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At least 19 recordsLinked to original sources

PubMed1979

Enzymic cis-trans isomerization of nitrofuran derivatives: isomerizing activity of xanthine oxidase, lipoyl dehydrogenase, DT-diaphorase and liver microsomes.

Xanthine oxidase (xanthine:oxygen oxidoreductase, EC 1.2.3.2) supplemented with an electron donor could catalyze the cis-trans isomerization of 3-(5-nitro-2-furyl)-2-(2-furyl)acrylamide, 3-(5-nitro-2-furyl)-2-phenylacrylamide and 3-(5-nitro-2-furyl)-2-(2-furyl)acrylonitrile. The direction of isomerization (cis leads to trans, cis in equilibrium trans or trans leads to cis) is dependent on the chemical structure of these nitrofuran derivatives. Lipoyl dehydrogenase (NADH:lipoamide oxidereductase, EC 1.6.4.3), DT-diaphorase (NAD(P)H:(quinone-acceptor) oxidoreductase, EC 1.6.99.2) and liver microsomes could also catalyze the conversion of cis-3-(5-nitro-2-furyl)-2-(2-furyl)acrylamide to its trans isomer in the presence of an appropriate electron donor. Such isomerizing activity of these enzymes is much higher than their nitro-reducing activity. In addition, the cis-trans isomerization of some nitrofuran derivatives was demonstrated with the liver slices and the small intestines of rats. A new cis-trans isomerization mechanism which is based on transfer of a single electron by an enzyme system to a nitrofuran derivative to give the radical-anion was proposed. This postulated mechanism was supported by the preliminary experiments using pulse radiolysis technique.

Animals↗

PubMedDate not supplied

[Gel-permeating chromatography of interacting multi-component systems. I. Study of protein isomerization by the method of gel-permeation chromatography. II. Method of determining the kinetic constant of isomerization].

A technique is suggested of determining the isomerization constants by means of gel-permeation chromatography. Chromatograms of proteins and expressions for statistical moments of their distribution along the chromatographic column obtained in the authors previous work [1], are used. A necessary condition for optimal setup of the GPCh experiments is found. Fulfilment of this condition provides a maximal accuracy of determination of the isomerization constants.

Chromatography, Gel↗

PubMed1979

Role of proline isomerization in folding of ribonuclease A at low temperatures.

In unfolded RNase A there is an interconversion between slow-folding and fast-folding forms (U(S) right harpoon over left harpoon U(F)) that is known to show properties characteristic of proline isomerization in model peptides. Here, we accept the evidence that U(S) molecules contain nonnative proline isomers and we ask about the isomerization of these proline residues during folding. The U(S) right harpoon over left harpoon U(F) reaction in unfolded RNase A is used both to provide data on the kinetics of proline isomerization in the unfolded protein and as the basis of an assay for measuring proline isomerization during folding.The tyrosine-detected folding kinetics at low temperatures have been compared to those of proline isomerization in unfolded RNase A. The comparison is based on the recent observation that the U(S) right harpoon over left harpoon U(F) kinetics are independent of guanidinium chloride concentration, so that they can be extrapolated to low guanidinium chloride concentrations, at which folding takes place. At 0 degrees C the tyrosine-detected folding reaction is 100-fold faster than the conversion of U(S) to U(F) in unfolded RNase A. Consequently, the folding reaction is not rate-limited by proline isomerization as it occurs in unfolded RNase A. An assay is given for proline isomerization during folding. The principle is that native RNase A yields U(F) on unfolding, whereas protein molecules that still contain nonnative proline isomers yield U(S). Unfolding takes place at 0 degrees C, at which proline isomerization is slow compared to unfolding. This assay yields two important results: (i) The kinetics of proline isomerization during folding are substantially faster than in unfolded RNase A-e.g., 40-fold at 0 degrees C. The mechanism of the rate enhancement is unknown. (ii) At low temperatures (0-10 degrees C), and also in the presence of (NH(4))(2)SO(4), the tyrosine-detected folding reaction occurs before proline isomerization and yields a folded intermediate I(N) that is able to bind the specific inhibitor 2'-CMP. The results demonstrate that a folding intermediate is spectrally detectable when folding occurs at low temperatures. They suggest that low temperatures provide suitable conditions for determining the kinetic pathway of folding by characterizing folding intermediates.

