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A C Storer

Publications and source records attributed to A C Storer.

At least 73 records · Page 4Linked to original sources
PubMed1988

Conformational states of N-acylalanine dithio esters: correlation of resonance Raman spectra with structures.

The conformational states of N-acylalanine dithio esters, involving rotational isomers about the RC(=O)NH--CH(CH3) and NHCH(CH3)--C(=S) bonds, are defined and compared to those of N-acylglycine dithio esters. The structure of N-(p-nitrobenzoyl)-DL-alanine ethyl dithio ester has been determined by X-ray crystallographic analysis; it is a B-type conformer with the amide N atom cis to the thiol sulfur. Raman and resonance Raman (RR) measurements on this compound and for the B conformers of solid N-benzoyl-DL-alanine ethyl dithio ester and N-(beta-phenylpropionyl)-DL-alanine ethyl dithio ester and its NHCH(CD3)C(=S) and NHCH(CH3)13C(=S) analogues are used to set up a library of RR data for alanine-based dithio esters in a B-conformer state. (Methyloxycarbonyl)-L-phenylalanyl-L-alanine ethyl dithio ester crystallizes in an A-like conformational state wherein the alanine N atom is nearly cis to the thiono S atom (C=S) [Varughese, K.I., Angus, R.H., Carey, P.R., Lee, H., & Storer, A.C. (1986) Can. J. Chem. 64, 1668-1673]. RR data for this solid material in its isotopically unsubstituted and CH(C-D3)C(=S) and CH(CH3)13C(=S) forms provide information on the RR signatures of alanine dithio esters in A-like conformations. RR spectra are compared for the solid compounds, for N-(p-nitrobenzoyl)-DL-alanine, N-(beta-phenylpropionyl)-DL-alanine, and (methyloxycarbonyl)-L-phenylalanyl-DL-alanine ethyl dithio esters, and for several 13C=S- and CD3-substituted analogues in CCl4 or aqueous solutions. The RR data demonstrate that the alanine-based dithio esters take up A, B, and C5 conformations in solution.(ABSTRACT TRUNCATED AT 250 WORDS)

Acylation↗
PubMed1988

Conformational variability in an enzyme's active site: resonance Raman evidence for different acyl group conformations in N-acylglycine and N-acylalanine dithioacyl papains.

It is demonstrated that the vibrational modes associated with the catalytically labile region of N-acylalanine dithioacyl papains undergo a major reorganization compared to the normal modes of corresponding model compounds. Thus, the resonance Raman (RR) spectrum of, e.g., N-benzoylalanine dithioacyl papain and its response to isotopic labeling cannot be understood completely on the basis of the RR spectrum of N-benzoylalanine ethyl dithio ester in one of its known conformational states [detailed in Lee, H., Angus, R. H., Storer, A. C., Varughese, K. I., & Carey, P. R. (1988) Biochemistry (preceding paper in this issue)]. This situation contrasts sharply to that for N-acylglycine dithioacyl papains whose RR spectra closely resemble those of the corresponding N-acylglycine ethyl dithio esters in a conformational state known as conformer B. For the N-acylalanine intermediates two possible causes are put forward to explain the rearrangement of the normal modes. First, the acyl groups based on alanine may bind in papain's active site in a conformation whose torsional angles near the -C(=S)S-group differ markedly from those of characterized model compounds. The second, and presently favored, explanation is that the N-acylalanine moiety is binding in the active site in an A- or C5-like conformation and that, in addition, there is significant vibrational coupling between some of the normal modes of the bound substrate and the normal modes associated with parts of the enzyme in contact with the substrate. The finding that deacylation for N-acylglycine or N-acylalanine dithioacyl papains must proceed from structures which are different is an indication that the mechanism of deacylation may not have strict stereochemical requirements.(ABSTRACT TRUNCATED AT 250 WORDS)

Acylation↗
PubMed1988

Comparison of the kinetics of the papain-catalyzed hydrolysis of glycine- and alanine-based esters and thiono esters.

