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Galanakis CM, Patsioura A, Gekas V. Enzyme Kinetics Modeling as a Tool to Optimize Food Industry: A Pragmatic Approach Based on Amylolytic Enzymes. Crit Rev Food Sci Nutr 2014; 55:1758-70. [DOI: 10.1080/10408398.2012.725112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fruton JS. The specificity and mechanism of pepsin action. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 33:401-43. [PMID: 4916858 DOI: 10.1002/9780470122785.ch9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Morihara K. Comparative specificity of microbial proteinases. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 41:179-243. [PMID: 4213643 DOI: 10.1002/9780470122860.ch5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Murakami Y, Chiba K, Oda T, Hirata A. Novel kinetic analysis of enzymatic dipeptide synthesis: effect of pH and substrates on thermolysin catalysis. Biotechnol Bioeng 2001; 74:406-15. [PMID: 11427942 DOI: 10.1002/bit.1131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The point of maximum activity is specific to a particular substrate-enzyme system but may vary with different substrates and the same enzyme. The specificity of enzymes has, however, been generally reported only at their "optimal" pH. In this article, we introduce the Michaelis-Menten equation taking pH into account, and apply it to the pH-activity profile of the thermolysin-catalyzed dipeptide synthesis. It has been reported to date that the pH-activity profile of thermolysin follows a bell-shaped curve with a maximal activity at or near pH 7.0. The profiles obtained in this study, however, indicated that the optimal pH varied from 5.8 (for F-AspPheOMe) to 7.3 (for Z-ArgPheOMe), and the order of thermolysin activity was greatly dependent on the pH of reaction media. We have succeeded in evaluating the substrates-induced change of the dissociation states of the active site of thermolysin using the hydrophobicity of substrates. We have obtained apparent kinetic parameters which are independent of the pH of reaction media. The apparent specificity of thermolysin which were independent of pH of the reaction media was in order L-Leu > L-Asp > L-Arg > L-Ala > L-Gly > L-Val and Z > Boc = F at P1 and P2 positions, respectively.
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Affiliation(s)
- Y Murakami
- Department of Chemical Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555; Japan.
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Ligné T, Pauthe E, Monti JP, Gacel G, Larreta-Garde V. Additional data about thermolysin specificity in buffer- and glycerol-containing media. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1337:143-8. [PMID: 9003446 DOI: 10.1016/s0167-4838(96)00142-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthesis and use of various substrates permit an improved approach to thermolysin-peptide recognition and elucidation of several new criteria affecting enzyme specificity. Nature and position of the recognized residue, role of adjacent amino acids, lateral chain hydrophobicity, and volume and length of peptides were all considered. Hydrolysis reactions were also carried out in the presence of glycerol; the effect of microenvironment modifications was quantitative, for example in inducing variations in catalytic reaction rates, and also qualitative, such as in influencing affinity.
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Affiliation(s)
- T Ligné
- Laboratoire de Technologie Enzymatique, URA 1442 CNRS, Compiègne University, France
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7
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Wetmore DR, Wong SL, Roche RS. The efficiency of processing and secretion of the thermolysin-like neutral protease from Bacillus cereus does not require the whole prosequence, but does depend on the nature of the amino acid sequence in the region of the cleavage site. Mol Microbiol 1994; 12:747-59. [PMID: 8052127 DOI: 10.1111/j.1365-2958.1994.tb01062.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using deletion mutants, it is shown that part of the prosequence, the omega-peptide (-4, -24), of the thermolysin-like neutral protease (TNP) from Bacillus cereus, Cnp, is not required for efficient processing and secretion of fully functional mature protease. It is demonstrated that the rate and selectivity of proprotein processing is dependent on both the flexibility and primary sequence of the processing site. Processing is found to be particularly sensitive to the nature of the amino acid three residues upstream from the site of cleavage. A consensus sequence for TNP proprotein processing has been identified, which provides further insights. Finally, a larger deletion of a portion of the Cnp prosequence upstream from the omega-peptide that includes amino acids conserved among TNPs reduces the rate of processing and secretion of Cnp and results in the accumulation of export-incompetent pre-proprotein in the cell fraction.