Ammonium Sulfate↗

PubMed1978

Acid catalysis of the formation of the slow-folding species of RNase A: evidence that the reaction is proline isomerization.

Unfolded RNase A is known to contain an equilibrium mixture of two forms, a slow-folding form (U(1)) and a fast-folding form (U(2)). If U(1) is produced after unfolding by the slow cis-trans isomerization of proline residues about X-Pro imide bonds, then the formation of U(1) should be catalyzed by strong acids. Therefore, the rate of formation of U(1) has been measured at different HClO(4) concentrations. After rapid unfolding of the native protein in concentrated HClO(4) at 0 degrees , the slow formation of U(1) was measured by use of refolding assays. Catalysis of its formation was found at HClO(4) concentrations above 5 M. The uncatalyzed reaction follows apparent first-order kinetics but, in the acid-catalyzed range, two reactions are found. The faster reaction produces two-thirds of the slow-folding species and shows acid catalysis above 5 M HClO(4). Catalysis of the slower reaction begins at 8 M HClO(4). The faster reaction shows a 100-fold increase in rate at 10.6 M HClO(4) over the rate of the uncatalyzed reaction of 5 M. The activation enthalpy of the uncatalyzed reaction has been measured in two sets of unfolding conditions: DeltaH(double dagger) is 21.5 kcal/mol (1 kcal = 4.2 x 10(3) J) in 3.3 M HClO(4) and 21.0 kcal/mol in 5 M guanidine HCl, pH 2.5.Both acid catalysis of the formation of U(1) and its high activation enthalpy are consistent with the rate-limiting step being cis-trans isomerization either of X-Pro imide bonds or of peptide bond. The rate of the uncatalyzed reaction is in the range expected for proline isomerization and is 0.1% of that of peptide bond isomerization; thus, the simplest explanation for the formation of U(1) is proline isomerization. Earlier data, showing that the kinetic properties of the U(1) right arrow over left arrow U(2) reaction in refolding conditions differ from those of proline isomerization, can be explained if there is kinetic coupling between early steps in the folding of U(1) and its conversion to U(2).The existence of two acid-catalyzed reactions that are distinguished by the HClO(4) concentration at which catalysis begins suggests that at least two essential proline residues produce slow-folding species of RNase A by isomerization after unfolding. Because protonation of imide bonds is responsible for acid catalysis of proline isomerization, the slower reaction probably involves an imide bond with a low pK. It may be the bond connecting Lys-41 and Pro-42, because the positive charge on Lys-41 could make this bond more difficult to protonate.

Catalysis↗

PubMed1992

Kinetic coupling between protein folding and prolyl isomerization. I. Theoretical models.

Kinetic models were developed to describe the influence of prolyl peptide bond isomerization on the kinetics of reversible protein folding for cases in which structural intermediates do not occur. In the simulations, the number of prolyl residues and the relative rates of folding and isomerization were varied. The experimentally observed rate constants were found to be identical with the intrinsic rate constants of folding and isomerization only when folding remains much faster than prolyl isomerization throughout the transition region. When the rate of folding becomes similar to or lower than the rate of isomerization, the observed kinetic parameters are complex functions of all microscopic rate constants. In particular, the observed folding rates in the transition region decrease with the number of prolyl residues. Pseudo two-state kinetics with single folding and unfolding reactions are observed in several cases, although the apparent folding rates depend strongly on prolyl isomerization reactions in the unfolded chain. This virtual simplicity can easily lead to misinterpretation of kinetic data. Additional phases can be resolved when refolding is started from the fast-folding species (UF). The coupling between folding and prolyl peptide bond isomerization also modifies the dependence on denaturant concentration of the apparent rate constants of folding. We suggest several tests to detect and characterize the contributions of folding and isomerization steps to the observed folding kinetics.

