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In this study, we evaluated the cis/trans-lycopene content in commercial ketchup, and investigated the effect of cooking of fermented tomato sour soup added with one of seven oils including peanut oil (PO), sesame oil (SO), corn oil (CO), tung seed oil (TSO), olive oil (OO), Litsea cubeba oil (LCO), and mustard oil (MO) on lycopene isomerization. The results showed significant differences in the contents of total lycopene and cis-lycopene among six brands of ketchup (P < 0.05), with cis-lycopene accounting for only 20.84%-24.56% of the total lycopene. The contents of total lycopene and cis-lycopene were significantly different among the seven cooked fermented tomato sour soup samples (P < 0.05), and their proportions of cis-isomers (51.40%-78.23%) were 1.2-1.9 times higher than that of the blank group and 2.09-3.75 times higher than those of the six brands of ketchup. Specifically, the sample with added MO had the highest proportion of cis-lycopene (78.23%), followed by those with SO and PO (75.34% and 71.65%, respectively). The total lycopene and cis-lycopene contents of the sample with added PO were 6.6 and 11.4 times higher than those of the blank control group, respectively, indicating that the former has great market potential. Therefore, the results of this study could provide a scientific basis for the further processing of fermented tomato sour soup for high-value functional products.

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The cis/trans isomerization of peptidyl‐prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4‐substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4‐thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half‐life of the refolding reaction decreased from ~2 h to ~35 s. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild‐type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the CγH2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment. [ABSTRACT FROM AUTHOR]

Porphyrin compound-based photochemical molecules and biomaterials have been synthesized for photosensitivity and bioimaging experiments. However, most porphyrin photosensitizers have limited application in biological environments owing to severe aggregation in aqueous solutions. In the present study, we prepared amphipathic and photosensitive copolymers using zinc porphyrin via consecutive atom transfer-free radical polymerizations (ATRPs) comprising photoresponsive and thermosensitive chain segments. Furthermore, we evaluated the photocatalytic activity of the copolymer for methylene blue (MB) in water.Methods: First, we synthesized a photoresponsive ain segment of poly (6-[4-(4-methoxyphenylazo)phenoxy]hexyl methacrylate) (ZnPor-PAzo); then, ZnPor-PAzo was used as a macroinitiator and was polymerized with N-isopropylacrylamide (NIPAM) via ATRPs to obtain a novel photochemical and thermoresponsive diblock biomaterial with end-functionalized zinc porphyrin [(ZnPor-PAzo)–PNIPAMs].Results: The polydispersity index (Mw/Mn) of (ZnPor-PAzo)–PNIPAMs was 1.19–1.32. Furthermore, its photoresponsive and thermosensitive characteristics were comprehensively studied.Discussion: The end-functionalized diblock copolymer (ZnPor-PAzo)–PNIPAM exhibits obvious fluorescence and efficient photocatalytic activity for aqueous MB under visible light.

Reactions of isocyanates/isothiocyanates with primary and secondary phosphines without solvent at room temperature afforded phosphinecarboxamide/phosphinecarbothioamide, respectively, in excellent yields. Furthermore, palladium complex Pd(COD)Cl2 was allowed to react with Ph2PC(O)NHPh (1a) to afford [Pd{Ph2PC(O)NHPh-κP}2Cl2] (3). On the other hand, the reaction of Pd(COD)Cl2 with 1 eq. of Ph2PC(S)NHPh (2a) afforded [PdCl2{Ph2PC(S)NHPh-κP,S}] (4). In the case of a 1:2 molar ratio, [PdCl{Ph2PC(S)NHPh-κP,S}{Ph2PC(S)NHPh-κP}]Cl (5) was formed. The newly obtained compounds were fully characterized using multielement NMR measurements and elemental analyses. In addition, the molecular structures of Ph2PC(O)NH(CH2)2Cl (1j), Ph2PC(S)NHPh(4-Cl) (2c), and 3–5 were determined using single-crystal X-ray diffraction. [ABSTRACT FROM AUTHOR]

Background: Intrinsically disordered proteins and protein regions (IDPs/IDRs) are important in diverse biological processes. Lacking a stable secondary structure, they display an ensemble of conformations. One factor contributing to this conformational heterogeneity is the proline cis/trans isomerization. The knowledge and value of a given cis/trans proline ratio are paramount, as the different conformational states can be responsible for different biological functions. Nuclear Magnetic Resonance (NMR) spectroscopy is the only method to characterize the two co-existing isomers on an atomic level, and only a few works report on these data. Methods: After collecting the available experimental literature findings, we conducted a statistical analysis regarding the influence of the neighboring amino acid types (i ± 4 regions) on forming a cis-Pro isomer. Based on this, several regularities were formulated. NMR spectroscopy was then used to define the cis-Pro content on model peptides and desired point mutations. Results: Analysis of NMR spectra prove the dependence of the cis-Pro content on the type of the neighboring amino acid—with special attention on aromatic and positively charged sidechains. Conclusions: Our results may benefit the design of protein regions with a given cis-Pro content, and contribute to a better understanding of the roles and functions of IDPs.

