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Smolarsky M. Spectroscopic Probes Incorporated into Specific Substrates and Inhibitors of Papain for the Study of Acylenzyme Formation. Isr J Chem 2013. [DOI: 10.1002/ijch.197400048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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2
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Yin DT, Kazlauskas RJ. Revised Molecular Basis of the Promiscuous Carboxylic Acid Perhydrolase Activity in Serine Hydrolases. Chemistry 2012; 18:8130-9. [DOI: 10.1002/chem.201200052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/09/2012] [Indexed: 11/08/2022]
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3
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Fernandez MM, Clark DS, Blanch HW. Papain kinetics in the presence of a water-miscible organic solvent. Biotechnol Bioeng 2009; 37:967-72. [PMID: 18597322 DOI: 10.1002/bit.260371011] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The effects of various concentrations of a water-miscible organic solvent [a 7:3 (v/v) mixture of N, N dimethylformamide and dimethylsulfoxide] on the kinetics of papain have been investigated. The parameters k(cat) and K(m) for the amidase and esterase activity of papain using N-alpha-benzoyl-DL-arginine-p-nitroanilide (BAPNA) and N-alpha-benzoyl-L-arginine ethyl ester (BAEE) as substrates were determined. For both types of activity, k(cat) initially increased (up to about 15% solvent), and then decreased with increasing concentrations of organic solvent. In contrast, K(m) increased sharply with the organic solvent concentration. Active site titration at 0 and 50% solvent indicated no change in the amount of active enzyme. Fluorometric measurements of the emission spectrum of papain did not indicate any major conformational changes with increasing concentrations of organic solvent.
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Affiliation(s)
- M M Fernandez
- Department of Chemical Engineering, University of California at Berkeley, California 94720, USA
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4
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Drøhse HB, Breddam K, Christensen U. Mechanism of Carboxypeptidase Y Catalyzed Hydrolysis and Aminolysis Reactions. ACTA ACUST UNITED AC 2009. [DOI: 10.3109/10242429109014859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Helle B. Drøhse
- Chemical Laboratory IV, University of Copenhagen, Universitetsparken, 5, DK-2100, Copenhagen, Denmark
| | - Klaus Breddam
- Chemical Laboratory IV, University of Copenhagen, Universitetsparken, 5, DK-2100, Copenhagen, Denmark
| | - Ulla Christensen
- Chemical Laboratory IV, University of Copenhagen, Universitetsparken, 5, DK-2100, Copenhagen, Denmark
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5
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Schellenberger V, Aaviksaar A, Jakubke HD. Salt-Enhanced Aminolysis of Acyl-α-Chymotrypsins by Dipeptides. ACTA ACUST UNITED AC 2009. [DOI: 10.3109/10242429109000692] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- V. Schellenberger
- Department of Biochemistry, Biosciences Division, Leipzig University, Talstr. 33, D-0-7010, Leipzig, Germany
| | - A. Aaviksaar
- Laboratory of Bioorganic Chemistry, Institute of Chemical Physics and Biophysics of the Estonian Academy of Sciences, PO Box 670, Tallinn, 200026, USSR
| | - H.-D. Jakubke
- Department of Biochemistry, Biosciences Division, Leipzig University, Talstr. 33, D-0-7010, Leipzig, Germany
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6
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Chaudhary AK, Beckman EJ, Russell AJ. Nonequal reactivity model for biocatalytic polytransesterification. AIChE J 2006. [DOI: 10.1002/aic.690440323] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Alkema WBL, de Vries E, Floris R, Janssen DB. Kinetics of enzyme acylation and deacylation in the penicillin acylase-catalyzed synthesis of beta-lactam antibiotics. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:3675-83. [PMID: 12950251 DOI: 10.1046/j.1432-1033.2003.03728.