However, in the case of BSA the cis-to-trans isomeric shift is incomplete. Using the fluorescence data, the effective binding constants of the trans-isomers with albumins (Ka) and the detection limits of albumin molecules (LD and LQ) were determined. The data obtained are indicative of high selectivity of some dyes to HSA compared to BSA. The results of molecular docking experiments correspond to the data obtained from the spectra. The influence of the dyes on intrinsic fluorescence of HSA and BSA was also studied, and fluorescence quenching, static in nature, was detected.

Conformational preference of bicyclic β-amino acid dipeptides.

Bridged bicyclic amino acids have high potential applicability as self-organized, conformationally constrained synthetic building blocks that do not require assistance from hydrogen bond formation. We systematically investigated the intrinsic conformational propensities of dipeptides of bridged bicyclic β-amino acids by means of accelerated molecular dynamics simulation and density functional theory (DFT) calculations in methanol, chloroform, and water. While the main-chain conformation, represented by φ and θ values, is fixed by the nature of the bicyclic ring structure, rotation of the C-terminal carbonyl group (ψ) is also restricted, converging to one or two minima. In endo-type dipeptides, in which the two N- and C-terminal amides are spatially close to each other, the C-terminal amide plane is placed horizontally. In exo-type dipeptides, in which the two amides are on opposite sides of the ring plane, the C-terminal carbonyl group can take two types of positions: either parallel/antiparallel with the N-terminal carbonyl or beneath the bicyclic ring, forcing the amide NHMe moiety to lie outside of the ring. We also examined the cis-trans preference of model bicyclic amides. Although the parent amides exhibit cis-trans equilibrium without any preference, addition of a methyl group on one of the bridgehead positions tips the equilibrium towards trans.

Quantification of reaction cycle parameters for an essential molecular switch in an auxin-responsive transcription circuit in rice

Protein-based molecular switches play critical roles in biological processes. The importance of the prolyl cis-trans switch is underscored by the ubiquitous presence of peptidyl prolyl isomerases such as cyclophilins that accelerate the intrinsically slow isomerization rate. In rice, a tryptophan-proline (W-P) cis-trans switch in transcription repressor protein OsIAA11 along with its associated cyclophilin LRT2 are essential components in a negative feedback gene regulation circuit that controls lateral root initiation in response to the plant hormone auxin. Importantly, no quantitative characterizations of the individual (microscopic) thermodynamic and kinetic parameters for any cyclophilin-catalyzed W-P isomerization have been reported. Here we present NMR studies that determine and independently validate these parameters for LRT2 catalysis of the W-P motif in OsIAA11, providing predictive power for understanding the role of this switch in the auxin-responsive circuit and the resulting lateral rootless phenotype in rice. We show that the observed isomerization rate is linearly dependent on LRT2 concentration but is independent of OsIAA11 concentration over a wide range, and LRT2 is optimally tuned to maintain OsIAA11 at its cis-trans equilibrium to supply the slower downstream cis-specific proteasomal degradation with maximal OsIAA11 substrate. This indicates that accelerating the LRT2-catalyzed isomerization would not accelerate OsIAA degradation, whereas decreasing this rate via targeted mutation could reveal relationships between circuit dynamics and lateral root development. Moreover, we show that sequences flanking the highly conserved Aux/IAA W-P motif do not impact LRT2 catalysis, suggesting that the parameters determined here are broadly applicable across highly conserved cyclophilins and their Aux/IAA targets.

Application of C-Terminal 7-Azabicyclo[2.2.1]heptane to Stabilize β-Strand-like Extended Conformation of a Neighboring α-Amino Acid.