Cytochrome c -type cis / trans fatty acid isomerase (CTI) has been proposed to control cis / trans isomerism of unsaturated fats in lipid-related food products. A gene encoding wildtype CTI from Pseudomonas putida KT2440 was introduced into the pET26b/pEC86 co-expression system, and the heme C cofactor was covalently bound into the expressed CTI protein through in vivo cytochrome c maturation. The recombinant CTI, purified from Escherichia coli BL21(DE3), catalyzed the cis / trans isomerization of three edible monounsaturated fatty acids. It exhibited strong substrate selectivity for palmitoleic acid (C 16:1 , cis -Δ9), reaching an 80.93 ± 1.78% conversion at reaction equilibrium. Notably, its promiscuity for other fatty acids (oleic acid: 29.21 ± 5.01% and cis -vaccenic acid: 51.21 ± 0.05%) was observed. Under the optimum reaction conditions (pH 7.5 and 15 °C), the kinetic parameters (V max , K m , and k cat) of CTI were derived as 0.035 mM min−1, 0.267 mM, and 0.141 sec−1, respectively, and the final catalytic efficiency (k cat /K m) was calculated as 5.26 × 102 M−1 s−1. Furthermore, structural properties of CTI were analyzed using deep learning-based protein structure prediction, suggesting the potential for specificity variability by altering loop dynamics and helix interactions surrounding the heme-binding motif. The following results would provide theoretical and practical information for CTI enzymes as novel promising industrial catalysts to control cis / trans isomerism of lipids in food products. [Display omitted] • Cis / trans fatty acid isomerase (CTI) is a bacterial cytochrome c -type hemoprotein. • The recombinant CTI was expressed in the pET26b/pEC86 co-expression system. • The recombinant CTI showed substrate promiscuity towards unsaturated fatty acids. • The recombinant CTI showed strong substrate selectivity against palmitoleic acid. • Deep learning-based structural prediction demonstrated the mode of action of CTI. [ABSTRACT FROM AUTHOR]

Reactions of isocyanates/isothiocyanates with primary and secondary phosphines without solvent at room temperature afforded phosphinecarboxamide/phosphinecarbothioamide, respectively, in excellent yields. Furthermore, palladium complex Pd(COD)Cl2 was allowed to react with Ph2PC(O)NHPh (1a) to afford [Pd{Ph2PC(O)NHPh-κP}2Cl2] (3). On the other hand, the reaction of Pd(COD)Cl2 with 1 eq. of Ph2PC(S)NHPh (2a) afforded [PdCl2{Ph2PC(S)NHPh-κP,S}] (4). In the case of a 1:2 molar ratio, [PdCl{Ph2PC(S)NHPh-κP,S}{Ph2PC(S)NHPh-κP}]Cl (5) was formed. The newly obtained compounds were fully characterized using multielement NMR measurements and elemental analyses. In addition, the molecular structures of Ph2PC(O)NH(CH2)2Cl (1j), Ph2PC(S)NHPh(4-Cl) (2c), and 3–5 were determined using single-crystal X-ray diffraction.

Strigolactones and abscisic acid (ABA) are apocarotenoid-derived plant hormones. Their biosynthesis starts with the conversion of trans-carotenes into cis forms, which serve as direct precursors. Iron-containing DWARF27 isomerases were shown to catalyse or contribute to the trans/cis conversions of these precursor molecules. D27 converts trans-β-carotene into 9-cis-β-carotene, which is the first committed step in strigolactone biosynthesis. Recent studies found that its paralogue, D27-LIKE1, also catalyses this conversion. A crucial step in ABA biosynthesis is the oxidative cleavage of 9-cis-violaxanthin and/or 9-cis-neoxanthin, which are formed from their trans isomers by unknown isomerases. Several lines of evidence point out that D27-like proteins directly or indirectly contribute to 9-cis-violaxanthin conversion, and eventually ABA biosynthesis. Apparently, the diversity of D27-like enzymatic activity is essential for the optimization of cis/trans ratios, and hence act to maintain apocarotenoid precursor pools. In this review, we discuss the functional divergence and redundancy of D27 paralogues and their potential direct contribution to ABA precursor biosynthesis. We provide updates on their gene expression regulation and alleged Fe-S cluster binding feature. Finally, we conclude that the functional divergence of these paralogues is not fully understood and we provide an outlook on potential directions in research., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

