An ab initio study of cis/trans isomerization in the XONO systems (X  F,Cl)

Hartree-Fock level and post Hartree-Fock level molecular orbital calculations are reported for the cis and trans isomers of the FONO and ClONO molecules in their electronic ground states for the transition states which are associated with their isomerization from the cis to trans forms.Geometries have been determined together with respective vibrational frequencies, and the energy barrier for the isomerization reaction calculated. The barrier was found to be 67 kJ/mol for FONO and 67 kJ/mol for ClONO. The calculated isomerization energies are 16 kJ/mol and 20 kJ/mol respectively. We also report certain spectroscopic properties for the molecules.     

Reaction of cis and trans isomers of platinum(II) diamminedichloride with purine,adenine and its derivatives in dilute solutions

Reactions of the cytostatic and antitumour agent, cis-platinum(II) diamminedichloride, and its trans isomer with purine, adenine and its N-9 derivatives were followed spectrophotometrically in dilute aqueous solutions. While the cis isomer formed with all compounds studied complexes with the metal-to-ligand ratios ML, ML₂ and M₂L, it was found that the trans isomer did not form the complexes ML₂ with adenosine and AMP. The values of dissociation constants, reaction rate constants and activation energies of the reactions of the cis and trans isomers with purine, adenine and its derivatives were in most cases comparable. Lower stability was exhibited only by the complexes of trans-platinum(II) diamminedichloride (trans-Pt(II)) with AMP as well as by its complexes M₂L with adenine and adenosine. The ability of cis-platinum(II) diamminedichloride (cis-Pt(II)) to react with two adenine residues can explain the greater tendency of the cis isomer to form intrastrand cross-links in nucleic acids as compared with the trans isomer.     

Anisotropic intersubunit and inter-ring interactions revealed in the native bullet-shaped chaperonin complex from Thermus thermophilus

Background

The recent morphological studies on chaperonins have revealed that nearly equivalent amount of symmetric GroEL–(GroES)₂ (football-shaped) and asymmetric GroEL–GroES (bullet-shaped) complexes coexist during the chaperonin reaction cycle, which prompted us to reexamine the equatorial split observed for chaperonin from Thermus thermophilus by implementing semi-empirical molecular orbital (MO) calculations, since it is now believed that the symmetric formation is a precursor to the equatorial split.

Methods

Semi-empirical MO calculations were employed to investigate the intersubunit interactions within the bullet-shaped T. thermophilus chaperonin capturing the substrate of folding intermediates. Interaction energies between each cis-GroEL subunit and closely related remaining subunits in cis-GroEL ring, or in trans-GroEL ring across the equatorial plane, and further, interaction energies between each GroES subunit and adjacent subunits in the same GroES ring and in cis-GroEL ring were simulated.

Results

Anisotropic intensities and energy distribution of the subunits were revealed by the calculations, which are consistent with two conformations of the subunits forming cis-GroEL ring as revealed by X-ray crystal structure, and with an anisotropic critical binding site on cis-GroEL ring for chaperonin functioning.

Conclusions

This is the first application of semi-empirical MO calculations to the macromolecular complex of the native bullet-shaped chaperonin (GroEL–GroES–ADP homolog) from T. thermophilus.

General significance

The results also appear to support the occurrence of the equatorial split for T. thermophilus chaperonin observed via electron microscopy, but has not yet been fully observed for Escherichia coli GroEL–GroES system.     

Nmr studies of the molecular conformations in the linear oligopeptides H-(L-Ala)n-L-Pro-OH