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Penicillin acylase catalyses the hydrolysis and synthesis of semisynthetic beta-lactam antibiotics via formation of a covalent acyl-enzyme intermediate. The kinetic and mechanistic aspects of these reactions were studied. Stopped-flow experiments with the penicillin and ampicillin analogues 2-nitro-5-phenylacetoxy-benzoic acid (NIPAOB) and d-2-nitro-5-[(phenylglycyl)amino]-benzoic acid (NIPGB) showed that the rate-limiting step in the conversion of penicillin G and ampicillin is the formation of the acyl-enzyme. The phenylacetyl- and phenylglycyl-enzymes are hydrolysed with rate constants of at least 1000 s-1 and 75 s-1, respectively. A normal solvent deuterium kinetic isotope effect (KIE) of 2 on the hydrolysis of 2-nitro-5-[(phenylacetyl)amino]-benzoic acid (NIPAB), NIPGB and NIPAOB indicated that the formation of the acyl-enzyme proceeds via a general acid-base mechanism. In agreement with such a mechanism, the proton inventory of the kcat for NIPAB showed that one proton, with a fractionation factor of 0.5, is transferred in the transition state of the rate-limiting step. The overall KIE of 2 for the kcat of NIPAOB resulted from an inverse isotope effect at low concentrations of D2O, which is overridden by a large normal isotope effect at large molar fractions of D2O. Rate measurements in the presence of glycerol indicated that the inverse isotope effect originated from the higher viscosity of D2O compared to H2O. Deacylation of the acyl-enzyme was studied by nucleophile competition and inhibition experiments. The beta-lactam compound 7-aminodesacetoxycephalosporanic acid (7-ADCA) was a better nucleophile than 6-aminopenicillanic acid, caused by a higher affinity of the enzyme for 7-ADCA and complete suppression of hydrolysis of the acyl-enzyme upon binding of 7-ADCA. By combining the results of the steady-state, presteady state and nucleophile binding experiments, values for the relevant kinetic constants for the synthesis and hydrolysis of beta-lactam antibiotics were obtained.
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Affiliation(s)
- Wynand B L Alkema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands
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8
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Youshko MI, Chilov GG, Shcherbakova TA, Svedas VK. Quantitative characterization of the nucleophile reactivity in penicillin acylase-catalyzed acyl transfer reactions. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1599:134-40. [PMID: 12479414 DOI: 10.1016/s1570-9639(02)00413-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophile reactivity of two most known nuclei of penicillins and cephalosporins, 6-aminopenicillanic (6-APA) and 7-aminodesacetoxycephalosporanic (7-ADCA) acids, was quantitatively characterized. In penicillin acylase (PA)-catalyzed acyl transfer reactions the relative reactivity of the added nucleophile compared to the water (i.e. nucleophile reactivity) is defined by two complex kinetic parameters beta(0) and gamma, and depends on the nucleophile concentration. In turn, parameters beta(0) and gamma were shown to be dependent on the structure of both reactants involved: nucleophile and acyl donor. Analysis of the kinetic scheme revealed that nucleophile reactivity is one of a few key parameters controlling efficiency of PA-catalyzed acyl transfer to the added nucleophile in an aqueous medium. Computation of the maximum nucleophile conversion to the product using determined nucleophile reactivity parameters in the synthesis of three different antibiotics, ampicillin, amoxicillin and cephalexin, showed good correlation with the results of corresponding synthetic experiments. Suggested approach can be extended to the quantitative description and optimization of PA-catalyzed acyl transfer reactions in a wide range of experimental conditions.
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Affiliation(s)
- Maxim I Youshko
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
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9
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Hänsler M, Ullmann G, Jakubke HD. The application of papain, ficin and clostripain in kinetically controlled peptide synthesis in frozen aqueous solutions. J Pept Sci 1995; 1:283-7. [PMID: 9223006 DOI: 10.1002/psc.310010502] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The capability of the cysteine proteases ficin, papain and clostripain to form peptide bonds in frozen aqueous solutions was investigated. Freezing the reaction mixture resulted in increased peptide yields in kinetically controlled coupling of Bz-Arg-OEt with various amino acid amides and dipeptides. Under these conditions, peptide yields increased up to 70% depending on the enzyme and the amino component used. Enzyme-catalysed peptide syntheses were carried out under optimized reaction conditions (temperature, amino component concentration and pH before freezing) using the condensation of Bz-Arg-OEt and H-Leu-NH2 as a model reaction.