The cis/trans isomerization of peptidyl-prolyl peptide bonds is often the bottleneck of the refolding reaction for proteins containing cis proline residues in the native state. Proline (Pro) analogues, especially C4-substituted fluoroprolines, have been widely used in protein engineering to enhance the thermodynamic stability of peptides and proteins and to investigate folding kinetics. 4-thiaproline (Thp) has been shown to bias the ring pucker of Pro, to increase the cis population percentage of model peptides in comparison to Pro, and to diminish the activation energy barrier for the cis/trans isomerization reaction. Despite its intriguing properties, Thp has been seldom incorporated into proteins. Moreover, the impact of Thp on the folding kinetics of globular proteins has never been reported. In this study, we show that upon incorporation of Thp at cisPro76 into the thioredoxin variant Trx1P the half-life of the refolding reaction decreased from ~2 h to ~35 s. A dramatic acceleration of the refolding rate could be observed also for the protein pseudo wild-type barstar upon replacement of cisPro48 with Thp. Quantum chemical calculations suggested that the replacement of the C γ H 2 group by a sulfur atom in the pyrrolidine ring, might lower the barrier for cis/trans rotation due to a weakened peptide bond. The protein variants retained their thermodynamic stability upon incorporation of Thp, while the catalytic and enzymatic activities of the modified Trx1P remained unchanged. Our results show that the Pro isostere Thp might accelerate the rate of the slow refolding reaction for proteins containing cis proline residues in the native state, independent from the local structural environment., (© 2023 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Porphyrin compound-based photochemical molecules and biomaterials have been synthesized for photosensitivity and bioimaging experiments. However, most porphyrin photosensitizers have limited application in biological environments owing to severe aggregation in aqueous solutions. In the present study, we prepared amphipathic and photosensitive copolymers using zinc porphyrin via consecutive atom transfer-free radical polymerizations (ATRPs) comprising photoresponsive and thermosensitive chain segments. Furthermore, we evaluated the photocatalytic activity of the copolymer for methylene blue (MB) in water. Methods: First, we synthesized a photoresponsive ain segment of poly (6-[4-(4-methoxyphenylazo)phenoxy]hexyl methacrylate) (ZnPor-PAzo); then, ZnPor-PAzo was used as a macroinitiator and was polymerized with N -isopropylacrylamide (NIPAM) via ATRPs to obtain a novel photochemical and thermoresponsive diblock biomaterial with end-functionalized zinc porphyrin [(ZnPor-PAzo)-PNIPAMs]. Results: The polydispersity index ( M w / M n ) of (ZnPor-PAzo)-PNIPAMs was 1.19-1.32. Furthermore, its photoresponsive and thermosensitive characteristics were comprehensively studied. Discussion: The end-functionalized diblock copolymer (ZnPor-PAzo)-PNIPAM exhibits obvious fluorescence and efficient photocatalytic activity for aqueous MB under visible light., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Qiu, Pan, Hu and Hui.)

Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less wellexamined homolog human Par14/17 with respect to structure, catalytic and cellular function. [ABSTRACT FROM AUTHOR]

trans-Resveratrol was evaluated in a stability study. Reverse-phase high-performance liquid chromatography with a diode array detector was used for the comparison of stressed and reference samples. Aqueous ethanolic solutions were examined under variable conditions. The following parameters were investigated: the time of storage, exposure to sunlight for up to 30 days, temperature from 5 to 80°C, pH from 2.9 to 10.2, trans-resveratrol concentrations from 0.5 to 100 mg L−1, and 3, 10, 20, and 50% ethanol. The cis/trans equilibrium position was significantly influenced by the resveratrol concentration. The trans-resveratrol isomer was stable only at solutions more concentrated than 25 mg L−1that were stable for 30 days in a refrigerator or at room temperature protected from light. Degradation of no more than 10% was observed at temperatures lower than 50°C and pH values lower 7.43. [ABSTRACT FROM PUBLISHER]

Background: Intrinsically disordered proteins and protein regions (IDPs/IDRs) are important in diverse biological processes. Lacking a stable secondary structure, they display an ensemble of conformations. One factor contributing to this conformational heterogeneity is the proline cis/trans isomerization. The knowledge and value of a given cis/trans proline ratio are paramount, as the different conformational states can be responsible for different biological functions. Nuclear Magnetic Resonance (NMR) spectroscopy is the only method to characterize the two co-existing isomers on an atomic level, and only a few works report on these data., Methods: After collecting the available experimental literature findings, we conducted a statistical analysis regarding the influence of the neighboring amino acid types ( i ± 4 regions) on forming a cis -Pro isomer. Based on this, several regularities were formulated. NMR spectroscopy was then used to define the cis- Pro content on model peptides and desired point mutations., Results: Analysis of NMR spectra prove the dependence of the cis- Pro content on the type of the neighboring amino acid-with special attention on aromatic and positively charged sidechains., Conclusions: Our results may benefit the design of protein regions with a given cis -Pro content, and contribute to a better understanding of the roles and functions of IDPs., Competing Interests: The authors declare no conflict of interest., (© 2023 The Author(s). Published by IMR Press.)

The default explanation for good to high diastereomeric excess when reducing N-chiral imines possessing only mediocre cis/trans-imine ratios (>15% cis-imine) has invariably been in situ cis-to-trans isomerization before reduction; but until now no study unequivocally supported this conclusion. The present study co-examines an alternative hypothesis, namely that some classes of cis-imines may hold conformations that erode the inherent facial bias of the chiral auxiliary, providing more of the trans-imine reduction product than would otherwise be expected. The ensuing experimental and computational (DFT) results favor the former, pre-existing, explanation.

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry.