The kinetic constants for the papain-catalyzed hydrolysis of a series of substrates with glycine or alanine in the P1 position are discussed. The substrates have N-benzoyl, N-(p-nitrobenzoyl), N-(beta-phenylpropionyl), or N-(methyloxycarbonyl)phenylalanine attached to the P1 moiety, and kinetic constants are obtained for both esters and thiono esters. The results for the hydrolysis of esters can be readily interpreted in terms of the known specificity of papain. For any glycine ester the change in kcat/Km upon substituting C=S for C=O or upon substituting an alpha-CH3 group is minimal. However, upon making both these substitutions, i.e., going from a glycine ester to an alanine thiono ester substrate, larger changes are seen for this ratio. Data for N-benzoyl- and N-(beta-phenylpropionyl)glycine and -alanine methyl thiono esters show that k2 is the parameter most affected by the double C=S and alpha-CH3 substitution. A further conclusion is that the deacylation rate constants for any pair of glycine and alanine dithioacyl papains are similar; e.g., for the intermediates based on the "good" substrates PheAla and PheGly k3 differs by only 20%. This is a surprising finding in light of the very different conformations and interactions of the bound acyl groups revealed by resonance Raman spectroscopy and raises the possibility that specific stereochemical effects, such as the oxyanion hole and general base catalysis, are not operating in the hydrolysis of dithioacyl papains.

Alanine↗
PubMed1986

Mechanistic origin of the sigmoidal rate behaviour of rat liver hexokinase D ('glucokinase').

Two recent proposals to account for the kinetic co-operativity of hexokinase D ('glucokinase') from rat liver are examined. A model in which the deviations from Michaelis-Menten kinetics result from a random order of binding of the substrates [Pettersson (1986) Biochem. J. 233, 347-350] accounts satisfactorily for the behaviour as a function of glucose concentrations, but it also predicts observable substrate inhibition by MgATP, which is in fact not observed. An alternative proposal in which the deviations arise from recycling of an enzyme-MgADP complex [Pettersson (1986) Eur. J. Biochem. 154, 167-170] also accounts satisfactorily for some of the data, but the required enzyme-MgADP complex could not be detected in isotope-exchange measurements. Thus the mnemonical mechanism proposed originally [Storer & Cornish-Bowden (1977) Biochem. J. 165, 61-69], which explains the deviations in terms of a relatively slow interconversion between two forms of free enzyme, remains the most parsimonious explanation of the behavior of hexokinase D.

Adenosine Triphosphate↗
PubMed1986

Benzoylamidoacetonitrile is bound as a thioimidate in the active site of papain.

13C NMR spectroscopy has been used to demonstrate that 13CN-labeled benzoylamidoacetonitrile forms a covalent adduct with the thiol group of cysteine 25 in the active site of papain. Spectral comparison with model compounds indicates that the adduct is a thioimidate. On the basis of a proposed mechanism for the formation of the thioimidate, it is concluded that the -CH2C(= NH)S--imino nitrogen does not sit in the active site in the same manner as the thiol ester carbonyl oxygen of the thiol acyl enzyme (or the oxyanion of the tetrahedral intermediate). Thus, in this sense the stabilization of the thioimidate does not reflect a similarity in structure between the bound thioimidate and the transition state.

Acetonitriles↗
PubMed1986

Conformational activation of acylpapains and acylcathepsin B's: resonance Raman and kinetic evidence.