β-Strands are formed by extended linear peptide chains that are usually paired to form β-sheet structure through interstrand hydrogen bonding. Linking a structured organic molecule with α-amino acid(s) can enforce or stabilize β-strand-like extended structures of the jointed amino acids. Spectroscopic and simulation studies indicated that the presence of a C-terminal 7-azabicyclo[2.2.1]heptane amine (Abh) favors a β-strand-like extended conformation of the adjacent α-amino acid on the N side. The bridgehead substitution of the Abh unit biases the amide cis-trans equilibrium of the adjacent α-amino acid residue to cis conformation. The proximity, specified by the presence of bond paths (such as H-H bond path) between the bridgehead proton of Abh and the α-proton of the α-amino acid provides a driving force favoring the extended conformation, which is independent of solvents. These results provide a basis for de novo design of β-strand-mimicking extended peptides by using β-strand enforcer/stabilizer even in the absence of the interstrand hydrogen bonding.

Spectral and Fluorescent Studies of the Interaction of an Anionic Oxacarbocyanine Dye with Bovine Serum Albumin

The influence of the formation of noncovalent intermolecular complexes with bovine serum albumin (BSA) on the spectral and fluorescent properties of the anionic oxacarbocyanine dye 3,3′-di-(γ-sulfopropyl)-5,5′-diphenyl-9-ethyloxacarbocyanine betaine (OCC) was studied. Binding of OCC to BSA increased significantly the dye fluorescence. Changes in the absorption and fluorescence spectra of OCC upon interaction with BSA argued in favor of a shift of the dye cis–trans equilibrium in the complex. The effects of adding albumin-denaturing compounds (urea, sodium dodecyl sulfate) on the spectral and fluorescent properties of the dye in the OCC–BSA complex were studied. It was concluded that OCC can act as a probe for albumins and can be used to study protein denaturing.

UV–vis spectral study of the isomeric equilibrium for the anionic polymethine dyes – oxonols in different solvents

Absorption spectra of meso-substituted anionic polymethine dyes – oxonols were studied in solvents of different polarity. Two bands observed in the absorption spectra were shown to belong to two isomers of the dyes: trans-isomer (with a shorter-wavelength absorption band) and cis-isomer (with a longer-wavelength shoulder or band), being in equilibrium. A decrease in the solvent polarity shifts the trans-cis equilibrium toward trans-isomer for the fluoro-substituted oxonol and cis-isomer for the methyl-substituted oxonol, which can be explained by different structure of oxonol ion pairs formed in low-polarity medium. Spectral measurements at different temperatures permitted estimation of the energetic difference between the isomers.

A contribution to the coordination chemistry of (E)-N,N′-bis(2-pyridyl)iminoisoindoline (2-pyimiso): Synthesis, characterization, and DFT calculations of trans-[PtCl2(dmso-κS)(2-pyimiso-κN)

Examples of coordination entities bearing (E)-N,N′-bis(heteroaryl)iminoisoindolines are scarce in the literature. This scarcity has prompted us to investigate the coordination chemistry of (E)-N,N′-bis(2-pyridyl)iminoisoindoline (2-pyimiso), a polydentate ligand exhibiting three potentially coordinating nitrogen atoms. In this paper we report the synthesis, spectroscopic characterization and DFT calculations of trans-[PtCl2(dmso-κS)(2-pyimiso-κN)] (trans-1), which contains 2-pyimiso as a monodentate ligand. DFT calculations in the gas phase, using either B3LYP, M06 or PBE0 hybrid functionals along with the LACV3P∗∗ and LACV3P∗∗++ basis sets, have revealed that in trans-1, 2-pyimiso coordinates to Pt(II) through the 2-pyridyl group attached to the imine nitrogen atom. Solvation free energies of both cis- and trans-1 in acetonitrile were computed at the M06/LACV3P∗∗ level of calculation using the Poisson–Boltzmann solvation model. The ΔG298 value calculated for the cis–trans equilibrium of 1 in acetonitrile is −5.5kcalmol−1, which agrees with our 1H NMR data in acetonitrile-d3.