Urea derivatives are ubiquitously found in many chemical disciplines. N, N′-substituted ureas may show different conformational preferences depending on their substitution pattern. The high energetic barrier for isomerization of the cis and trans state poses additional challenges on computational simulation techniques aiming at a reproduction of the biological properties of urea derivatives. Herein, we investigate energetics of urea conformations and their interconversion using a broad spectrum of methodologies ranging from data mining, via quantum chemistry to molecular dynamics simulation and free energy calculations. We find that the inversion of urea conformations is inherently slow and beyond the time scale of typical simulation protocols. Therefore, extra care needs to be taken by computational chemists to work with appropriate model systems. We find that both knowledge-driven approaches as well as physics-based methods may guide molecular modelers towards accurate starting structures for expensive calculations to ensure that conformations of urea derivatives are modeled as adequately as possible. [ABSTRACT FROM AUTHOR]

ABSTRACT Self-association of proteins can be triggered by a change in the distribution of the conformational ensemble. Posttranslational modification, such as phosphorylation, can induce a shift in the ensemble of conformations. In the brain of Alzheimer's disease patients, the formation of intra-cellular neurofibrillary tangles deposition is a result of self-aggregation of hyper-phosphorylated tau protein. Biochemical and NMR studies suggest that the cis peptidyl prolyl conformation of a phosphorylated threonine-proline motif in the tau protein renders tau more prone to aggregation than the trans isomer. However, little is known about the role of peptidyl prolyl cis/trans isomerization in tau aggregation. Here, we show that intra-molecular electrostatic interactions are better formed in the trans isomer. We explore the conformational landscape of the tau segment containing the phosphorylated-Thr231-Pro232 motif using accelerated molecular dynamics and show that intra-molecular electrostatic interactions are coupled to the isomeric state of the peptidyl prolyl bond. Our results suggest that the loss of intra-molecular interactions and the more restricted conformational ensemble of the cis isomer could favor self-aggregation. The results are consistent with experiments, providing valuable complementary atomistic insights and a hypothetical model for isomer specific aggregation of the tau protein. Proteins 2015; 83:436-444. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Abstract: The preparation of six phenylphosphonates (and phosphonic acid derivatives) bearing a sulfur group in ortho position was accomplished via either a [1,3]- or a [1,4]-sigmatropic rearrangement. Their complexation with different platinum sources has been studied and the new platinum complexes obtained were characterized by NMR spectroscopy (1H, 13C, 31P and 195Pt). Three runs of experiments were performed. The first was the reaction of ligands 1 and 2 bearing one sulfide and a phosphonate diester functions with potassium tetrachloroplatinate. In the obtained complexes, two molecules of ligand chelate the metal only by the sulfur atom. We were able to observe by 195Pt and 31P NMR spectroscopy the trans to cis rearrangement of a dichloro-methyl-(o-phosphorylbenzyl)sulfide platinum(II) complex upon time, leading to two new species, which are diastereomers of the cis-complex. The second set of experiments involved ligands 1, 2 and 3 bearing one sulfide or sulfoxide and a phosphonate diester moieties, cisplatin and one equivalent of silver nitrate. In the resulting complexes the platinum is coordinated by the sulfur atom of one molecule of ligand. In the third run, the reaction between ligands 4, 5, and 6 bearing one sulfide or sulfoxide and one phosphonic acid or one phosphonic monoester group and the cisplatin diaqua form led to O,S–Pt chelates. [Copyright &y& Elsevier]

Enthalpies (Δ H), Gibbs free energies (Δ G), and equilibrium constants (log K) for the trans → cis isomerization of various 3,3′-, 4,4′-, and 5,5′- disubstituted 2,2′-diphenoquinones with a range of electron withdrawing and releasing moieties (methyl, fluoro, chloro, bromo, trifluoromethyl, and amino) were calculated in the gas phase and in the solvent phase ( n-hexane, benzene, n-octanol, acetonitrile, and water). In the gas phase, the trans isomer of the parent and all substituted 2,2′-diphenoquinones is predicted to be more thermodynamically stable than the cis configuration, with log K ranging from −2.8 to −7.0. For all compounds, increasing solvent polarity/proticity progressively favors shifting the cis/ trans equilibrium towards greater contributions of the cis configuration and substantially increases the log K by up to 5.1 units relative to the gas phase. In polar protic and polar aprotic solvents, the estimated log K ranges as low as −0.4, indicating significant populations of the cis isomers should be present. The findings support the polar solvent phase mechanistic predictions for a cis configuration of 2,2′-diphenoquinones participating in the thermal transformation of trans-2,2′-diphenoquinones to oxepino[2,3-b]benzofurans. With limited exceptions for some amino derivatives, the cis-2,2′-diphenoquinone to oxepino[2,3-b]benzofuran isomerization is expected to be thermodynamically favorable for all substituents/phases under consideration. The cis-2,2′-diphenoquinone to oxepino[2,3-b]benzofuran rearrangement is predicted to become less thermodynamically favored with increasing solvent polarity/proticity. [ABSTRACT FROM AUTHOR]