Kinetics↗

PubMed1992

Disposition of the atrioventricular conduction tissues in the heart with isomerism of the atrial appendages: its relation to congenital complete heart block.

OBJECTIVES: Our goal was to compare histologically the mechanisms producing congenital complete heart block in normally structured hearts and in hearts with isomerism of the atrial appendages. BACKGROUND: It is known that several different histologic patterns can underscore the existence of congenital complete heart block in the normally structured heart, and that block is particularly frequent in the setting of isomerism of the atrial appendages. The histologic findings in the latter setting were compared and contrasted with those found in the normally structured heart. METHODS: Serial section techniques were used to study 14 hearts with isomerism of the atrial appendage (12 with left isomerism and 2 with right isomerism) and 7 normally structured hearts. RESULTS: Discontinuity between the atrioventricular (AV) node and the ventricular conduction tissues was found in 10 of the 12 hearts with left isomerism; the other 2 hearts had a normally formed conduction axis and heart block was not present in these cases. In both hearts with right isomerism, "slings" of ventricular conduction tissue connected dual AV nodes; congenital complete heart block was not present in either case. In six of the seven cases with a normally structured heart, anti-Ro antibodies had been found in the maternal serum. All six of these hearts had discontinuity between the atrial tissues and the ventricular conduction axis. Intraventricular discontinuity was found in the seventh case, in which anti-Ro antibodies were not found in the mother. CONCLUSIONS: The pattern of congenital complete heart block in cases with left isomerism is discontinuity between the AV node and the conduction axis, in contrast to the pattern of atrial-axis discontinuity produced in the normally structured heart when anti-Ro antibodies are found in the maternal serum.

Abnormalities, Multiple↗

PubMed1976

The isomerization of 2,5- and 9,12-octadecadienoic acids by an extract of Butyrivibrio fibrisolvens.

A cell-free particulate preparation from Butyrivibrio fibrisolvens was used to study the relative rates of isomerization of all cis,cis-methylene-interrupted isomers of octadecadienoic acid. Only two isomers were found to be substrates, the 9,12-isomer was isomerized at 41 +/- 4 mumol/min per mg protein, and the 2,5-isomer at 11 +/- 1 mumol/min per mg. The product of the isomerization of the 2,5-isomer had an ultraviolet absorption maximum at 233 nm indicating that it was the 3,5-isomer. The isomerization of the 2,5-isomer was studied in detail. Its rate of isomerization was linear with protein concentration up to 0.047 mg/ml, and was linear with substrate concentration up to 48 muM. The pH optimum was 6.8. Below pH 6, the substrate was also subject to spontaneous isomerization. The inhibition of isomerization of the 9,12-isomer by the other isomers was studied. Those isomers in which the double bonds are close to the carboxyl group were the most effective inhibitors. The preparation was also found capable of hydrogenating the conjugated diene product from the 2,5-isomer to a monoene after prolonged incubation.

Fatty Acids, Unsaturated↗

PubMed1992

[Echocardiographic diagnosis and significance of atrial isomerism].

Forty-nine patients with atrial isomerism (right atrial isomerism 27, left atrial isomerism 22) diagnosed by 2DE of the abdominal great vessels were reported in this paper. Compared with the results of high kilovolt filtered chest film and autopsy, atrial situs determined by 2DE was concordant with bronchial morphology in 43 patients, 25 (93%) of right atrial isomerism, 18 (82%) of left isomerism. 25 patients who had angiocardiography or autopsy were associated with other cardiac malformations which were severe and complicated in right atrial isomerism. The results of this series showed that ultrasonography of the abdominal great vessels could be a reliable guide to the diagnosis of atrial isomerism, 2DE diagnosis is useful for angiocardiography.

Child↗

PubMed1979

s-Cis and s-trans isomerism of the His-Pro peptide bond in angiotensin and thyroliberin analogues.