Fatty acids attached to all-trans-astaxanthin alter its cis–trans equilibrium, and consequently its stability, upon light-accelerated autoxidation

Fatty acid esterification, common in naturally occurring astaxanthin, has been suggested to influence both colour stability and degradation of all-trans-astaxanthin. Therefore, astaxanthin stability was studied as influenced by monoesterification and diesterification with palmitate. Increased esterification decelerated degradation of all-trans-astaxanthin (RP-UHPLC–PDA), whereas, it had no influence on colour loss over time (spectrophotometry). This difference might be explained by the observation that palmitate esterification influenced the cis–trans equilibrium. Free astaxanthin produced larger amounts of 9-cis isomer whereas monopalmitate esterification resulted in increased 13-cis isomerization. The molar ratios of 9-cis:13-cis after 60min were 1:1.7 (free), 1:4.8 (monopalmitate) and 1:2.6 (dipalmitate). The formation of 9-cis astaxanthin, with its higher molar extinction coefficient than that of all-trans-astaxanthin, might compensate for colour loss induced by conjugated double bond cleavage. As such, it was concluded that spectrophotometry is not an accurate measure of the degradation of the all-trans-astaxanthin molecule.

Initiation efficacy of halo-chelated cis-dichloro-configured ruthenium-based second-generation benzylidene complexes in ring-opening metathesis polymerization

The initiation efficacy of eight differently substituted halo-chelated cis-dichloro-configured ruthenium-based second-generation benzylidene complexes was assessed in the ring-opening metathesis polymerization of a norbornene derivative in two solvents and at three temperatures. From the evaluation of the number average molecular masses and the molecular mass distributions of the resulting polymers a conclusion on the level of initiation was possible and it was found that the metathesis-inactive cis-dichloro-configured pre-initiators quickly isomerize to their metathesis-active trans-dichloro isomers leading to remarkably high initiation efficiencies in toluene at 80 °C. Even controlled polymerization is feasible under these conditions. Further, the diverse initiation efficacies of the eight pre-initiators at ambient temperature are discussed with the emphasis to identify whether the position of the cis–trans equilibrium or the speed of the isomerization is responsible for the results obtained in the polymerization experiments.

A theoretical view on the thermodynamic cis–trans equilibrium of dihalo ruthenium olefin metathesis (pre-)catalysts

This work was conducted to provide an overview on the position of the thermodynamic cis–trans equilibrium of 85 conventional and X-chelated alkylidene-ruthenium complexes (X=O, S, Se, N, P, Cl, I, Br). The reported energies (ΔE) were obtained through single-point calculations with M06 functional and TZVP basis set from BP86/SVP-optimized cis- and trans-dichloro geometries and using the polarizable continuum model to simulate the influence of the solvent. Dichloromethane and toluene were selected as examples for solvents with high and low dielectric constants. The obtained relative stabilities of the cis- and trans-dihalo derivatives of the respective alkylidene complexes will serve for a better explanation of their catalytic activity as has been disclosed herein with selected examples.

Robust trans-amide helical structure of oligomers of bicyclic mimics of β-proline: impact of positional switching of bridgehead substituent on amide cis-trans equilibrium.

Because homooligomers of 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acid, a bridged β-proline analogue with a substituent installed at the remote C4-bridgehead position, completely biased the amide cis-trans equilibrium to the cis-amide structure, we expected that introduction of a substituent at the C1-bridgehead position adjacent to the carboxylic acid moiety, rather than the remote C4-bridgehead position, would tip the cis-trans amide equilibrium toward trans-amide structure without the aid of hydrogen bonding. Thus, in this work we established an efficient synthetic route to an optically active bicyclic analogue of 1,1-disubstituted β-proline, bearing a substituent at the C1-bridgehead position. Crystallographic, spectroscopic, and computational studies showed that indeed oligomers of this analogue take a consistent helical structure involving all-trans-amide linkages, independently of the number of residues, from the dimer up to the octamer. Oligomers composed of (R)-β-amino acid units form an extended left-handed helix with about 2.7 residues per turn and an approximately 4.0 Å rise per residue, characterized by complete lack of main-chain hydrogen bonding. This unique helical structure shows some similarity in shape to the trans-amide-based polyproline II (PPII) helix. The present helix was stable in various kinds of solvents such as alcohols. The present work provided a fundamental structural basis for future applications.