Abstract: The influence of α-cis- and α-trans-polyprenols on the structure and properties of model membranes was analyzed. The interaction of Ficaprenol-12 (α-cis-Prenol-12, α-Z-Prenol-12) and Alloprenol-12 (α-trans-Prenol-12, α-E-Prenol-12) with model membranes was compared using high performance liquid chromatography (HPLC), differential scanning calorimetry (DSC) and fluorescent methods. l-α-Phosphatidylcholine from egg yolk (EYPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) as the main lipid components of unilamellar (SUVs) and multilamellar (MLVs) vesicles were used. The two-step extraction procedure (n-pentane and hexane, respectively) allowed to separately analyze the fractions of polyprenol as non-incorporated (PrenolNonInc) and incorporated (PrenolInc) into liposomes. Consequently, distribution coefficients, P′, describing the equilibrium of prenol content between phospholipid (EYPC) membrane and the aqueous phase gave different log P′ for α-cis- and α-trans-Prenol-12, indicating that the configuration of the α-terminal residue significantly alters the hydrophobicity of the polyisoprenoid molecule and consequently the affinity of polyprenols for EYPC membrane. In fluorescence experiments α-trans-Pren-12 increased up to 1.7-fold the permeability of EYPC bilayer for glucose while the effect of α-cis-Pren-12 was almost negligible. Considerable changes of thermotropic behavior of DPPC membranes in the presence of both prenol isomers were observed. α-trans-Pren-12 completely abolished the pretransition while in the case of α-cis-Pren-12 it was noticeably reduced. Furthermore, for both prenol isomers, the temperature of the main phase transition (T m ) was shifted by about 1°C to lower values and the height of the peak was significantly reduced. The DSC analysis profiles also showed a new peak at 38.7°C, which may suggest the concomitant presence of more that one phase within the membrane. Results of these experiments and the concomitant occurrence of alloprenols and ficaprenols in plant tissues suggest that cis/trans isomerization of the α-residue of polyisoprenoid molecule might comprise a putative mechanism responsible for modulation of the permeability of cellular membranes. [Copyright &y& Elsevier]

Abstract: The SlyD (sensitive to lysis D) protein of Escherichia coli is a folding enzyme with a chaperone domain and a prolyl isomerase domain of the FK506 binding protein type. Here we investigated how the two domains and their interplay are optimized for function in protein folding. Unfolded protein molecules initially form a highly dynamic complex with the chaperone domain of SlyD, and they are then transferred to the prolyl isomerase domain. The turnover number of the prolyl isomerase site is very high and guarantees that, after transfer, prolyl peptide bonds in substrate proteins are isomerized very rapidly. The Michaelis constant of catalyzed folding reflects the substrate affinity of the chaperone domain, and the turnover number is presumably determined by the rate of productive substrate transfer from the chaperone to the prolyl isomerase site and by the intrinsic propensity of the refolding protein chain to leave the active site with the native prolyl isomer. The efficiency of substrate transfer is high because dissociation from the chaperone site is very fast and because the two sites are close to each other. Protein molecules that left the prolyl isomerase site with an incorrect prolyl isomer can rapidly be re-bound by the chaperone domain because the association rate is very high as well. [Copyright &y& Elsevier]

Abstract: In protein structures the peptide bond is found to be in trans conformation in the majority of the cases. Only a small fraction of peptide bonds in proteins is reported to be in cis conformation. Most of these instances (>90%) occur when the peptide bond is an imide (X-Pro) rather than an amide bond (X-nonPro). Due to the implication of cis/trans isomerization in many biologically significant processes, the accurate prediction of the peptide bond conformation is of high interest. In this study, we evaluate the effect of a wide range of features, towards the reliable prediction of both proline and non-proline cis/trans isomerization. We use evolutionary profiles, secondary structure information, real-valued solvent accessibility predictions for each amino acid and the physicochemical properties of the surrounding residues. We also explore the predictive impact of a modified feature vector, which consists of condensed position-specific scoring matrices (PSSMX), secondary structure and solvent accessibility. The best discriminating ability is achieved using the first feature vector combined with a wrapper feature selection algorithm and a support vector machine (SVM). The proposed method results in 70% accuracy, 75% sensitivity and 71% positive predictive value (PPV) in the prediction of the peptide bond conformation between any two amino acids. The output of the feature selection stage is investigated in order to identify discriminatory features as well as the contribution of each neighboring residue in the formation of the peptide bond, thus, advancing our knowledge towards cis/trans isomerization. [Copyright &y& Elsevier]

• Contents of trans fatty acids in oils was determined by 1H NMR spectroscopy in association with multivariate calibration. • The 1H NMR spectra of edible and cis-trans isomerized oils are different in three chemical shift regions. • The difference of the 1H NMR spectra of cis and tans unsaturated fatty acids was analyzed. • The PLS method were successfully applied to predict the contents of unsaturated fatty acids in oils. In this work, cis and trans fatty acid (FA) contents in edible oils was determined using 1H nuclear magnetic resonance (1H NMR) spectroscopy. The comparison of 1H NMR spectra of edible oil and cis-trans isomerized oil showed that they were different in three regions: (1) 2.880 - 2.650 ppm caused by bis-allylic protons; (2) 2.140 - 1.900 ppm due to allylic protons; and (3) 1.030 - 0.930 ppm due to methyl protons of linolenic acyl groups. The 1H NMR signals in these regions were combined with partial least squares method to predict contents of cis/trans fatty acids in edible oils. The results showed that the predicted values were consistent with the gas chromatography-measured values and had a good linear relationship with a correlation coefficient (R2) of above 0.98. This work demonstrates that 1H NMR spectroscopy was successfully used to determine the composition of both cis and trans fatty acids in edible oils. [ABSTRACT FROM AUTHOR]

