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Plapp BV, Gakhar L, Subramanian R. Dependence of crystallographic atomic displacement parameters on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenase. Acta Crystallogr D Struct Biol 2022; 78:1221-1234. [PMID: 36189742 PMCID: PMC9527765 DOI: 10.1107/s2059798322008361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022] Open
Abstract
Enzymes catalyze reactions by binding and orienting substrates with dynamic interactions. Horse liver alcohol dehydrogenase catalyzes hydrogen transfer with quantum-mechanical tunneling that involves fast motions in the active site. The structures and B factors of ternary complexes of the enzyme with NAD+ and 2,3,4,5,6-pentafluorobenzyl alcohol or NAD+ and 2,2,2-trifluoroethanol were determined to 1.1-1.3 Å resolution below the `glassy transition' in order to extract information about the temperature-dependent harmonic motions, which are reflected in the crystallographic B factors. The refinement statistics and structures are essentially the same for each structure at all temperatures. The B factors were corrected for a small amount of radiation decay. The overall B factors for the complexes are similar (13-16 Å2) over the range 25-100 K, but increase somewhat at 150 K. Applying TLS refinement to remove the contribution of pseudo-rigid-body displacements of coenzyme binding and catalytic domains provided residual B factors of 7-10 Å2 for the overall complexes and of 5-10 Å2 for C4N of NAD+ and the methylene carbon of the alcohols. These residual B factors have a very small dependence on temperature and include local harmonic motions and apparently contributions from other sources. Structures at 100 K show complexes that are poised for hydrogen transfer, which involves atomic displacements of ∼0.3 Å and is compatible with the motions estimated from the residual B factors and molecular-dynamics simulations. At 298 K local conformational changes are also involved in catalysis, as enzymes with substitutions of amino acids in the substrate-binding site have similar positions of NAD+ and pentafluorobenzyl alcohol and similar residual B factors, but differ by tenfold in the rate constants for hydride transfer.
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Affiliation(s)
- Bryce V. Plapp
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
| | - Lokesh Gakhar
- Protein and Crystallography Facility, Carver College of Medicine, The University of Iowa, Iowa City, IA 52252, USA
| | - Ramaswamy Subramanian
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52252, USA
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Wang M, Zhu C, Kohne M, Warncke K. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems. Methods Enzymol 2015; 563:59-94. [PMID: 26478482 PMCID: PMC6186429 DOI: 10.1016/bs.mie.2015.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.
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Affiliation(s)
- Miao Wang
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Chen Zhu
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Meghan Kohne
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA
| | - Kurt Warncke
- Department of Physics, Emory University, N201 Mathematics and Science Center, Atlanta, Georgia, USA.
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Elsner C, Ernst C, Buchmeiser MR. Miniaturized biocatalysis on polyacrylate-based capillary monoliths. J Appl Polym Sci 2010. [DOI: 10.1002/app.32657] [Citation(s) in RCA: 8] [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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Zakharchenko NL, Ermakova EA, Zuev YF. Effect of trypsin microenvironment on the rate constants of elementary stages of the hydrolysis reaction of N α-Benzoyl-L-arginine ethyl ester. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:404-8. [DOI: 10.1134/s1068162008030199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Gonnelli M, Strambini GB. Intramolecular Quenching of Tryptophan Phosphorescence in Short Peptides and Proteins¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00234.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Douzou P. Enzymology at subzero temperatures. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 45:157-272. [PMID: 335820 DOI: 10.1002/9780470122907.ch3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Gonnelli M, Strambini GB. Intramolecular Quenching of Tryptophan Phosphorescence in Short Peptides and Proteins¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-11-09-ra-367.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Peerce BE, Peerce B, Clarke RD. Phosphophloretin sensitivity of rabbit renal NaPi-IIa and NaPi-Ia. Am J Physiol Renal Physiol 2004; 286:F955-64. [PMID: 15075191 DOI: 10.1152/ajprenal.00245.2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The effect of phosphorylated phloretins on Na+-dependent phosphate uptake into rabbit renal brush-border membrane vesicles (BBMV) was examined. Na+-dependent phosphate uptake into isolated rabbit cortex BBMV was sensitive to 2′-phosphophloretin (2′-PP) and 2′-phospho-4′,4,6′-trimethoxy phloretin (PTMP) in a dose-dependent and pH-dependent manner. PTMP inhibition of Na+-dependent phosphate uptake was maximum at alkali pH, and 2′-PP inhibition of Na+-dependent phosphate uptake was maximum at acidic pH. Increasing Na+concentrations did not increase PTMP inhibition of renal cortex BBMV Na+-dependent phosphate uptake at pH 6. The effect of phosphophloretins on Na+-dependent phosphate uptake was examined in BBMV isolated from purified proximal tubules and distal tubules. 2′-PP and PTMP inhibition of Na+-dependent phosphate uptake into BBMV isolated from purified proximal tubules was similar to the inhibition seen with BBMV from renal cortex. 2′-PP, but not PTMP, inhibited Na+-dependent phosphate uptake into BBMV isolated from purified distal tubules. The pH dependence of inhibition, the absence of PTMP inhibition of Na+-dependent phosphate uptake into distal tubule BBMV, and the inhibition of Na+-dependent phosphate uptake into distal tubule BBMV suggest that NaPi-Ia is 2′-PP sensitive and NaPi-IIa is PTMP sensitive.
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Affiliation(s)
- Brian E Peerce
- Department of Physiology and Biophysics, Univesity of Texas Medical Branch, Galveston, TX 77555-0641, USA.