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly.

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m's stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition--incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein--modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation.

Conformational Diversity in Contryphans from Conus Venom: cis–trans Isomerisation and Aromatic/Proline Interactions in the 23‐Membered Ring of a 7‐Residue Peptide Disulfide Loop

Conformational diversity or "shapeshifting" in cyclic peptide natural products can, in principle, confer a single molecular entity with the property of binding to multiple receptors. Conformational equilibria have been probed in the contryphans, which are peptides derived from Conus venom possessing a 23-membered cyclic disulfide moiety. The natural sequences derived from Conus inscriptus, GCV(D)LYPWC* (In936) and Conus loroisii, GCP(D)WDPWC* (Lo959) differ in the number of proline residues within the macrocyclic ring. Structural characterisation of distinct conformational states arising from cis-trans equilibria about Xxx-Pro bonds is reported. Isomerisation about the C2-P3 bond is observed in the case of Lo959 and about the Y5-P6 bond in In936. Evidence is presented for as many as four distinct species in the case of the synthetic analogue V3P In936. The Tyr-Pro-Trp segment in In936 is characterised by distinct sidechain orientations as a consequence of aromatic/proline interactions as evidenced by specific sidechain-sidechain nuclear Overhauser effects and ring current shifted proton chemical shifts. Molecular dynamics simulations suggest that Tyr5 and Trp7 sidechain conformations are correlated and depend on the geometry of the Xxx-Pro bond. Thermodynamic parameters are derived for the cis↔trans equilibrium for In936. Studies on synthetic analogues provide insights into the role of sequence effects in modulating isomerisation about Xxx-Pro bonds.

Study of cis-trans equilibrium of oxacarbocyanine dyes in solution and in a complex with DNA

Cis-trans equilibrium for a number of meso-substituted oxacarbocyanine dyes, 3,3′-diethyloxacarbocyanine iodide (K1), 3,3′-diethyl-9-methyloxacarbocyanine iodide (K2), 3,3′-dimethyl-9-ethyloxacarbocyanine iodide (K3), 3,3′,9-triethyl-6,6′-dimethoxyoxacarbocyanine iodide (K4), and 3,3′,9-triethyl-5,5′-dimethyloxacarbocyanine iodide (K5), has been studied in solutions and in a complex with DNA by spectral and fluorescent methods. A shift of the cis-trans isomer equilibrium toward the formation of the trans-isomer was observed in the presence of DNA, which determined in many respects the spectral effects observed upon the complexation of the oxacarbocyanine dyes. A steep rise of fluorescence (due to binding of the trans-isomer) in a complex with DNA is favorable for using oxacarbocyanine dyes to determine DNA.

Water-Stable Helical Structure of Tertiary Amides of Bicyclic β-Amino Acid Bearing 7-Azabicyclo[2.2.1]heptane. Full Control of Amide Cis−Trans Equilibrium by Bridgehead Substitution

Helical structures of oligomers of non-natural β-amino acids are significantly stabilized by intramolecular hydrogen bonding between main-chain amide moieties in many cases, but the structures are generally susceptible to the environment; that is, helices may unfold in protic solvents such as water. For the generation of non-hydrogen-bonded ordered structures of amides (tertiary amides in most cases), control of cis-trans isomerization is crucial, even though there is only a small sterical difference with respect to cis and trans orientations. We have established methods for synthesis of conformationally constrained β-proline mimics, that is, bridgehead-substituted 7-azabicyclo[2.2.1]heptane-2-endo-carboxylic acids. Our crystallographic, 1D- and 2D-NMR, and CD spectroscopic studies in solution revealed that a bridgehead methoxymethyl substituent completely biased the cis-trans equilibrium to the cis-amide structure along the main chain, and helical structures based on the cis-amide linkage were generated independently of the number of residues, from the minimalist dimer through the tetramer, hexamer, and up to the octamer, and irrespective of the solvent (e.g., water, alcohol, halogenated solvents, and cyclohexane). Generality of the control of the amide equilibrium by bridgehead substitution was also examined.