Bacillus sp. ORAs2 and Pseudomonas sp. ORAs5, two arsenic-resistant bacterial strains previously isolated from sediments of the Orbetello Lagoon, Italy, were tested for their adaptation to mixed contaminants on the level of membrane fatty acid composition. The two bacterial strains were characterized by high levels of arsenic resistance, and Pseudomonas sp. ORAs5 was also shown to be solvent-tolerant. The bacterial strains were exposed to mixtures of two toxic compounds: arsenic at fixed concentrations and toluene in variable amounts or, alternatively, toluene at constant values along with arsenic added at variable concentrations. Both strains react to the contaminants by changing the composition of their membrane fatty acids. Bacillus sp. strain ORAs2 showed a correlation between growth rate decreases and fatty acids degree of saturation increases in both cases, although pointedly in the presence of 1, 2, and 3 mM of toluene and different additions of arsenic, counteracting membranes fluidity induced by toxic compounds. In Pseudomonas sp. ORAs5, adaptive changes in membrane composition was observed both in terms of increases in the degree of saturation and in the trans/ cis ratio of unsaturated fatty acids in the presence of varying toluene and constant arsenic concentrations, whereas only minor changes occurred with increasing arsenic and constant toluene concentrations. Thus, on the level of membrane composition, Bacillus sp. ORAs2 showed a higher potential for adaptation to the presence of mixed pollutants, suggesting its probable suitability for bioremediation purposes. [ABSTRACT FROM AUTHOR]

Abstract: The peptide bond preceding proline residues realizes a cis/trans conformational switch with high switching resistance in native proteins and folding intermediates. Therefore, individual isomers have the potential to differ in bioactivity. However, information about isomer-specific bioactivities is difficult to obtain because of the risk of affecting isomeric distribution by bioactivity assay components. Here we present an approach that allows for the measurement of the recovery of enzymatic activities of wild-type RNase T1 and RNase T1 variants during refolding under conditions where the population of enzyme–substrate or enzyme–product complexes is negligible. Recovery of enzymatic activity was continuously monitored within the visible range of the spectrum by addition of a fluorescence-labeled nucleotide substrate to the refolding sample. We found that a nonnative trans conformation at Pro39 renders the RNase T1 almost completely inactive. A folding intermediate having a nonnative trans conformation at Pro55 shows about 46% of the enzymatic activity referred to the native state. Pro55, in contrast to the active site located Pro39, is situated in a solvent-exposed loop region remote from active-site residues. In both cases, peptidyl prolyl cis/trans isomerases accelerate the regain of nucleolytic activity. Our findings show that even if there is a considerable distance between the site of isomerization and the active site, conformational control of the bioactivity of proteins is likely to occur, and that the surface location of prolyl bonds suffices for the control of buried active sites mediated by peptidyl prolyl cis/trans isomerases. [Copyright &y& Elsevier]

Abstract: In a previous paper, we demonstrated that tissue trans fatty acids can not only derive from the diet but also be endogenously formed. The central focus of this study was to prove that the in vivo isomerization occurs via a radical process. Two different models of radical insult were used: CCl4 and AAPH injection to rats fed a diet completely free of trans isomers. Following this acute radical stress, a significant increase in unnatural trans fatty acid content of erythrocyte, kidney, and heart, but not liver, was observed. These results can be mainly explained by the high content, particularly in the liver, of antioxidant vitamins A and E that exhibit also an “anti-isomerizing” effect. Since during ageing cellular components are exposed to increasing radical insults, the observation of a significant trans fatty acid accumulation in 30-month-old rats could confirm that the in vivo formation of unnatural isomers is due to a radical process. Trans fatty acids can influence the physical characteristics of bilayer microdomains, affecting membrane properties and functions; thus, knowledge of biological radical species responsible for cis/trans isomerization and their possible sources can provide protective systems for preserving lipid geometry. [Copyright &y& Elsevier]

Cis/trans isomerization of peptide C&bond;N bonds is involved in the configurational changes and are definitive for the bioactivity of peptides and proteins. The basic molecular character and origin of the restricted rotation of the peptide C&bond;N bonds are briefly introduced, as well as the methods used for study of the cis/trans isomerization, such as the chymotrypsin-coupled assay, pH-mediated solvent jump, and UV-resonance Raman spectroscopy, etc. The control of the peptide bond configuration with photoresponsive (photochromic) groups such as azobenzene or thioamide bonds is also reviewed. Copyright © 2007 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Abstract: The kinetics of Z-(cis)/E-(trans) isomerization of enalapril was investigated by reversed phase high-performance liquid chromatography (RP-HPLC) using a monolith ODS column under a series of different temperature and pH conditions. At a neutral pH 7, the rate (k obs) of Z-(cis)/E-(trans) isomerization of enalapril at 4°C (9.4×10−3 min−1) is much lower than at 23°C (1.8×10−1 min−1), while the fractional concentration of Z-(cis) isomer is always higher than that of E-(trans) isomer in the pH range 2–7. The fractional concentration of the E-(trans) isomer becomes a maximum (about 40%) in the pH range 3–6, where enalapril exists as a zwitterion. The hydrophobicity (log P O/W) of both isomers was estimated by high-speed counter-current chromatography (HSCCC). Normal phase HSCCC separation using a tert-butyl methyl ether–acetonitrile–20mM potassium phosphate buffer (pH 5) two-phase solvent system (2:2:3, v/v/v) at 4°C was effective in partially separating the isomers, and the partition coefficient (K) of each isomer was directly calculated from the retention volume (V R). The log P O/W values of Z-(cis) and E-(trans) isomers were −0.46 and −0.65, respectively. [Copyright &y& Elsevier]