The molecular conformations of the linear oligopeptides H-(L -Ala)_n-L -Pro-OH, with n = 1,2 and 3, have been investigated. ¹³C nmr observation of the equilibrium between the cis and trans forms of the Ala-Pro peptide bond indicated the occurrence of nonrandom conformations in solutions of these flexible peptides. The formation of the nonrandom species containing the cis form of the Ala-Pro bond was found to depend on the deprotonation of the carboxylic acid group of proline, the solvent, and the ionic strength in aqueous solution. The influence of intramolecular hydrogen bonding on the relative conformational energies of the species containing the cis and trans Ala-Pro peptide bond was studied by comparison of the peptides H-(Ala)_n-Pro-OH with analogous molecules where hydrogen bond formation was excluded by the covalent structure. In earlier work a hydrogen bond between the protonated terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue had been suggested to stabilize conformations including trans proline. For the systems described here this hypothesis can be ruled out, since the cis:trans ratio is identical for molecules with methyl ester protected and free protonated terminal carboxylic acid groups of proline. Direct evidence for hydrogen bond formation between the deprotonated terminal carboxylic acid group and the amide proton of the penultimate amino acid residue in the molecular species containing cis proline was obtained from ¹H nmr studies. However, the cis:trans ratio of the Ala-Pro bond was not affected by N-methylation of the penultimate amino acid residue, which prevents formation of this hydrogen bond. Overall the experimental observations lead to the conclusion that the relative energies of the peptide conformations including cis or trans proline are mainly determined by intramolecular electrostatic interactions, whereas in the molecules considered, intramolecular hydrogen bonding is a consequence of specific peptide backbone conformations rather than a cause for the occurrence of energetically favored species. Independent support for this conclusion was obtained from model consideration which indicated that electrostatic interactions between the terminal carboxylic acid group and the carbonyl oxygen of the penultimate amino acid residue could indeed account for the observed relative conformational energies of the species containing cis and trans proline, respectively.     

Partial purification and properties of a cis-3: trans-2-enal isomerase from cucumber fruit

An enzyme, which catalyses the isomerisation of cis-3-enals to trans-2-enals, has been partially purified from cucumber fruit. The isomerase activity has been resolved from significant contamination by the related activities, lipoxygenase and hydroperoxide cleavage enzymes. An examination of the substrate specificity of the isomerase enzyme showed it to be specific for the cis-3-enals. The most efficient isomerisation was achieved with cis-3-hexenal and cis-3-nonenal which are, physiologically, the two most significant substrates. The trans-3-enal and cis-3-enol were not suitable substrates for the enzyme.     

Cis-trans isomerization of proline in the peptide (his 105-Val 124) of ribonuclease a containing the primary nucleation site

Conformational energy calculations have been carried out to determine the relative stabilities of the C-terminal sequence 105–124 of ribonuclease A, withcis andtrans forms, respectively, of Asn 113-Pro 114. Thecis form of Pro 114 is the one that occurs in the native protein. This peptide contains the sequence 106–118, which, on the basis of both theoretical and experimental studies, is thought to constitute the primary nucleation site for the folding of ribonuclease A. It is shown that both conformations of the isolated peptide (with Pro 114 in thecis andtrans forms, respectively) are of approximately equal stability. Both forms have similar conformations from residues 105–110 and 118–124, while they differ in the bend region involving residues 111–117. Calculations have also been carried out to deduce the possible low-energy paths for the interconversion between thecis andtrans forms of both Pro 114 and Pro 117. It is shown that there are two low-energy paths (with a minimum activation energy of 16.5 kcal/mole) for the interconversion of Pro 114. Attractive nonbonded interaction energies stabilize the transition state on these paths. Only one relatively low-energy path (with an activation energy of 18 kcal/mole) could be found for the isomerization of Pro 117, which occur in thetrans form in the native protein; in this case, allcis forms have significantly higher energy than thetrans form. These calculations thus show that native-like forms for the isolated peptide can exist with Pro 114 in either thecis or thetrans form and that these forms are readily interconvertible.     

Retinoic acid as a survival factor in neuronal development of the grasshopper,Locusta migratoria

Based on experience with cell cultures of adult insect neurons, we develop a serum-free culture system for embryonic locust neurons. Influences of trophic substances on survival and neurite outgrowth of developing neurons are investigated. For the first time, a positive trophic effect of 9-cis retinoic acid (9-cis RA) was shown in vitro on embryonic neurons of an insect. We observed longer cell survival of 50 % developmental stage neurons in cultures supplemented with 0.3 nM 9-cis RA. Furthermore, an influence on neuron morphology was revealed, as the addition of 9-cis RA to cell culture medium led to an increase in the number of neurites per cell. Although an RA receptor gene, LmRXR (Locusta migratoria retinoid X receptor), was expressed in the central nervous system throughout development, the influence of 9-cis RA on neuronal survival and outgrowth was restricted to 50 % stage embryonic cells.     