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Affiliation(s)
- M Hänsler
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, Leipzig University, Germany
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10
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Gololobov MY, Stepanov VM, Voyushina TL, Adlercreutz P. The second nucleophile molecule binds to the acyl-enzyme-nucleophile complex in alpha-chymotrypsin catalysis. Kinetic evidence for the interaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 217:955-63. [PMID: 8223653 DOI: 10.1111/j.1432-1033.1993.tb18326.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
alpha-Chymotrypsin-catalyzed acyl transfer was studied using three acyl-group donors (Mal-L-Ala-L-Ala-L-PheOMe, Bz-L-TyrOEt and Ac-L-TrpOEt; Mal, maleyl; Bz, benzoyl; OMe, methyl ester; OEt, ethyl ester) and a series of amino-acid amides. Most of the reactions studied can be described by the simplest kinetic model without the nucleophile binding to the acyl-enzyme. The alpha-chymotrypsin-catalyzed transfer of the Mal-L-Ala-L-Ala-L-Phe group to the amides of L-Phe and L-Tyr showed a linear dependence of the partition constant, p, on the nucleophile concentration which can be interpreted by the hydrolysis of the acyl-enzyme-nucleophile complex. The alpha-chymotrypsin-catalyzed transfer of the Bz-L-Tyr and Ac-L-Trp groups to several amino-acid amides showed unusual behavior which can be interpreted by the kinetic model involving formation of a complex of the acyl-enzyme with two nucleophile molecules. These observations can explain the conflicting conclusions concerning the kinetics of alpha-chymotrypsin-catalyzed acyl transfer evident in previous studies.
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Affiliation(s)
- M Y Gololobov
- Department of Biotechnology, University of Lund, Sweden
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11
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Ménard R, Carmona E, Plouffe C, Brömme D, Konishi Y, Lefebvre J, Storer AC. The specificity of the S1' subsite of cysteine proteases. FEBS Lett 1993; 328:107-10. [PMID: 8344413 DOI: 10.1016/0014-5793(93)80975-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The specificity of the S1' subsite of the cysteine proteases cathepsin B, L, S and papain has been investigated using a series of intramolecularly quenched fluorogenic substrates (Dansyl-Phe-Arg-AA-Trp-Ala) where the P1' amino acid (AA) has been varied. Taken individually, each enzyme displays a relatively broad S1' subsite specificity and this subsite cannot be considered as a primary site of specificity. Notable differences do exist however between the various proteases. Cathepsin B prefers large hydrophobic residues in the P1' position of a substrate while cathepsin L has an opposite trend, favoring amino acids with small (Ala, Ser) or long but non-branched (Asn, Gln, Lys) side chains. Cathepsin S and papain display a somewhat broader S1' subsite specificity.
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Affiliation(s)
- R Ménard
- Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec
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12
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Schellenberger V, Jakubke HD. Proteasekatalysierte kinetisch kontrollierte Peptidsynthese. Angew Chem Int Ed Engl 1991. [DOI: 10.1002/ange.19911031105] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Abstract
Carboxypeptidase C partially purified from the flavedo of citrus fruit by a new, simple procedure was studied as a catalyst for peptide-bond formation. Dipeptides were obtained in high yields (80-95%) with Bz--Tyr--OEt as carboxyl-compound, and amino acid amides and amino acid alkylesters as nucleophiles. To characterize the synthesis reaction, a number of parameters such as pH, excess of the nucleophile, and the molarity of the buffer were evaluated. The yield of dipeptides depends on the side chain of the amino acid alkylester used as the carboxyl component as well as on the N-terminal protecting group. Esterase activity was minimal in the absence of a nucleophile, suggesting a modified mechanism for the synthesis reaction compared to other serine proteases. No secondary hydrolysis of the peptides formed was observed.
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Affiliation(s)
- D Steinke
- Institut für Enzymtechnologie, Heinrich Heine Universität Düsseldorf, Jülich, FRG
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14
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Gololobov MYu, Petrauskas A, Pauliukonis R, Koschke V, Borisov IL, Svedas V. Increased nucleophile reactivity of amino acid beta-naphthylamides in alpha-chymotrypsin-catalyzed peptide synthesis. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1041:71-8. [PMID: 2223849 DOI: 10.1016/0167-4838(90)90124-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Alpha-chymotrypsin-catalyzed acyl transfer from Boc-L-MetONp, Ac-L-TyrOEt, Bz-L-TyrOMe, Mal-L-PheOMe to the C-protected amino acids (L-AlaNH2, L-LeuNH2, L-ArgOMe and beta-naphthylamides of L-Arg, L-Leu, L-Ala and L-Glu) has been studied. Modification of the carboxylic groups with beta-naphthylamide was shown to increase the reactivity of nucleophiles in these reactions by a factor of more than 100 in comparison with amides and esters of the same amino acids. This effect can be accounted for by the effective formation of the nucleophile-acylenzyme complex due to hydrophobic interactions of the beta-naphthylamide moiety with the corresponding subsite of alpha-chymotrypsin. The reaction kinetics follows the scheme involving hydrolysis of the nucleophile-acylenzyme intermediate. The contribution of this pathway depends on the structures of both the acyl-group donor and the added nucleophile. The competitive inhibition by amino acid beta-naphthylamides is also observed. The results obtained show that modification of the COOH-group of added nucleophiles by beta-naphthylamide strongly affects the reactivity of these compounds in the alpha-chymotrypsin-catalyzed peptide synthesis.