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Affiliation(s)
- D R Wetmore
- Department of Biological Sciences, University of Calgary, Alberta, Canada
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Abstract
Antigen receptor genes are assembled by site-specific DNA rearrangement. The recombination activator genes RAG-1 and RAG-2 are essential for this process, termed V(D)J rearrangement. The activity and stability of the RAG-2 protein have now been shown to be regulated by phosphorylation. In fibroblasts RAG-2 was phosphorylated predominantly at two serine residues, one of which affected RAG-2 activity in vivo. The threonine at residue 490 was phosphorylated by p34cdc2 kinase in vitro; phosphorylation at this site in vivo was associated with rapid degradation of RAG-2. Instability was transferred to chimeric proteins by a 90-residue portion of RAG-2. Mutation of the p34cdc2 phosphorylation site of the tumor suppressor protein p53 conferred a similar phenotype, suggesting that this association between phosphorylation and degradation is a general mechanism.
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Affiliation(s)
- W C Lin
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Poncz L. Substrate inhibition of Pseudomonas aeruginosa elastase by 3-(2-furyl)acryloyl-glycyl-L-phenylalanyl-L-phenylalanine. Arch Biochem Biophys 1988; 266:508-15. [PMID: 3142360 DOI: 10.1016/0003-9861(88)90283-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The kinetics of hydrolysis by Pseudomonas aeruginosa elastase at 37 degrees C and pH 7.3 of 3-(2-furyl)acryloyl-glycyl-L-phenylalanyl-L-phenylalanine is compatible with nonproductive substrate inhibition, i.e., v = V.[S]/(Km + [S] + [S]2/K1), and the values of Km, Ki, and kappa cat are 1.4 mM, 5.0 mM, and 240 s-1, respectively. Product inhibition experiments are in agreement with an ordered release of product, with L-phenylalanyl-L-phenylalanine, the amino-containing product, being released first from the elastase.product complex. The values of Ki for L-phenylalanyl-L-phenylalanine and 3-(2-furyl)acryloyl-glycine are 1.5 and 4.0 mM, respectively. Kinetic experiments indicate that the second molecule of substrate combines with elastase.substrate to form a dead-end elastase . (substrate)2 complex.
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Affiliation(s)
- L Poncz
- Case Western Reserve University, Department of Pediatrics, Cleveland, Ohio 44106
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Berdal BP, Bøvre K, Olsvik O, Omland T. Patterns of extracellular proline-specific endopeptidases in Legionella and Flavobacterium spp. demonstrated by use of chromogenic peptides. J Clin Microbiol 1983; 17:970-4. [PMID: 6348081 PMCID: PMC272785 DOI: 10.1128/jcm.17.6.970-974.1983] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Some Legionella strains possess a strong extracellular proline-specific endopeptidase (PSE) activity. Using an enlarged selection of chromogenic peptides representing a variety of N-terminal amino-acids binding to a -prolyl-proline, paranitroanilide chain, PSE activity of Legionella and Flavobacterium strains was examined. Differences in PSE activity emphasized the importance of the chemical structure at the nonchromogenic end of the peptide substrates. There seem to be distinct patterns of N-terminal specificity of PSE in the two bacterial groups.
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11
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Hiromi K, Ohnishi M, Tanaka A. Subsite structure and ligand binding mechanism of glucoamylase. Mol Cell Biochem 1983; 51:79-95. [PMID: 6406831 DOI: 10.1007/bf00215589] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
1. The basic concept and outline of the subsite theory were described, which correlates quantitatively the subsite structure (the arrangement of subsite affinities) to the action pattern of amylases in a unified manner. 2. The subsite structures of several amylases including glucoamylase were summarized. 3. In parallel with the theoretical prediction obtained therefrom, the binding subsites of glucose, gluconolactone and linear substrates to Rhizopus glucoamylase were investigated experimentally, by using steady-state inhibition kinetics, difference absorption spectrophotometry, and fluorometric titration. 4. From several lines of evidence, it was concluded that gluconolactone, a transition state analogue, is bound at Subsite 1 (nonreducing end side) where a tryptophan residue is located. 5. The stopped-flow kinetic studies have revealed that all the ligand bindings studied consist of two-step mechanism in which a bimolecular association between the enzyme and a ligand to form a loosely bound complex (EL) followed by the unimolecular isomerization process in which EL converts to the final firmly bound EL complex. For substrates the EL may be the productive complex and the fluorescence of the tryptophan located at Subsite 1 is quenched in their isomerization process, most probably a relocation of ligand to occupy this subsite.