Formation of cis-Coniferin in Cell-Free Extracts of Fagus grandifolia Ehrh Bark

American beech (Fagus grandifolia Ehrh) bark exclusively accumulates cis-monolignols and their glucosidic conjugates; no evidence for the accumulation of trans-monolignols has been found. The glucosyltransferase from this source exhibits a very unusual substrate specificity for cis, and not trans, monolignols. This is further evidence that cis monolignols are involved in lignin formation in these plant tissues. Preliminary evidence for the existence of a novel trans-cis monolignol isomerase was obtained, in agreement with our contention that this isomerization is not photochemically mediated.     

Further characterization of an E. coli strain resistant to the toxic and mutagenic action of cis-diamminedichloroplatinum(II)

An increased resistance to the toxic and mutagenic activity of the antitumor drug cis-diamminedichloroplatinum(II) (cis-DDP) in the E. coli strain BS21 compared to its wild-type parent, F26, has been reported. This resistance was neither due to different binding of cis-DDP to DNA nor to adaptive DNA repair (Germanier et al., 1984) In the present work, we found that mutation of the uvrA, recA and polA genes did not abolish the resistance of BS21 to the toxic action of cis-DDP. The lower mutability of BS21 was not influenced by the polA mutation, while uvrA greatly reduced and recA eliminated the mutagenic activity of cis-DDP in both strains. Treatment of BS21 and F26 with equal doses of cis-DDP produced the same initial number of platinum-DNA lesions. Little excision repair was detected in vivo in either strain during 6-h post-treatment incubation, the F26 strain being the most efficient of the two for this process. In contrast, F26 and BS21 were transformed identically by pBR322 DNA which had been treated with cis-DDP in vitro. Analysis of the platinum-DNA adducts which were formed between cis-DDP and salmon sperm DNA in the buffer conditions of this experiment suggests that plasmid DNA contains 80% monofunctional adducts and 20% bifunctional bis-guanine adducts.These data indicate that the selective toxicity and mutagenicity of these two strains in vivo are neither a result of different numbers of Pt-DNA lesions nor of their repair. The selectivity disappeared when the two bacterial strains were transformed by pBR322 DNA containing identical platinum-DNA lesions, suggesting that the biochemical events which process platinum-DNA lesions are the same in both strains. Hence, it appears that cis-DDP may form qualitatively different platinum-DNA adducts in the BS21 and F26 strains which are responsible for the different toxicity and mutagenicity.     

The Outcome of the Oxidations of Unusual Enediamide Motifs Is Governed by the Stabilities of the Intermediate Iminium Ions

We compare the results from the oxidation of two unusual “enediamide” motifs (3,4-dihydropyrazin-2(1H)-ones), where a double bond is flanked by two amides. In one case the oxidation led to a ring-opened product arising from the cleavage of the double bond, and in the other a rare cis-dioxygenated compound was obtained. Both products have been characterized by X-ray crystallography. The outcomes of the key reactions are rationalized based on calculated free energies of intermediates.     

Enzymatic preparation of cis and trans-3-amino-4-hydroxytetrahydrofurans and cis-3-amino-4-hydroxypyrrolidines

The lipase catalyzed resolution of cis and trans-3-amino-4-hydroxytetrahydrofurans and cis-3-amino-4-hydroxypyrrolidines have been studied. For all the heterocycles, the best enantioselectivity was obtained using Candida antarctica lipases A and B as catalysts in hydrolytic processes. The absolute configuration of the optically pure obtained heterocycles has been assigned.     

cis–trans isomerization of carbon double bonds in monounsaturated triacylglycerols via generation of free radicals