It is shown that, by extending the size of the substrate to meet papain's specificity requirement, conformational changes occur in bonds adjacent to the scissile linkage in the acyl enzyme. The resonance Raman (RR) spectra of the dithioacylpapains CH3OC(=O)-Phe-NHCH2C(=S)S-papain, CH3O(=O))-Gly-Phe-NHCH2C(=S)S-papain, and CH3OC(=O)-Gly-Gly-Phe-NHCH2C(=S)S-papain, formed from thiono ester substrates, are found to be very similar, indicating that each dithioacyl enzyme takes up an identical B-type conformation in the -NHCH2C(=S)SCH2-linkages. Moreover, the kcat and kcat/Km parameters for the reactions involving these intermediates are similar (in the ranges 0.51-0.67 s-1 and 44 100-68 200 M-1 s-1, respectively). For these reactions kcat = k3, the rate constant for deacylation. The strong structural similarities in the region undergoing catalytic transformation, taken with the similar k3's, show that placing glycine residues in papain's S3 and S4 subsites has little effect on the deacylation process. However, there are marked RR spectral and kinetic differences between the intermediates formed from these three substrates, all of which meet papain's requirement for Phe at the S2 subsite, and N-(beta-phenylpropionyl)glycine dithioacylpapain, C6H5(CH2)2C(=O)NHCH2C(=S)S-papain. The RR spectral differences indicate that changes occur in the torsional angles of the -NH-CH2-C(=S)-S-CH2- fragment upon going to the di-, tri-, and tetrapeptide-based substrates. The changes in these torsional angles are consistent with slight conformational activation since higher k3 values are found for the di-, tri-, and tetrapeptide-based substrates (0.51-0.67 s-1) compared to the k3 for C6H5(CH2)2C(=O)NHCH2C-(=S)S-papain of 0.165 s-1.(ABSTRACT TRUNCATED AT 250 WORDS)

Acylation↗
PubMed1986

Chymopapain A. Purification and investigation by covalent chromatography and characterization by two-protonic-state reactivity-probe kinetics, steady-state kinetics and resonance Raman spectroscopy of some dithioacyl derivatives.

Chymopapain A was isolated from the dried latex of papaya (Carica papaya) by ion-exchange chromatography followed by covalent chromatography by thiol-disulphide interchange. The latter procedure was used to produce fully active enzyme containing one essential thiol group per molecule of protein, to establish that the chymopapain A molecule contains, in addition, one non-essential thiol group per molecule and to recalculate the literature value of epsilon 280 for the enzyme as 36 000 M-1 X cm -1. The Michaelis parameters for the hydrolysis of L-benzoylarginine p-nitroanilide and of benzyloxy-carbonyl-lysine nitrophenyl ester at 25 degrees C, and I 0.1 at several pH values catalysed by chymopapain A, papaya proteinase omega, papain (EC 3.4.22.2) and actinidin (EC 3.4.22.14) were determined. Towards these substrates chymopapain A has kcat./km values similar to those of actinidin and of papaya proteinase omega and significantly lower than those of papain or ficin. The environment of the catalytic site of chymopapain A is markedly different from those of other cysteine proteinases studied to date, as evidenced by the pH-dependence of the second-order rate constant (k) for the reaction of the catalytic-site thiol group with 2,2'-dipyridyl disulphide. The striking bell-shaped component that is a characteristic feature of the reactions of S-/ImH+ (thiolate/imidazolium) ion-pair components of many cysteine-proteinase catalytic sites with the 2,2'-dipyridyl disulphide univalent cation is not present in the pH-k profile for the chymopapain A reaction. The result is consistent with the presence of an additional positive charge in, or near, the catalytic site that repels the cationic form of the probe reagent. Resonance Raman spectra were collected at pH values 2.5, 6.0 and 8.0 for each of the following dithioacyl derivatives of chymopapain A: N-benzoylglycine-, N-(Beta-phenylpropionl)glycine- and N-methoxycarbonylphenylalanylglycine-. The main conclusion of the spectral study is that in each case the acyl group binds as a single population known as conformer B in which the glycinic N atom is in close contact with the thiol S atom of the catalytic-site cysteine residue, as is the case also for papain and other cysteine proteinases studied. Thus the abnormal catalytic-site environment of chymopapain A detected by the reactivity-probe studies, which may have consequences for the acylation step of the catalytic act, does not perturb the conformation of the bound acyl group at the acyl-enzyme-intermediate stage of catalysis.

2,2'-Dipyridyl↗
PubMed1985

Comparison of the kinetics and mechanism of the papain-catalyzed hydrolysis of esters and thiono esters.