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Affiliation(s)
- Gololobov MYu
- Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow University, U.S.S.R
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15
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Pazhanisamy S, Govardhan CP, Pratt RF. Beta-lactamase-catalyzed aminolysis of depsipeptides: amine specificity and steady-state kinetics. Biochemistry 1989; 28:6863-70. [PMID: 2819039 DOI: 10.1021/bi00443a013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
beta-Lactamases catalyze not only the hydrolysis but also the aminolysis of certain depsipeptides [Pratt, R. F., & Govardhan, C. P. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 1302-1306]. This paper explores further the specificity of the aminolysis reaction with respect to the structure of the amine and also the steady-state kinetics of the reaction. The amines preferred by the class C beta-lactamase of Enterobacter cloacae P99 appear to be aromatic D-alpha-amino acids. The general order of substrate effectiveness at pH 7.5 appears to be aromatic D-alpha-amino acids greater than large aliphatic D-alpha-amino acids greater than small aliphatic D-alpha-amino acids approximately small aliphatic L-alpha-amino acids greater than large L-alpha-amino acids. Charges on the aliphatic side chains seem unimportant. Ineffective as acyl acceptors were beta-amino acids, alpha-amino phosphonic acids, and, in general, amines, including amino acid carboxyl derivatives and peptides. There is thus strong evidence for specific interaction between the amine and the enzyme. A detailed kinetics study was made of the P99 beta-lactamase-catalyzed aminolysis of m-[[(phenylacetyl)glycyl]oxy]benzoic acid by D-phenylalanine. The steady-state kinetics were complex because of the presence of parallel enzyme-catalyzed hydrolysis and aminolysis reactions. An empirical rate equation was obtained for the total reaction. This has important elements in common with that previously found for the aminolysis of specific peptides by the DD-peptidases of various Streptomyces strains [e.g., Frere, J.-M., Ghuysen, J.-M., Perkins, H.R., & Nieto, M. (1973) Biochem. J. 135, 483-492].(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S Pazhanisamy
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06457
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16
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Hansch C, Kim D, Leo AJ, Novellino E, Silipo C, Vittoria A. Toward a quantitative comparative toxicology of organic compounds. Crit Rev Toxicol 1989; 19:185-226. [PMID: 2653732 DOI: 10.3109/10408448909037471] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Correlation equations between logP (P = octanol water partition coefficient) and the biological activity of alcohols has been derived for 101 examples on all sorts of systems, from simple proteins to whole animals. This provides an overview of the toxic nature of hydrophobic compounds which can be used as a basis for comparison of more complex chemicals. About 100 examples of the hydrophobic effects of chemicals, other than alcohols, to various living systems or their parts are presented for comparison. It is clear that hydrophobic xenobiotics are toxic to almost every form of life, including humans (or parts there of).