We investigated the heat-induced cis/trans isomerization of double bonds in monounsaturated lipids. When triolein (9-cis, 18:1) was heated around 180 °C, small amounts of isomerization products were obtained depending on the heating period. The heat-induced isomerization of triolein was considerably suppressed by the addition of different antioxidants or under nitrogen stream, and these additives simultaneously inhibited the thermal oxidation of double bonds in triolein. Therefore, an intermediate of the thermal oxidation reaction might be responsible for the heat-induced isomerization of the double bonds in triolein. The thermodynamics of the heat-induced isomerization of triolein (9-cis, 18:1) and trielaidin (9-trans, 18:1) were investigated using Arrhenius plot. The Arrhenius activation energies of cis double bonds in triolein and trans double bonds in trielaidin were 106 kJ/mol and 137 kJ/mol, respectively. The calculated internal rotational barrier heights of these double bonds were similar to those of the double bond of 2-butene radical and significantly lower than those of non-radicalized double bonds in 2-butene. These results suggest that heat-induced cis/trans isomerization of triolein and trielaidin occurs mainly through the formation of radical species, which are the intermediates produced during thermal oxidation. The activation energy difference between the two forms suggests that trans trielaidin radicals are more stable than cis triolein radicals. The high thermodynamic stability of the trans double bonds in lipid radicals would influence the population of cis and trans isomers in edible oils and contribute to slight accumulation of trans-18:1 isomers during heating or industrial processing.     

A study of the complexes of borate ions and some cyclitols using 11B-n.m.r. spectroscopy

Complexes between borate ion and cyclohexane-cis-1,2-diol, cyclohexane-cis,cis-1,3,5-triol, and myo- and epi-inositol have been investigated by ¹¹B-n.m.r. spectroscopy. Three different complexes of myo-inositol have been identified. Formation constants have been determined for the borate complexes of each cyclitol. Where the complex is formed from the less-stable chair conformer, MNDO calculations have been performed to determine the enthalpies of inversion. For myo-inositol, an iterative method of calculation gave a set of constants which provided a good match with experimental data and supported the proposed formulation of its borate complexes.     

13C-NMR of double and triple bond carbon atoms of unsaturated fatty acid methyl esters

The carbon magnetic resonance spectra of many fatty acid methyl esters with cis and trans double bonds and triple bonds at various positions and in many different combinations have been investigated.The influence of the ester group on double and triple bonds in the fatty acid chain depends strongly on the positions of these bonds. For a given position the influence is constant, even if one or more other double or triple bonds are present.Together with the evaluated chemical shift parameters for the effects of double and triple bonds on each other, complete assignments are possible and spectra of various types of unsaturated esters can be predicted with high accuracy (±0.1 ppm).     

Binding study of the drug cis-dichlorodiammineplatinum(II)to G p5′ and dGp5′ by high resolution proton and carbon-13 NMR spectroscopy

The molecular mode of action leading to the anticancer activity of the drug cis-diamminedichloroplatinum(II), cis-DDP or cis-platinum is still the subject of speculation. In the present high field (400 MHz) ¹H NMR study the results on coupling constants for cis- and trans-diammine bis(guanosine- 5′-monophosphate) and (d-guanosine-5′-monophosphate)platinum(II) complexes are presented and discussed. The ¹H and ¹³C NMR chemical shifts obtained are consistent with the drug binding to N7 of each guanine. It has been found that the drug induces different conformational changes in the nucleotide from the trans-DDP isomer.     

13C Chemical shifts of long-chain epoxides,alcohols and hydroperoxides

¹³C-NMR shifts are reported for a number of long-chain and cyclic epoxides (cis and trans, saturated and unsaturated) and of several primary alcohols and hydroperoxides. The influence of each of these three functional groups on the chemical shift of nearby carbons has been determined and some new additivity parameters are reported.     