The kinetic constants for the papain-catalyzed hydrolysis of the methyl thiono esters of N-benzoylglycine and N-(beta-phenylpropionyl)glycine are compared with those for the corresponding methyl ester substrates. The k2/Ks values for the thiono esters are 2-3 times higher than those for the esters, and both show bell-shaped pH dependencies with similar pKa's (approximately 4 and 9). The k3 values for the thiono esters are 30-60 times less than those for the esters and do not exhibit a pH dependency. Solvent deuterium isotope effects on k2/Ks and k3 were measured for the ester and thiono ester substrates of both glycine derivatives. Each thiono ester substrate showed an isotope effect similar to that for the corresponding ester substrate. Moreover, use of the proton inventory technique indicated that, as for esters, one proton is transferred in the transition state for deacylation during reactions involving thiono esters and the degree of heavy atom reorganization in the transition state is very similar in both cases. The k3 values for the hydrolysis of a series of para-substituted N-benzoylglycine esters were found to correlate with the k3 values for the corresponding para-substituted thiono esters [Carey, P. R., Lee, H., Ozaki, Y., & Storer, A. C. (1984) J. Am. Chem. Soc. 106, 8258-8262], showing that the rate-determining step for the deacylation of both thiolacyl and dithioacyl enzymes probably involves the disruption of a contact between the substrate's glycinic nitrogen atom and the sulfur of cysteine-25. It is concluded that the hydrolysis of esters and thiono esters proceeds by essentially the same reaction pathway. Due to an oxygen-sulfur exchange process the product released in the case of the N-(beta-phenylpropionyl)glycine thiono ester substrate is the dioxygen acid; however, for the N-benzoylglycine thiono ester substrate, the thiol acid is the initial product. This thiol acid then acts as a substrate for papain and reacylates the enzyme to eventually give the dioxygen acid product. It is shown that thiol acids are excellent substrates for papain.

Esters↗
PubMed1984

Identity of acyl group conformations in the active sites of papain and cathepsin B by resonance Raman spectroscopy.

Resonance Raman spectroscopic data provide conclusive evidence for the existence of an acyl-enzyme intermediate during the reaction of a thionoester substrate, N-methyloxycarbonylphenylalanylglycine methyl thionoester (CH3OC(=O)-Phe-NHCH2C(=S) OCH3), with cathepsin B from porcine spleen. The resonance Raman spectrum of CH3OC(=O)-Phe-NHCH2C(=S)S-cathepsin B, where the thiol S is from the active-site cysteine residue, is compared to that of the corresponding papain acyl-enzyme. Within the limits of experimental error (+/-2 cm-1 for peak positions), there are no detectable spectral differences. Since the resonance Raman spectrum is sensitive to the torsional angles in the glycinic bonds and the cysteine linkages, the conformations are identical in those parts of the acyl-enzymes where chemical transformation occurs. A conformational analysis of the model compound CH3OC(=O)-Phe-NHCH2C(=S)SC2H5 demonstrates that the dithioacyl group in both dithioacyl-enzymes is present as a single population of a form known as conformer B. Conformer B is characterized by a small torsional angle about the glycinic NHCH2-CS(thiol) bond such that the nitrogen and S (thiol) atoms are in close contact. This conformer is widespread among the dithioacyl intermediates of plant cysteine proteinases, and it is apparent that the same chemistry is retained in a mammalian cysteine proteinase. Steady-state kinetic parameters are also reported for CH3OC(=O)-Phe-NHCH2C(=S)OCH3 reacting with papain and cathepsin B. The similarity of the Kcat values, 0.53 and 1.15 s-1, for papain and cathepsin B, respectively, provides further evidence for a conserved deacylation process.

Animals↗
PubMed1984

Comparative resonance Raman spectroscopic and kinetic studies of acyl-enzymes involving papain, actinidin and papaya peptidase II.