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Affiliation(s)
- C Hansch
- Department of Chemistry, Pomona College, Claremont, California
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17
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Yu. Gololobov M, Borisov IL, Belikov VM, ?vedas VK. Acyl group transfer by proteases forming acyl-enzyme intermediate: Kinetic model analysis. Biotechnol Bioeng 1988; 32:866-72. [DOI: 10.1002/bit.260320704] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Chipman DM, Jencks WP. Specificity of the sarcoplasmic reticulum calcium ATPase at the hydrolysis step. Biochemistry 1988; 27:5707-12. [PMID: 2972313 DOI: 10.1021/bi00415a047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The coupling of Ca2+ transport to ATP hydrolysis by the SR ATPase requires that the enzyme operate with considerable specificity, which is different at different steps. The limits of specificity of the calcium-free phosphorylated enzyme for transfer of its phosphoryl group to water have been examined. The rate of transfer of the phosphoryl group to the simple nucleophile methanol was compared to its transfer to water by following the formation of methyl phosphate from inorganic phosphate. The reverse reaction, hydrolysis of methyl phosphate, was compared to phosphate-water oxygen exchange. The reactions involving methanol as nucleophile or leaving group are at least 2-3 orders of magnitude slower than those involving water. This result indicates that the transition state for this reaction involves strong and specific interactions of the H2O molecule with the enzyme. These interactions may also involve the bound Mg2+ ion. The results also suggest that the difference in specificity between Ca2+ free and Ca2+ bound states of the enzyme involves significant differences in the structure of the catalytic site.
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Affiliation(s)
- D M Chipman
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254
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19
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Groeger U, Stehle P, Fürst P, Leuchtenberger W, Drauz K. Papain‐catalyzed synthesis of dipeptides. FOOD BIOTECHNOL 1988. [DOI: 10.1080/08905438809549686] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Barbas CF, Wong CH. One-pot tripeptide syntheses from three single amino acid derivatives catalyzed by papain. Tetrahedron Lett 1988. [DOI: 10.1016/0040-4039(88)85044-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Shima H, Fukuda M, Tanabe K, Ito T, Kunugi S. Wheat Carboxypeptidase-Catalyzed Peptide Synthesis by Aminolysis ofN-Acyl Amino Acid Ester. Indication of the Acyl-Enzyme Mechanism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1987. [DOI: 10.1246/bcsj.60.1403] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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22
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Brocklehurst K, Willenbrock F, Salih E. Chapter 2 Cysteine proteinases. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/s0167-7306(09)60016-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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23
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Kasche V, Haufler U, Riechmann L. Equilibrium and kinetically controlled synthesis with enzymes: semisynthesis of penicillins and peptides. Methods Enzymol 1987; 136:280-92. [PMID: 3316930 DOI: 10.1016/s0076-6879(87)36028-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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24
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Riechmann L, Kasche V. Reaction mechanism, specificity and pH-dependence of peptide synthesis catalyzed by the metalloproteinase thermolysin. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 872:269-76. [PMID: 3730402 DOI: 10.1016/0167-4838(86)90280-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The initial rates of peptide bond formation catalyzed by the metalloproteinase thermolysin were determined. The dependence of the formation rates on the concentration of the carboxyl donor and the acceptor can be explained by a rapid-equilibrium random bireactant mechanism, in which the binding of one substrate has a positive influence on the binding of the other (synergism). The specificity of the enzyme for the donor and acceptor in the condensation reaction was further investigated by determining the apparent kinetic parameters kcat and Km for various substrates. The pH-dependence of the initial rates of synthesis was found to be identical to the pH-dependence of the hydrolytic action of the enzyme. The rates are also shown to be independent of the pKa of the amino group of the acceptor, indicating that deprotonation of the attacking nucleophile in the synthetic reaction is not rate-limiting.
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25
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Kasche V. Mechanism and yields in enzyme catalysed equilibrium and kinetically controlled synthesis of β-lactam antibiotics, peptides and other condensation products. Enzyme Microb Technol 1986. [DOI: 10.1016/0141-0229(86)90003-7] [Citation(s) in RCA: 252] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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27
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Riechmann L, Kasche V. Peptide synthesis catalyzed by the serine proteinases chymotrypsin and trypsin. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 830:164-72. [PMID: 4016137 DOI: 10.1016/0167-4838(85)90024-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ratio of the initial rates of aminolysis and hydrolysis in peptide semisynthesis catalyzed by chymotrypsin (EC 3.4.21.1) and trypsin (EC 3.4.21.4) was found to depend non-linearly on the concentration of the added nucleophile. This is in agreement with a mechanism for the peptide semisynthesis where nucleophile binding to the acyl-enzyme precedes the aminolysis reaction. The acyl-enzyme-nucleophile complex can still be deacylated by water. A temperature optimum was observed for peptide synthesis for valinamide as nucleophile. This and the similarity of the P'1 specificity in peptide hydrolysis and nucleophile specificity in peptide semisynthesis also support the mechanism including the nucleophile binding. The influence of added nucleophiles on the acylation step during peptide synthesis was studied by determining kcat and Km for the appearance of the leaving group from the acyl donor. Acceptor (= nucleophile) specificity was shown to be more important for high ratios of aminolysis: hydrolysis than donor specificity. The maximum product concentration during kinetically controlled peptide semisynthesis was found to be independent of the enzyme content.