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Bayliss ME, Wilkes SH, Prescott JM. Aeromonas neutral protease: specificity toward extended substrates. Arch Biochem Biophys 1980; 204:214-9. [PMID: 7000005 DOI: 10.1016/0003-9861(80)90026-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Kam CM, Nishino N, Powers JC. Inhibition of thermolysin and carboxypeptidase A by phosphoramidates. Biochemistry 1979; 18:3032-8. [PMID: 465451 DOI: 10.1021/bi00581a019] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
We have developed a depolymerase computer model that uses a minimization routine. The model is designed so that, given experimental bond-cleavage frequencies for oligomeric substrates and experimental Michaelis parameters as a function of substrate chain length, the optimum subsite map is generated. The minimized sum of the weighted-squared residuals of the experimental and calculated data is used as a criterion of the goodness-of-fit for the optimized subsite map. The application of the minimization procedure to subsite mapping is explored through the use of simulated data. A procedure is developed whereby the minimization model can be used to determine the number of subsites in the enzymic binding region and to locate the position of the catalytic amino acids among these subsites. The degree of propagation of experimental variance into the subsite-binding energies is estimated. The question of whether hydrolytic rate coefficients are constant or a function of the number of filled subsites is examined.
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Chemical modifications of the subtilisins with special reference to the binding of large substrates. A review. ACTA ACUST UNITED AC 1976. [DOI: 10.1007/bf02906260] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Thoma JA, Allen JD. Subsite mapping of enzymes: collecting and processing experimental data--a case study of an amylase-malto-oligosaccharide system. Carbohydr Res 1976; 48:105-24. [PMID: 949715 DOI: 10.1016/s0008-6215(00)83518-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two research groups have independently developed the theory and experimental methodology for quantitatively assessing substrate monomer-subsite binding-energies for depolymerases. When the two approaches are applied to the same enzyme-substrate system they yield surprisingly divergent results. This paper outlines the application of the two approaches to an amylase-maltooligosaccharide system and points out the more important areas of disagreement. We show that by proper data-management, the conflicts between the tow laboratories are basically resolved. The complexities of the subsite model demand extensive data-gathering and exacting data-processing and verification that the computed model-parameters can faithfully reproduce the experimental data.
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Oka T, Morihara K. Comparative specificity of microbial acid proteinases for synthetic peptides. II. Effect of secondary interaction. Arch Biochem Biophys 1973; 156:552-9. [PMID: 4578121 DOI: 10.1016/0003-9861(73)90304-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Matthews BW, Jansonius JN, Colman PM, Schoenborn BP, Dupourque D. Three-dimensional structure of thermolysin. NATURE: NEW BIOLOGY 1972; 238:37-41. [PMID: 18663849 DOI: 10.1038/newbio238037a0] [Citation(s) in RCA: 137] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- B W Matthews
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
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23
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Raymond MN, Garnier J, Bricas E. Studies on the specificity of chymosin (rennin). I. Kinetic parameters of the hydrolysis of synthetic oligopeptide substrates. Biochimie 1972; 54:145-54. [PMID: 4563931 DOI: 10.1016/s0300-9084(72)80098-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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24
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Morihara K, Tsuzuki H. Comparative study of various neutral proteinases from microorganisms: specificity with oligopeptides. Arch Biochem Biophys 1971; 146:291-6. [PMID: 5004124 DOI: 10.1016/s0003-9861(71)80066-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Damoglou AP, Lindley H, Stapleton IW. The hydrolysis by thermolysin of dipeptide derivatives that conatin substituted cysteine. Biochem J 1971; 123:379-84. [PMID: 5126091 PMCID: PMC1176968 DOI: 10.1042/bj1230379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
1. The preparation of protected dipeptides of the form acetylglycylamino acid amides is described, where the amino acid is phenylalanine, leucine, valine, alanine, S-methylcysteine, S-ethylcysteine, S-benzylcysteine and S-phenylcysteine. 2. Kinetic parameters for the thermolytic hydrolysis of these blocked dipeptides are reported. The rate of hydrolysis was fastest when the amino acid was leucine or phenylalanine, slower when it was S-methylcysteine, valine or S-ethylcysteine, much slower when it was alanine, and negligible for S-phenylcysteine or S-benzylcysteine. 3. The results are compared with those for similar dipeptide derivatives with benzyloxycarbonyl and furylacryloyl blocking groups, which are hydrolysed faster.