The dipeptide His-Pro isomerizes from all-s-trans to partly s-cis when titrated in D2O from acidic to neutral pD as observed by 13C and 1H nuclear magnetic resonance of the proline side chain. This isomerization is reported by the His C-2 and C-4 protons and carbons which show distinct, well-resolved resonances for each isomer. The influence of the His-Pro peptide bond rotational state on the histidine protons far removed from the bond has not been previously observed in model compounds or peptides. The peptides thyroliberin (TRH), [3-MeHis2]-TRH, and [3-MeHis6]-, [Sar1,Al8]-, and Nalpha-acetylangiotensin II were found to similarly isomerize from all-s-trans to partly s-cis as reported by their His C-2 and C-4 proton resonances. The His C-2 and C-4 protons in the peptides [1,3-diMeHis2]-TRH and [1-MeHis6]-, and [homoHis6]-angiotensin do not report this isomerization. Angiotensin II has previously been found to exhibit the same isomerization. The reporting of the s-trans to s-cis isomerization by the His C-2 proton appears to be correlated with the known potencies of the five angiotensin peptides in rat uterine strips and of the three TRH peptides by radioimmunoassay of released thyrotropin.

Angiotensin II↗

PubMed1978

Alkaline isomerization of thermoresistant cytochrome c-552 and horse heart cytochrome c studied by absorption and resonance Raman spectroscopy.

The structure of the thermoresistant cytochrome c (552, Thermus thermophilus) has been investigated at neutral and alkaline pH by absorption and resonance Raman spectroscopy and compared with that of horse heart cytochrome c. The ligands of the ferricytochrome c-552 at neutral pH are considered to be histidine and methionine, whereas the ligands of ferrocytochrome c-552 are histidine and another nitrogen base, histidine or lysine. Ferric cytochrome c-552 undergoes an alkaline isomerization with a pK of 12.3 (25 degrees C), accompanied by a ligand exchange. Horse heart cytochrome c has at least three isomerization states at alkaline pH (pK 9.3, 12.9 and greater than 13.5 at 25 degrees C). The replacement of the sixth ligand may not be involved in the second isomerization. The thermodynamic parameters for the isomerization were also estimated. The entropy change upon isomerization of cytochrome c-552 is negative, whereas for that of horse heart cytochrome c the entropy change is positive.

Animals↗

PubMed1992

Intramolecular catalysis of a proline isomerization reaction in the folding of dihydrofolate reductase.

The cis/trans isomerization of the peptide bond preceding proline residues in proteins can limit the rate at which a protein folds to its native conformation. Mutagenic analyses of dihydrofolate reductase (DHFR) from Escherichia coli show that this isomerization reaction can be intramolecularly catalyzed by a side chain from an amino acid which is distant in sequence but adjacent in the native conformation. The guanidinium NH2 nitrogen of Arg 44 forms one hydrogen bond to the imide nitrogen and a second to the carbonyl oxygen of Pro 66 in wild-type DHFR. Replacement of Arg 44 with Leu results in a change of the nature of the two slow steps in refolding from being limited by the acquisition of secondary and/or tertiary structure to being limited by isomerization. The simultaneous replacement of Pro 66 with Ala (i.e., the Leu 44/Ala 66 double mutant) eliminates this isomerization reaction and once again makes protein folding the limiting process. Apparently, one or both of the hydrogen bonds between Arg 44 and Pro 66 accelerate the isomerization of the Gln 65-Pro 66 peptide bond. The replacement of Arg 44 with Leu affects the kinetics of the slow folding reactions in a fashion which indicates that the crucial hydrogen bonds form in the transition states for the rate-limiting steps in folding.

Arginine↗

PubMed1992

Kinetics and mechanism of isomerization of cyclosporin A.