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28
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Riechmann L, Kasche V. Kinetic studies on the mechanism and the specificity of peptide semisynthesis catalyzed by the serine proteases alpha-chymotrypsin and beta-trypsin. Biochem Biophys Res Commun 1984; 120:686-91. [PMID: 6732779 DOI: 10.1016/0006-291x(84)91310-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The mechanism of peptide semisynthesis catalyzed by alpha-chymotrypsin and beta-trypsin has been investigated. The dependence of the apparent ratio of the second order rate constants for the deacylation of the acyl-enzyme intermediate by water and other nucleophiles (amino acid amides) on the nucleophile concentration indicates a mechanism that involves two acyl-enzymes. One with and one without bound nucleophile that both can be deacylated by water. The nucleophile specificity in peptide semisynthesis catalyzed by the proteases was found to reflect the P1-specificity in the corresponding hydrolytic reaction.
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29
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30
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31
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Aerts GM, De Bruyne CK. Effects of alcohols on hydrolysis catalyzed by beta-D-glucosidase from Stachybotrys atra. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 660:317-24. [PMID: 6793076 DOI: 10.1016/0005-2744(81)90176-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The interaction of alcohols in the hydrolysis of aryl beta-D-glucopyranosides and aryl beta-D-xylopyranosides by beta-D-glucosidase (beta-D-glucoside glucohydrolase, EC 3.2.1.21) from Stachybotrys atra has been investigated. The results constitute support for the presence of a glycosyl-enzyme intermediate, formed during the first step (glycosylation) of the proposed two-step mechanism. Transfer of the glycosyl group to an alcohol, with the formation of an alkyl glycopyranoside, can take place in parallel to the transfer to a water molecule (second or deglycosylation step). The alcohol binds to the free enzyme and to the glycosyl-enzyme intermediate. The glycosyl-enzyme-alcohol complex undergoes hydrolysis in addition to the alcoholysis. For aryl beta-D-glucopyranosides the deglycosylation step is rate-limiting. For aryl beta-D-xylopyranosides two kinds of substrate behaviour can be observed. Depending on the substituent group on the phenyl ring, either both steps are rate-controlling or the first step is rate-limiting. Electron-withdrawing substituents increase the rate at which the substrate aglycon group is released.
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Ascenzi P, Menegatti E, Bortolotti F, Guarneri M, Antonini E. Steady-state and pre-steady-state kinetics of the trypsin-catalysed hydrolysis of alpha-CBZ-L-lysine-p-nitrophenyl ester. BIOCHIMICA ET BIOPHYSICA ACTA 1981; 658:158-64. [PMID: 6783103 DOI: 10.1016/0005-2744(81)90259-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The catalytic properties of bovine tyrpsin (EC 3.4.21.4) have been investigated using a synthetic chromogenic substrate: alpha-CBZ-L-lysine-p-nitrophenyl ester (ZLNPE). The use of ZLNPE allows the determination of trypsin down to a concentration of 2 . 10(-9) M. Steady-state and pre-steady-state data have been in the framework of the minimum three-step mechanism: (Formula: see text). The pH-dependence of the kinetic parameters shows that at acid pH values (congruent to 2.6) the k+3 step is rate limiting in catalysis, whereas for pH values higher than 4.8 k+2 becomes rate limiting. This change in rate-limiting step with pH illustrates the danger in the assumption that kcat vs. pH profiles for protease action on substrates with good leaving groups are equivalent to k+3 vs. pH profiles.