Importance of the sphingosine base double-bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers

The precise role of the sphingosine base trans double bond for the unique properties of sphingomyelins (SMs), one of the main lipid components in raftlike structures of biological membranes, has not been fully explored. Several reports comparing the hydration, lipid packing, and hydrogen-bonding behaviors of SM and glycerophospholipid bilayers found remarkable differences overall. However, the atomic interactions linking the double-bond geometry with these thermodynamic and structural changes remained elusive. A recent report on ceramides, which differ from SMs only by their hydroxyl headgroup, has shown that replacing the trans double bond of the sphingosine base by cis weakens the hydrogen-bonding potential of these lipids and thereby alters their biological activity. Based on data from extensive (a total 0.75 μs) atomistic molecular dynamics simulations of bilayers composed of all-trans, all-cis, and a trans/cis (4:1 ratio) racemic mixture of sphingomyelin lipids, here we show that the trans configuration allows for the formation of significantly more hydrogen bonds than the cis. The extra hydrogen bonds enabled tighter packing of lipids in the all-trans and trans/cis bilayers, thus reducing the average area per lipid while increasing the chain order and the bilayer thickness. Moreover, fewer water molecules access the lipid-water interface of the all-trans bilayer than of the all-cis bilayer. These results provide the atomic basis for the importance of the natural sphingomyelin trans double-bond conformation for the formation of ordered membrane domains.     

trans-10,cis-12 Conjugated linoleic acid promotes bone formation by inhibiting adipogenesis by peroxisome proliferator activated receptor-γ-dependent mechanisms and by directly enhancing osteoblastogenesis from bone marrow mesenchymal stem cells

The bone undergoes continuous remodeling of osteoblastic bone formation and osteoclastic bone resorption to maintain proper bone mass. It is also reported that bone marrow adiposity has a reciprocal role in osteoblasts due to their same origin from mesenchymal stem cells. In addition, one of the key mediators of adipogenesis, peroxisome-proliferator activated receptor-γ (PPARγ), plays a significant role in osteoblastogenesis in bone marrow mesenchymal stem cells. One dietary component that is known to have significant impact on adiposity and bone mass is conjugated linoleic acid (CLA). However, the link between controlling adiposity to improving bone mass by CLA has not been studied intensively. Thus, the purpose of this study is to determine the role of CLA on bone marrow adiposity and bone formation using murine mesenchymal stem cells. The results confirmed that the trans-10,cis-12 CLA, but not the cis-9,trans-11 CLA isomer, significantly inhibited adipogenesis and promoted osteoblastogenesis from mesenchymal stem cells. The inhibition of adipogenesis by the trans-10,cis-12 CLA was mediated by PPARγ; however, the trans-10,cis-12 CLA had a direct effect on osteoblastogenesis which was independent to PPARγ in this model. The trans-10,cis-12 CLA also had significant effects on osteoclastogenesis inhibitory factor, which suggests potential influence of CLA on osteoclastogenesis. Overall, the results suggest that the trans-10,cis-12, but not the cis-9,trans-11 CLA isomer, has a positive impact on bone health by both PPARγ mediated and independent mechanisms in mesenchymal stem cells.     

Quantitative determination of diol metabolites of CS-670, a new antiinflammatory agent,by capillary column gas chromatography-mass spectrometry

CS-670(I), being developed as a non-steroidal anti-inflammatory agent, is a racemic prodrug. It has been found to be readily metabolized to active metabolites: trans and unsaturated mono-ols (trans-OH, unsaturated-OH). We report here a method for the quantitative determination of the eight diol stereoisomers excreted in urine after administration I. The diols were well separated and quantitated using capillary column GC-MS after a rather simple derivatization with diazomethane-trifluoroacetic anhydride. Sex differences in rats and species differences between rats and mice were observed in the metabolism of I: the trans-diols originating from trans-OH were predominantly excreted in male and female rat urine but the excretion rate was greater in the male rats; the cis-diols originating from cis mono-ol (cis-OH) were the major urinary metabolites in mice. The hydroxy groups were mainly introduced at the respective equatorial hydrogen atoms at the 4′-carbon of trans-OH and the 5′-carbon of cis-OH. The 4′- and 5′-hydroxy groups in the diols were in the cis conformation with respect to the original 2′-hydroxy group. As approximately 9% of the trans-diols were excreted in urine after administration of cis-OH to rats, the chiral inversion from cis-OH to trans-OH was suggested to occur through the saturated ketone intermediate.