The kinetics of isomerization of cyclosporin A to isocyclosporin A were studied in various nonaqueous solvents as a function of temperature and added methanesulfonic acid. The rate of isomerization was found to be acid-catalyzed over the acid concentration range studied. The choice of organic solvent significantly altered the rate of isomerization. For a series of alcohols, the rate was enhanced with increasing dielectric constant of the media, however, this correlation did not hold upon introduction of the dipolar aprotic solvent, tetrahydrofuran. Conversion of cyclosporin A to isocyclosporin A in tetrahydrofuran was found to contain diminished side reactions as compared to alcoholic solvents. The rate of conversion of isocyclosporin A to cyclosporin A was determined in aqueous buffers as a function of pH, buffer concentration, and temperature. The rates of conversion were extremely rapid compared to the forward reaction. Based on the pH dependencies of dilute solution reactivities, isocyclosporin A displayed a kinetically generated pKa value of 6.9 for the secondary amine moiety. From pH 8 to pH 10 the pH-rate profile plot is linear, with a slope approximately equal to unity, indicating apparent hydroxide ion catalysis. The break in pH-rate profile suggests a change in the rate-determining step upon protonation of isocyclosporin A. The rate of isomerization in plasma was comparable with that found in a pH 7.4 buffer solution, indicating that plasma proteins do not significantly alter the isomerization kinetics of isocyclosporin A to cyclosporin A.

Buffers↗

PubMed1977

Relaxation spectra of yeast hexokinases. Isomerization of the enzyme.

Yeast hexokinase isozymes P1 and P11 exhibit a pH dependent, rapid relaxation process at 15 degrees C at enzyme concentrations of 100-474 muM and over a pH range of 6-8. The process was detected by equilibrium temperature jump spectroscopy using the indicator probe phenol red. The value of 1/tau varies from about 6 ms-1 at pH 8 for both isozymes to 50 ms-1 for P1 and 85 ms-1 for P11 at pH 6. The data are consistent with a mechanism involving an enzyme isomerization coupled to an ionization. The forward rate constant for the isomerization of the proposed mechanism varies between 3 and 7 ms-1; the ratio of the reverse rate constant to the ionization Ka is between 0.5 and 2 X 10(11) M-1 S-1; the estimated pKa varies between 5.5 and 6.1. The ranges of values in rate constants and pKa represent variations observed between preparations of the same isozyme and between isozymes. The isomerization rate is at least 50 times faster than catalysis under all conditions and the pKa is lower than that controlling activity. The rate of isomerization is unchanged by addition of sugar and nucleotide ligands, but the amplitude of the process is perturbed. These data imply that isomerizing and ionizing forms are sensitive to events at the active site. These equilibria between forms of hexokinase are fast enough, and have the right properties, to be important to the mechanism and regulation of the enzyme.

Adenosine Triphosphate↗

PubMed1992

Structural analysis of non-volatile compounds by liquid chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry: thermal isomerization of benzylpenicillin in a Plasmaspray interface.

Isomerization and degradation of benzylpenicillin ((2S,5R,6R)-3,3-dimethyl-7-oxo-6-(2-phenylacetamido)-4-thia-1- azabicyclo[3.2.0]heptane-2-carboxylic acid) were studied using a combination of Plasmaspray (PSP) liquid chromatography/tandem mass spectrometry (LC/MS/MS) and liquid secondary ion tandem mass spectrometry (LSI MS/MS). Benzylpenicillin was isomerized to benzylpenicillenic acid (3-mercapto-N-[[5-oxo-2-(phenylmethyl)-4(5H)- oxazolylidene]methyl]valine) in the PSP interface/ion source. The isomerization was inferred from the probe temperature dependence of PSP LC tandem mass spectra and discrepancies in the daughter ions between PSP LC and LSI tandem mass spectra. High temperature at the PSP interface was responsible for the isomerization, since the difference between PSP LC and LSI tandem mass spectra became smaller as the probe temperature was lowered. It was also found that benzylpenicillin was decomposed to benzylpenilloic acid (5,5-dimethyl-2-[(phenylacetamido)methyl]thiazolidine-4-carboxylic acid), N-(phenylacetyl)glycine, N-(phenylacetyl)glycinal and 3-mercaptovaline in the PSP interface/ion source. The degradation products formed in the interface/ion source were identical to those formed in acidic solution. The results show that degradation of penicillins can be investigated by PSP LC/MS and PSP LC/MS/MS.