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Widmer F, Johansen JT. Enzymatic peptide synthesis. Carboxypeptidase Y catalyzed formation of peptide bonds. ACTA ACUST UNITED AC 1979. [DOI: 10.1007/bf02910870] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Yuthavong Y, Suttimool W. Rate constants of individual steps in papain-catalysed reactions. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 523:198-206. [PMID: 629988 DOI: 10.1016/0005-2744(78)90022-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rate constants for acylation of papain (EC 3.4.22.2) by specific substrates and its subsequent deacylation are derived from kinetic analysis of the reactions in the presence of aminoacetonitrile and methanol. Methyl and ethyl hippurate and methyl N-benzyloxycarbonylglycinate have marginally higher values of rate constants for acylation than for deacylation, while the reverse is true for ethyl N-benzoyl-L-arginate. Both acylation and deacylation are rate-determining for these substrates, while only deacylation irate-determining for methyl-N-acetyl-L-phenylalanylglycinate. Deacylation is the only rate-determining step for p-nitrophenyl esters of hippuric acid, N-benzyloxycarbonylglycine and N-acetyl-L-phenylalanylglycine. These results are discussed in relation to those from inactivation of the enzyme by alkylating agent in the presence of substrate.
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Abstract
alpha-Chymotrypsin (EC 3.4.21.1)-catalysed syntheses of peptides were performed with various N-acylated amino acid or peptide esters as donors, and amino acid derivatives, peptides or their derivatives as acceptors. Under optimal conditions the synthesis was almost quantitative. As acceptor nucleophiles, free amino acids or the ester derivatives were inadequate, but amino acid amides or hydrazides, di- or tri-peptides, or the amides, hydrazides and esters of the peptides were useful. The nucleophile specificity for synthesis was markedly similar to the leaving-group specificity in hydrolysis; hydrophobic or bulky amino acid residues were most effecient at both P1' and P2' positions [notation of Schechter & Berger (1967) Biochem. Biophys. Res. Commun. 27, 157-162], but L-proline as well as D-amino acid residues were the worst choices. The synthesis was further dependent on the solubility of the products synthesized; a higher yield of products was expected with lower solubility. As donor esters, good substrates were all useful. Accordingly, fragment condensation was possible by using N-acylated peptide esters and various peptides. The present study suggested that alpha-chymotrypsin may become a useful tool for peptide synthesis.
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Abstract
As a first step in the investigation of papain catalysis using subzero temperatures to detect, accumulate, and characterize enzyme-substrate intermediates, we have studied some potential cryosolvents and carried out preliminary intermediate trapping experiments. The effects of subzero temperatures and aqueous dimethyl sulfoxide solutions on the papain-catalyzed hydrolysis of Nalpha-carbobenzoxy-L-lysine p-nitrophenyl ester have been investigated in detail. At 0 degrees C, the value of kcat decreases with increasing dimethyl sulfoxide concentration, decreasing in proportion to the decreased water concentration; however, the value of Km increases exponentially. The effect on Km can be accounted for by a combination of both dielectric and competitive inhibition effects. The Arrhenius plot for the deacylation reaction in 7.65 M (60% v/v) dimethyl sulfoxide is linear over the temperature range 0 to -45 degrees C and extrapolates to a calculated value of kcat at 25 degrees C in excellent agreement with that obtained in the absence of organic solvent. The pH-rate profile is not substantially perturbed by the presence of 7.65 M dimethyl sulfoxide. At -45 degrees C and below, turnover occurs extremely slowly, and is essentially negligible, although acylation is still quite rapid. Consequently, the acyl enzyme, Na-carbobenzoxy-L-lysyl-papain, can be readily accumulated and trapped at temperatures below -50 degrees C. At these low temperatures, under conditions of excess substrate, the amount of p-nitrophenol liberated in the acylation reaction is equivalent to the active-site normality of the enzyme, indicating a 1:1 stoichiometry in formation of the acyl enzyme. The effect of dimethyl sulfoxide up to 7.65 M, on the intrinsic ultraviolet, fluorescence, and circular dichroic properties of the enzyme shows no evidence of any solvent-induced structural changes. All experimental observations are consistent with the conclusion that 7.65 M dimethyl sulfoxide and subzero temperatures have no deleterious effects on papain-catalyzed reactions. A related series of experiments indicate that aqueous ethanol cryosolvents up to 13.7 M (80% v/v) are also suitable. Preliminary experiments at subzero temperatures using Na-carbobenzoxy-L-lysine methyl ester suggest the existence of three enzyme-substrate intermediates which can be detected and accumulated.