Resonance Raman spectra are reported for a series of dithioacyl-enzymes involving actinidin (EC 3.4.22.14) and papaya peptidase II (the more basic monothiol cysteine proteinase of Carica papaya). The acyl groups are N-benzoylglycine and N-(beta-phenylpropionyl)glycine containing C = S or 13C = S at the ester function. Comparison of the data with those for the corresponding papain (EC 3.4.22.2) analogues [Storer, Lee & Carey (1983) Biochemistry 22, 4789-4796] allows us to define the conformation of the dithioacyl group in the catalytic site. In each case the dithioacyl group is bound in a single conformation known as conformer B, in which the glycinic nitrogen atom comes into close contact with the sulphur atom of the catalytic-site cysteine residue. For the N-(beta-phenylpropionyl)glycine dithioacyl-enzymes the torsional angles of the NH-CH2-C(= S) bonds assume values typical of an essentially relaxed non-strained state. However, for the N-benzoylglycine dithioacyl-enzymes there is evidence for a slightly perturbed conformer B, and the perturbation is most pronounced for N-benzoylglycine dithioacyl-actinidin. Values of k+2/Ks and k+3 for the reactions of papain, actinidin and papaya peptidase II with N-benzoylglycine and N-(beta-phenylpropionyl)glycine methyl thionoesters were obtained by a pre-steady-state kinetic study. Wide variation was found in k+2/Ks, but the values of k+3 are all similar. This general picture is supported by the results from a steady-state kinetic study of the reactions of the three enzymes with N-benzoyl-L-arginine-p-nitroanilide and with N-benzyloxycarbonyl-L-lysine p-nitrophenyl ester. The similarity of the values of k+3, together with the invariance of conformer B geometry at the P1 site, suggests that the chemistry of the deacylation process is highly conserved among these three cysteine proteinases.

Acylation↗
PubMed1983

Comparison of the substrate conformations in the active sites of papain, chymopapain, ficin and bromelain by resonance Raman spectroscopy.

The resonance Raman spectra of several enzyme-substrate intermediates of papain, chymopapain, ficin and bromelain are reported. The intermediates are dithioacyl enzymes formed during the catalyzed hydrolysis of N-acylglycine thionoester substrates. Interpretation of the resonance Raman spectra allows us to compare, for the first time, the substrate geometries in a series of functioning intermediates from different enzymes. The substrates assume essentially identical conformations for papain, chymopapain and ficin and a similar, but not identical, conformation in the active site of bromelain. Each dithioacyl enzyme population appears to be made up of a single homogeneous conformational state. This state has been characterised in earlier studies of dithioacyl papains. It is designated as conformer B and is characterized by an attractive contact between the substrate's glycinic N atom and the active site cysteine S atom. It is now apparent that conformer B is of general significance in the mechanism of cysteine proteases.

Binding Sites↗
PubMed1983

Conformational states of N-acylglycine dithioesters in solution: resonance Raman studies of isotopically substituted models for enzyme-substrate complexes.

Resonance Raman (RR) and FTIR spectroscopic studies, taken with X-ray crystallographic data, are used to define the three major conformational states of N-acylglycine dithioesters in solution and to set up spectra-structure correlations. Importantly, each conformer has a characteristic RR signature, and thus the RR spectrum can be used to follow conformational events within dithioester enzyme-substrate intermediates. The signatures are further defined in the present work by the synthesis and spectroscopic characterization of 13C and 15N derivatives of N-benzoylglycine ethyl dithioester and N-(beta-phenylpropionyl)glycine ethyl dithioester. The observed isotope shifts offer insight into the normal mode character of the RR bands and provide standards with which to compare the shifts in the corresponding enzyme-substrate intermediates.

Enzymes↗
PubMed1983

Relaxed and perturbed substrate conformations in enzyme active sites: evidence from multichannel resonance raman spectra.