Model tetrapeptide system was designed to investigate the cis/trans isomerization of peptidyl-prolyl imide bond of Ser-Pro motif. To establish the side-chain O-phosphorylation effect in regulating the peptides conformations, molecular dynamics (MD) simulations where carried out on the designed tetrapeptides and their corresponding phosphorylated forms by MD Insight II Discovery3 approach. The most stable configurations and the statistic cis/trans concentration distribution demonstrated that the phosphorylation evidently influences the peptidyl-prolyl imide bond isomerization and works as a key effect in regulating the peptide conformations. The charge state and the site provided for the charge of the phosphate moiety might be an important key. The results also demonstrated that phosphorylation changes the cis conformation ratio of the peptide and the maximum cis value is obtained when the phosphate group has no negative charge. [ABSTRACT FROM AUTHOR]

Abstract: Trans isomers of unsaturated fatty acids are absorbed from the diet, due to their presence in diary fat and hydrogenated vegetable oils, and health concern has risen due to their effects on lipid risk factors in cardiovascular diseases. On the basis of the efficiency of the thiyl-radical-catalyzed cis/trans isomerization in vitro and the presence of many sulfur-containing compounds in the cell, the aim of this study was to demonstrate that trans geometry of lipid double bonds can be endogenously generated within membrane phospholipids. The study reports trans fatty acids occurrence in tissue and erythrocyte phospholipids of young adult rats fed a diet completely free of trans isomers. Results show that tissues are differently prone to the endogenous isomerization and that, following a free radical attack, trans fatty acids can reach very high amounts. The effectiveness of this process is considerably inhibited in the presence of all-trans retinol, confirming previous data in model membranes. Our results suggest that geometrical isomerization of unsaturated fatty acids, which causes a structural modification of membrane lipids and may influence basic membrane properties and vital biochemical functions, can occur under radical stress conditions and could be efficiently prevented by vitamin A. [Copyright &y& Elsevier]

Non-proline cis peptide bonds have been observed in numerous protein crystal structures even though the energetic barrier to this conformation is significant and no non-prolyl-cis/trans-isomerase has been identified to date. While some external factors, such as metal binding or co-factor interaction, have been identified that appear to induce cis/trans isomerization of non-proline peptide bonds, the intrinsic structural basis for their existence and the mechanism governing cis/trans isomerization in proteins remains poorly understood. Here, we report the crystal structure of a newly isolated neurotoxin, the scorpion α-like toxin Buthus martensii Karsch (BmK) M7, at 1.4Å resolution. BmK M7 crystallizes as a dimer in which the identical non-proline peptide bond between residues 9 and 10 exists either in the cis conformation or as a mixture of cis and trans conformations in either monomer. We also determined the crystal structures of several mutants of BmK M1, a representative scorpion α-like toxin that contains an identical non-proline cis peptide bond as that observed in BmK M7, in which residues within or neighboring the cis peptide bond were altered. Substitution of an aspartic acid residue for lysine at residue 8 in the BmK M1 (K8D) mutant converted the cis form of the non-proline peptide bond 9–10 into the trans form, revealing an intramolecular switch for cis-to-trans isomerization. Cis/trans interconversion of the switch residue at position 8 appears to be sequence-dependent as the peptide bond between residues 9 and 10 retains its wild-type cis conformation in the BmK M1 (K8Q) mutant structure. The structural interconversion of the isomeric states of the BmK M1 non-proline cis peptide bond may relate to the conversion of the scorpion α-toxins subgroups. [Copyright &y& Elsevier]

Peptidyl–prolyl cis/trans isomerization, observed in the native state of an increasing number of proteins, is of considerable biological significance. The first evidence for an asymmetric transmission along the polypeptide chain of the structural effects of prolyl isomerization is now derived from the statistics of the Cα/Cα-atom distance distributions in the crystal structures of 848 non-homologous proteins. More detailed information on how isomerization affects segments adjacent to proline is obtained from crystal structures of proteins, that are more than 95% homologous, and that exhibit two different states of isomerization at a particular prolyl bond. The resulting 64 cases, which represent 3.8% of the database used, form pairs of coordinates which were analyzed for the existence of isomer-specific intramolecular nonbonded Cα/Cα-atom distances around the critical proline, and for the positional preferences for particular amino acids in the isomeric sequence segment. The probability that a native protein exhibits both prolyl isomers in the crystalline state increases in particular with a Pro at the third position N-terminal to the isomeric bond (−3 position), and with Ser, Gly and Asp at the position preceding the isomeric bond (−1 position). Structural alignment of matched pairs of isomeric proteins generates three classes with respect to position-specific distribution of Cα-atom displacements around an isomeric proline imide bond. In the majority of cases the distribution of these intermolecular isomer-specific Cα-atom distances shows a symmetric behavior for the N-terminal and C-terminal segment flanking the proline residue, and the magnitude did not exceed 1.3±0.6 A˚ including the Cα atoms in proximity to the prolyl bond. However, in the remaining 12 protein pairs the structural changes are unidirectional relative to the isomerizing bond whereby the magnitude of the isomer-specific effect exceeds 3.0±2.0 A˚ even at positions remote to proline. Interestingly, the magnitude of the intramolecular isomer-specific Cα atom displacements reveals a lever–arm amplification of the isomerization-mediated structural changes in a protein backbone. The observed backbone effects provide a structural basis for isomer-specific reactions of proline-containing polypeptides, and thus may play a role in biological recognition and regulation. [Copyright &y& Elsevier]