Chromatography, Liquid↗

PubMed1979

Isomerization of the double bonds of a conjugated fatty acid during beta-oxidation.

The beta-oxidation of an unsaturated fatty acid containing conjugated double bonds at odd-numbered carbon atoms has not previously been studied. It is, therefore, not clear whether, during the beta-oxidation of such an acid, the double bonds will be isomerized by enoyl-CoA isomerase (delta 3 - delta 2-enoyl-CoA isomerase) with the loss or retention of its conjugated nature. To investigate the problem, (E,E)-3,5-octadienoyl-CoA was synthesized for use as a model substrate, and enoyl-CoA isomerase was partially purified from bovine liver. The isomerization was followed by spectrophotometric and gas liquid chromatographic methods, and the results suggested that the isomerization of the model substrate proceeded with retention of a conjugated double bond system. It is, therefore, proposed that the beta-oxidation intermediate of alpha-eleostearic acid (delta 9,11,13 fatty acid) will also isomerize with retention of the conjugated double bond system.

Acyl Coenzyme A↗

PubMed1992

Kinetic coupling between protein folding and prolyl isomerization. II. Folding of ribonuclease A and ribonuclease T1.

The folding and unfolding kinetics within the transition region were measured for RNase A and for RNase T1. The data were used to evaluate the theoretical models for the influence of prolyl isomerization on the observed folding kinetics. These two proteins were selected, since the folding reaction of RNase A is faster than prolyl isomerization, whereas in RNase T1, folding is slower than isomerization in the transition region. Folding of RNase T1 was investigated for three variants with different numbers of cis prolyl residues. The results indicate that in the transition region the folding rates are indeed strongly dependent on the number of prolyl residues. The variant of RNase T1 that contains only one cis prolyl residue folds about ten times faster than two variants that contain two cis prolyl residues. For both RNase A and RNase T1, the apparent rates of folding and unfolding as well as the corresponding amplitudes depend on the concentration of denaturant in a manner that was predicted by the model calculations. When refolding was started from the fast-folding species, additional kinetic phases could be observed in the transition region for both proteins. The obtained values could be used to calculate the microscopic rate constants of folding and isomerization on the basis of theoretical models.

Exoribonucleases↗

PubMed1979

Voltage transients from photo-isomerizing azo dye in bilayer membranes.

Voltage transients are induced by brief light flashed on bilayer membranes with absorbed 3,3'-bis(alpha-(trimethylammonium)methyl)azobenzene (Bis-Q). The voltages are positive for trans-to-cis photo-isomerization, and negative for cis-to-trans photo-isomerization. The risetimes in phosphatidylethanolamine-decane bilayer membranes indicate that absorbed trans-Bis-Q is photo-isomerized to cis within 2 microseconds, and that cis is photo-isomerized to trans within 15 microseconds.

Azo Compounds↗

PubMed1992

Enzymatic catalysis of prolyl isomerization in an unfolding protein.

Prolyl isomerases are able to accelerate slow steps in protein refolding that are limited in rate by cis/trans isomerizations of Xaa-Pro peptide bonds. We show here that prolyl isomerizations in the course of protein unfolding are also well catalyzed. To demonstrate catalysis we use cytoplasmic prolyl isomerase from Escherichia coli as the enzyme and reduced and carboxymethylated ribonuclease T1 as the substrate. This form of ribonuclease T1 without disulfide bonds is nativelike folded only in the presence of moderate concentrations of NaCl. Unfolding can be induced by reducing the NaCl concentration at ambient temperature and in the absence of denaturants. Under these conditions prolyl isomerase retains its activity and it catalyzes prolyl cis/trans isomerization in the unfolding protein. Under identical conditions within the NaCl-induced transition unfolding and refolding are catalyzed with equal efficiency. The stability of the protein and thus the final distribution of unfolded and folded molecules attained at equilibrium is unchanged in the presence of prolyl isomerase. These results demonstrate that prolyl isomerase functions in protein folding as an enzyme and catalyzes prolyl isomerization in either direction.

Amino Acid Isomerases↗