A diode array based multichannel Raman spectrometer has made it possible to record complete, high quality, resonance Raman (RR) spectra of enzyme-substrate intermediates. The intermediates are dithioacylpapains in which the acyl group is either N-benzoylglycine or N-(beta-phenylpropionyl)glycine. RR data are reported for the unlabeled dithioacylpapains as well as for the intermediates labeled separately with ND, 15N, and 13C = S in the glycine residue. Comparison of the results for the dithioacylpapains with that of the corresponding labeled glycine ethyl dithioesters [Lee, H., Storer, A. C., & Carey, P. R. (1983) Biochemistry (preceding paper in this issue)] leads to the conclusion that for both substrates in the active site the dihedral angles in the glycine NH-C-C(= S) linkages assume an essentially relaxed type B conformation. Similarly, there is no evidence for distortion about the C(= O)-NH peptide bond which links the P1 and P2 sites on the substrate. However, for the N-benzoylglycine case there is evidence for some conformational distortion in the -S-C-C cysteine linkages. The present data favor a single homogeneous conformational population about the substrates' NH-C-C(= S) bonds in the native dithioacylpapains. However, below pH 3.0 the dithioacyl enzymes denature and the RR spectra of the 13C = S substituted species confirm that the conformational population reverts to the mixture of conformers A and B found for the corresponding ethyl dithioesters in solution.

Binding Sites↗
PubMed1981

Resonance Raman and electronic absorption spectral studies of some beta-(2-furyl)acryloylglyceraldehyde-3-phosphate dehydrogenases.

Electronic absorption and resonance Raman spectra, together with rates of arsenolysis, are used to show that the acylated subunits of the rabbit furylacryloylglyceraldehyde-3-phosphate dehydrogenase (FA-rabbit enzyme), but not the FA-sturgeon enzyme, exist as a mixed population of at least two forms. One form of the FA-rabbit enzyme has a high rate of arsenolysis, and its near-UV absorption maximum (lambda max) is red shifted on binding NAD+, while the other has a lower rate of arsenolysis, and its absorption spectrum appears to be unaffected by excess NAD+. The FA-sturgeon enzyme exists as a single population that has a high rate of arsenolysis, and its lambda max is red shifted on binding NAD+. This red shift and the concomitant position of v C==C, the band due to the ethylenic double bond stretching vibration in the resonance Raman spectrum, indicate that in the presence of NAD+ the pi electrons of the FA chromophore are polarized, i.e., a permanent dipole has been set up along the long axis of the FA group. It is argued that this does not result in activation of the carbonyl group by setting up polarization (i.e., delta + C--O delta -) within that group alone. A comparison of the vC==C's and lambda max's for a series of FA derivatives of the type (formula, see text) where X = H, N, or O, shows a clear correlation. However, when X = S as, e.g., in thiol esters, this correlation breaks down. This is explained in terms of a possible through-space d pi-p pi overlap between the ethylenic bond pi orbitals and the empty sulfur 3d orbitals.

Acrylates↗
PubMed1981

Kinetic and physical properties of the L-malate-NAD+ oxidoreductase from Methanospirillum hungatii and comparison with the enzyme from other sources.

The L-malate-NAD+ oxidoreductase of Methanospirillum hungatii was purified to homogeneity by using Blue Sepharose and ADP-Sepharose affinity chromatography. The molecular weight was estimated as 61 700 +/- 1900 by gel filtration and 64 200 +/- 1200 by ultracentrifugation. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis indicated that the protein is composed of two polypeptide chains, each corresponding to 31 350 +/- 2150 daltons. Inhibition patterns obtained for malate, alpha-oxoglutarate and ADP established that the sequential reaction mechanism was ordered, with NADH serving as the first substrate. Intracellular concentrations of oxaloacetate approximated the Km value of 27 microM, but NADH was present at less than Km values. Comparison of the amino-acid composition of the L-malate-NAD+ oxidoreductase of M. hungatii and 22 others from prokaryotic and eukaryotic cells revealed a significant direct relationship between average hydrophobicity and the frequency of non-polar side chains, as well as a significant indirect relationship between average hydrophobicity and the polarity ratio. Calculations based on amino-acid-composition data indicated significant composition similarity between pairs of mammalian-cytoplasmic or pairs of mitochondrial L-malate-NAD+ oxidoreductases from various sources, but no significant composition similarity between any of the pairs of bacterial species examined.

Amino Acids↗