Catalytic hydrogenation of linoleic acid was studied on Ir/Al2O3. A detailed analysis of geometrical and positional isomers of octadecenoic acid (18:1) in the products was performed by capillary gas-liquid chromatography with a new capillary column coated with isocyanopropyl trisilphenylene siloxane (TC-70). Well-resolved peaks of 10 species of 18:1 were observed in the product. In addition to monoenoic acid isomers, four species of trans-dienoic isomers and conjugated dienoic isomers were found. From the distribution of 18:1 isomers, it was found that the double bond closer to the methyl end (Δ12) showed higher reactivity than that closer to the carboxyl end (Δ9) for hydrogenation. Because cis-8 18:1 and trans-8 18:1 were not observed but cis-10 18:1 and trans-10 18:1 were observed in the products, the double-bond Δ9 did not migrate to the carboxyl end but migrated to the methyl end. On the other hand, the Δ12 bond migrated to both methyl and carboxyl ends. From the distribution of 18:1 isomers in the reaction pathway, the hydrogenation of linoleic acid proceeds via half-hydrogenation states. Cis-18:1 isomers were produced predominantly in the initial stage of the reaction, while trans-18:1 isomers were produced during progress of the reaction. The cis/trans and positional isomerization took place by readsorption of 18:1 produced by the partial hydrogenation of linoleic acid. [ABSTRACT FROM AUTHOR]

Catalytic activity and selectivity for hydrogenation of linoleic acid ( cis-9, cis-12 18:2) were studied on Pt, Pd, Ru, and Ir supported on Al2O3. Stearic acid (18:0) and 10 different octadecenoic isomers (18:1) in the products could be separated completely by using a new capillary column coated by isocyanopropyl trisilphenylene siloxane for gas-liquid chromatography. The monoenoic acid isomers and dienoic acid isomers in the products on the various catalysts showed different distributions. The catalysts exhibited nearly equal selectivity for stearic acid formation. The 12-position double bond in linoleic acid has higher reactivity than the 9-position double bond in catalytic hydrogenation on platinum-group metal catalysts. In addition to hydrogenation products of linoleic acid, geometrical and positional dienoic acid isomers ( trans-9, trans-12; trans-8, cis-12; cis-9, trans-13; trans-9, cis-13; cis-9, trans-12 18:2), due to isomerization of linoleic acid during hydrogenation, were contained in the reaction products. Ru/Al2O3 exhibited the highest activity for isomerization of linoleic acid with the noble metal catalysts. Conjugated octadecadienoic acid isomers have been observed in products of the reaction on Pt/Al2O3, Ru/Al2O3, and Ir/Al2O3. Catalytic activities of noble metals for positional and geometric isomerization of linoleic acid during hydrogenation decreased in the sequence of Ru ≥ Pt > Ir » Pd. [ABSTRACT FROM AUTHOR]

The monomers produced from thermal high-pressure conversion of meadowfoam or oleic acids into estolides were characterized as a complex mixture of fatty acids. Mild reaction conditions produced little change in the starting acids. However, vigorous reaction conditions, e.g. ≥3 h at 250°C with stirring, significantly altered the starting fatty acids. Cis/trans isomerization occurred readily, with the proportion of trans isomers reaching 57%. In addition, the double bonds migrated throughout all positions of the hydrocarbon chain with concentrations diminishing outward from the starting double bond position. Branching was also observed to a small extent under these conditions and was even more pronounced in the absence of water. Lactones were also identified in the reaction mixture, with contents near 16% in the meadowfoam series. All products can be explained via carbocation rearrangement mechanisms that result from protonation of the starting olefins. [ABSTRACT FROM AUTHOR]

Cis/trans isomerization of amide bonds is a key step in a wide range of biological and synthetic processes. Occurring through C-N amide bond rotation, it also coincides with the activation of amides in enzymatic hydrolysis. In recently described QM studies of cis/trans isomerization in secondary amides using density functional methods, we highlighted that a peptidic prototype, such as glycylglycine methyl ester, can suitably represent the isomerization and complexities arising out of a larger molecular backbone, and can serve as the primary scaffold for model structures with different substitution patterns in order to assess and compare the steric effect of the substitution patterns. Here, we describe our theoretical assessment of such steric effects using tert-butyl as a representative bulky substitution. We analyze the geometries and relative stabilities of both trans and cis isomers, and effects on the cis/trans isomerization barrier. We also use the additivity principle to calculate absolute steric effects with a gradual increase in bulk. The study establishes that bulky substitutions significantly destabilize cis isomers and also increases the isomerization barrier, thereby synergistically hindering the cis/trans isomerization of secondary amides. These results provide a basis for the rationalization of kinetic and thermodynamic properties of peptides with potential applications in synthetic and medicinal chemistry. [ABSTRACT FROM AUTHOR]