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Dawson RM. The reaction of choline and 3,3-dimethyl-1-butanol with the acetylenzyme from acetylcholinesterase. J Neurochem 1975; 25:783-7. [PMID: 1471 DOI: 10.1111/j.1471-4159.1975.tb04408.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Grimard M. N-alpha-benzoyl arginine ethylester hydrolysis by porcine plasmin. A kinetic study of diethyleneglycol influence on this hydrolysis. FEBS Lett 1975; 54:334-8. [PMID: 236932 DOI: 10.1016/0014-5793(75)80934-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
The specificity of the S(1)' subsite of the proteolytic enzyme papain was investigated by studying the effect of l-alpha-amino acid amides on the enzyme-catalysed hydrolysis of N-benzyloxycarbonylglycine p-nitrophenyl ester and by determining the kinetic parameters for the enzyme-catalysed hydrolysis of some N-benzyloxycarbonylglycyl-l-amino acid amides. These studies showed that the S(1)' subsite has a predilection for hydrophobic residues, in particular l-leucine and l-tryptophan. The specificity for these residues is manifest in both the binding and acylation steps. N-Benzyloxycarbonylglycine amide is not hydrolysed under comparable conditions, indicating that the amide group adjacent to and on the C-terminal side of the peptide bond about to be cleaved makes an important contribution to the rate of the papain-catalysed hydrolysis of peptides.
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Schuber F, Pinck M. On the chemical reactivity of aminoacyl-tRNA ester bond. 2. Aminolysis by tris and diethanolamine. Biochimie 1974; 56:391-5. [PMID: 4853443 DOI: 10.1016/s0300-9084(74)80147-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Fink AL, Gwyn C. Conformational changes in papain during catalysis and ligand binding. Biochemistry 1974; 13:1190-5. [PMID: 4814720 DOI: 10.1021/bi00703a601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Boland MJ, Hardman MJ. The actinidin-catalysed hydrolysis of N-a-benzyloxycarbonyl-L-lysine p-nitrophenyl ester. pH dependence and mechanism. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 36:575-82. [PMID: 4730966 DOI: 10.1111/j.1432-1033.1973.tb02947.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Hollaway MR, Hardman MJ. Evidence for a rate-limiting conformation change in the catalytic steps of the ficin and papain-catalysed hydrolyses of benzyloxycarbonyl-L-lysine p-nitrophenyl ester. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 32:537-46. [PMID: 4692223 DOI: 10.1111/j.1432-1033.1973.tb02639.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Werber MM, Greenzaid P. Chymotrypsin-catalyzed reactions of phenyl hippurate with alcohols. Kinetic evidence for a binding site for nucleophiles. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 293:208-16. [PMID: 4685277 DOI: 10.1016/0005-2744(73)90393-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dillingham EO, Mast RW, Bass GE, Autian J. Toxicity of methyl- and halogen-substituted alcohols in tissue culture relative to structure-activity models and acute toxicity in mice. J Pharm Sci 1973; 62:22-30. [PMID: 4734195 DOI: 10.1002/jps.2600620103] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Hersh LB. The Effect of Aliphatic Alcohols and Organic Solvents on Reactions Catalyzed by 5-Hydroxy-N-methylpyroglutamate Synthetase. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(19)45846-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Abstract
The specificity of the proteolytic enzyme, papain, for the peptide bond of the substrate adjacent to that about to be cleaved and for the acyl residue of some N-acylglycine derivatives is manifest almost exclusively in the formation of the acyl-enzyme from the enzyme-substrate complex. Models for the enzyme-substrate complex and acyl-enzyme intermediate are suggested that account for these observations. In particular it is suggested that the peptide bond of the substrate adjacent to that about to be cleaved, is bound in the cleft of the enzyme between the NH group of glycine-66 and the backbone C=O group of aspartic acid-158, and provides a sensitive amplification mechanism through which the specificity of the enzyme for hydrophobic amino acids such as l-phenylalanine is relayed. It is also suggested that the distortion in the enzyme-substrate complex and the binding of the peptide bond adjacent to that about to be cleaved are also linked and behave co-operatively, the distortion of the protein facilitating binding and the stronger binding facilitating distortion. The results imply that between the enzyme-substrate complex and the acyl-enzyme a relaxation of the protein conformation must occur.
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Glazer A, Smith EL. 14 Papain and Other Plant Sulfhydryl Proteolytic Enzymes. HYDROLYSIS: PEPTIDE BONDS 1971. [DOI: 10.1016/s1874-6047(08)60405-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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