Capture of the [Mo3S4]4+ Cluster within a {Mo18} Macrocycle Yielding a Supramolecular Assembly Stabilized by a Dynamic H-Bond Network

The use of the [Mo(3)S(4)(Hnta)(3)](2-) complex (nta(3-) = nitrilotriacetate) as structuring agent toward the self-condensation process of the [Mo(2)O(2)S(2)(OH(2))(6)](2+) cation leads to the largest oxothiomolybdenum ring. In the solid state, X-ray diffraction analysis reveals the presence of the targeted molecular compound (noted 1a), which consists of the {Mo(18)O(18)S(18)(OH)(18)} host templated by the [Mo(3)S(4)(Hnta)(3)](2-) guest. Nevertheless, the structure shows an additional molecular moiety corresponding to a dinuclear unit {Mo(2)O(2)S(2)} coordinated to two nta(3-) ligands, mutually arranged in a cis fashion (1b). In the solid state, both entities interact through two short hydrogen bonds to give a striking supramolecular adduct, noted {1a-1b}. Synthetic procedures to prepare the individual species as pure compounds were reported. 1a was obtained as a pure mixed Cs(+)/NMe(4)(+) salt while the dinuclear unit [Mo(2)O(2)S(2)(Hnta)(2)](2-) was obtained as mixed K(+)/Na(+) crystals. X-ray diffraction study of the latter reveals a trans isomer (noted 1b'), characterized by the specific coordination of both nta(3-) ligands. All the compounds were characterized in solution (D(2)O or DMSO) by multiexperiment (1)H NMR (1D, COSY, NOESY, and DOSY). The overall results were consistent with the retention of the adduct {1a-1b} which exhibits a supramolecular reactivity. The dinuclear individual species in solution gave rise to cis-trans equilibrium, while in the presence of the oxothiomolybdenum ring 1a, the dinuclear unit is maintained as a frozen cis complex. DOSY NMR provides a definitive argument for the integrity of the supramolecular assembly. In addition, preliminary electrochemical study of 1a is also reported.

Spectral and fluorescent study of the interaction of anionic cyanine dyes with serum albumins

The noncovalent interaction of two anionic cyanine dyes with human and bovine serum albumins was studied by spectral and fluorescent methods. Upon the interaction with albumins, a growth of fluorescence and, in most cases, a long-wavelength shift of the dye absorption band are observed. For the meso-substituted cyanine dye 3,3′-di-(γ-sulfopropyl)-9-methylthiacarbocyanine betaine (K1), a mobile cis-trans equilibrium is observed: the dye in the free state occurs mainly as the cis-isomer, whereas in the complex with albumins the equilibrium is shifted toward the trans-isomer (this shift is greater for human albumin). Dye K1 is recommended as a spectral and fluorescent probe for serum albumins.

Effect of neutral salts and methylglyoxal on the cis-trans equilibrium of n-methylacetamide. A 13-carbon nuclear magnetic resonance study

Cis-trans isomers of N-methylacetamide were observed by using 13C nuclear magnetic resonance spectroscopy. The addition of neutral salts altered the isomer ratio favoring the cis form. The salt-induced cis isomerization is reversible and depends on salt concentration. Methylglyoxal added to N-methylacetamide formed a stable cis isomer. It is proposed that concentrated salts and methylglyoxal, by binding to the peptide bond, affect the properties of proteins.