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27
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Desmazeaud MJ, Hermier JH. [Specificity of the nuclear protease produced by Micrococcus caseolyticus]. EUROPEAN JOURNAL OF BIOCHEMISTRY 1971; 19:51-5. [PMID: 5551628 DOI: 10.1111/j.1432-1033.1971.tb01286.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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28
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Affiliation(s)
- T Oka
- Shionogi Research Laboratory, Shionogi and Co., Ltd., Fukushima-ku, Osaka, Japan
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29
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Morihara K, Tsuzuki H. Thermolysin: kinetic study with oligopeptides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1970; 15:374-80. [PMID: 4993757 DOI: 10.1111/j.1432-1033.1970.tb01018.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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30
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The Action Pattern of Porcine Pancreatic α-Amylase in Relationship to the Substrate Binding Site of the Enzyme. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)62937-0] [Citation(s) in RCA: 235] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Thoma JA, Brothers C, Spradlin J. Subsite mapping of enzymes. Studies on Bacillus subtilis amylase. Biochemistry 1970; 9:1768-75. [PMID: 4985698 DOI: 10.1021/bi00810a016] [Citation(s) in RCA: 117] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Feder J, Schuck JM. Comparative kinetic studies on the neutral protease and thermolysin catalyzed hydrolysis of simple dipeptide substrates. Biotechnol Bioeng 1970. [DOI: 10.1002/bit.260120210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Morihara K, Oka T, Tsuzuki H. On the specificity of Bacillus subtilis neutral protease in relation to the compound active site. Arch Biochem Biophys 1969; 135:311-23. [PMID: 4983099 DOI: 10.1016/0003-9861(69)90545-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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35
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Millet J, Acher R, Aubert JP. Biochemical and physiological properties of an extracellular protease produced by Bacillus megaterium. Biotechnol Bioeng 1969; 11:1233-46. [PMID: 4983542 DOI: 10.1002/bit.260110617] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Morihara K, Oka T, Tsuzuki H. The compound active site of Bacillus subtilis neutral protease: some properties of six subsites. Arch Biochem Biophys 1969; 132:489-501. [PMID: 4978857 DOI: 10.1016/0003-9861(69)90393-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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37
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Millet J, Acher R. [Specificity of megateriopeptidase: an amino-endopeptidase with hydrophobic characteristics]. EUROPEAN JOURNAL OF BIOCHEMISTRY 1969; 9:456-62. [PMID: 4980359 DOI: 10.1111/j.1432-1033.1969.tb00631.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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38
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Matsubara H, Singer A, Sasaki RM. Effect of proline residue on the hydrolysis of substrates by thermolysin. Biochem Biophys Res Commun 1969; 34:719-24. [PMID: 4975980 DOI: 10.1016/0006-291x(69)90798-0] [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: 01/13/2023]
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39
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McQuade AB, Crewther WG. Peptide substrates for a proteinase of Clostridium histolyticum. BIOCHIMICA ET BIOPHYSICA ACTA 1968; 167:619-20. [PMID: 5722284 DOI: 10.1016/0005-2744(68)90055-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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