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10
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The role of pH change caused by the addition of water-miscible organic solvents in the destabilization of an enzyme. Enzyme Microb Technol 1995. [DOI: 10.1016/0141-0229(94)00028-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Virden R, Tan AK, Fink AL. Cryoenzymology of staphylococcal beta-lactamase: trapping a serine-70-linked acyl-enzyme. Biochemistry 1990; 29:145-53. [PMID: 2108714 DOI: 10.1021/bi00453a018] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Various cryosolvents were investigated for their suitability in cryoenzymological experiments with beta-lactamase from Staphylococcus aureus PC1. On the basis of the minimal effects on the catalytic and structural properties of the enzyme, ternary solvents containing ethylene glycol, methanol, and water were found most suitable. The interaction of beta-lactamase with a number of substrates was studied at subzero temperatures. In general, the reaction profiles were similar to those in aqueous solution at above-zero temperatures, with the exception of the slower rates. For cephalosporin substrates, such as PADAC, in which the 3'-substituent may leave to form a more stable form of the acyl-enzyme [Faraci, W., & Pratt, R. (1985) Biochemistry 24, 903-910], this intermediate could be readily stabilized at subzero temperatures. At -40 degrees C the slow rate of deacylation in the reaction with the chromophoric substrate 6 beta-[(furylacryloyl)amino]penicillanic acid permitted the acyl-enzyme to be stoichiometrically accumulated. This intermediate was then stabilized at low pH with trifluoroacetic acid. Isolation by centrifugal gel filtration, followed by pepsin digestion, gave a penicilloyl-labeled peptide which was isolated by HPLC. Subsequent trypsinolysis of this peptide gave a single labeled peptide, corresponding to the octapeptide surrounding the active-site serine, Ser-70.
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Affiliation(s)
- R Virden
- Department of Chemistry, University of California, Santa Cruz 95064
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12
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Bruice TW, Kenyon GL. Alkyl alkanethiolsulfonate sulfhydryl reagents: β-Sulfhydryl-modified derivatives of l-cysteine as substrates for trypsin and α-chymotrypsin. Bioorg Chem 1985. [DOI: 10.1016/0045-2068(85)90010-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Douzou P, Petsko GA. Proteins at Work: “Stop-Action” Pictures at Subzero Temperatures. ADVANCES IN PROTEIN CHEMISTRY 1984. [DOI: 10.1016/s0065-3233(08)60299-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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15
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Grace S, Dunaway-Mariano D. Examination of the solvent perturbation technique as a method to identify enzyme catalytic groups. Biochemistry 1983; 22:4238-47. [PMID: 6354250 DOI: 10.1021/bi00287a013] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present study was undertaken for the purpose of evaluating the solvent perturbation technique as a method to identify enzyme catalytic residues. For establishment of expected directions and sizes of pKa perturbations for different types of acids in different classes of solvents, a study of the pKa of a series of acids in mixed solvent systems was carried out. Consistent with previous findings, the presence of organic solvents (25% v/v) increased the pKa values of neutral acids while it decreased or did not change the pKa values of cationic acids. The size of the perturbation observed was dependent on the nature of the organic solvent and on the polarity of the neutral form of the acid. The solvent perturbation studies were then extended to the catalytic aspartate residue of yeast hexokinase. The pKa of this residue was determined from the MgATP V/K profile measured in the presence and absence of organic solvents (25% v/v). While dimethylformamide and methanol induced small but perhaps significant increases in the observed pKa, dimethyl sulfoxide and propylene glycol did not. The pKa values, from the MgATP V/K profiles measured in the presence of fully saturating glucose, were not significantly increased by the organic solvents. The pKi vs. pH profile for the competitive inhibitor lyxose was also measured in the presence and absence of organic solvents. While methanol (25% v/v), dimethylformamide (25% v/v), and dioxane (17.5% v/v) induced a large increase in the pKa, propylene glycol and dimethyl sulfoxide (25% v/v) did not. The results from this investigation indicate that the solvent perturbation technique should not be relied upon indiscriminately.
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Hoa GH, Bégard E, Beaudry P, Maurel P, Grunberg-Manago M, Douzou P. Analysis of cosolvent and divalent cation effects on association equilibrium and activity of ribosomes. Biochemistry 1980; 19:3080-7. [PMID: 6994808 DOI: 10.1021/bi00554a038] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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van Dijk C, Grande HJ, Mayhew SG, Veeger C. Properties of the hydrogenase of Megasphaera elsdenii. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 107:251-61. [PMID: 6995113 DOI: 10.1111/j.1432-1033.1980.tb04645.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The catalytic activities of Megasphaera elsdenii hydrogenase are stimulated by salts. The stimulation is due to the anion: the more chaotropic the anion, the greater the effect. Dithionite-reduced and dye-oxidised preparations of hydrogenase are inactivated by reaction with oxygen. The inactivation of the reduced enzyme by excess oxygen follows pseudo-first-order kinetics; the reaction order for the oxidised enzyme has not been established. The rate of oxygen-inactivation is decreased by bovine serum albumin. The hydrogen production activity decreases in the presence of dimethylsulphoxide and ethylene glycol. The hydrogen oxidation activity is stimulated by dimethylsulphoxide, and the activity remains linear with time at concentrations up to 50% (v/v). Above 70% dimethylsulphoxide the steady-state activity of hydrogenase is abolished for both types of activity. The enzyme is more stable in a hydrogen atmosphere than in an argon atmosphere, and the oxidized enzyme is more stable than the reduced enzyme. The enzyme is isolated in the presence of dithionite and it is therefore reduced. When the enzyme is oxidized by treatment with 2,6-dichloroindophenol or with (bi)sulphite, its activity increases by up to 65%; this activation is not reversed when the enzyme is re-reduced. The increase in activity is associated with a change of the redox potential of the incubation medium to a less negative value; half of the maximum activation occurs at -0.41 V. The electron paramagnetic resonance spectrum of the dithionite-reduced hydrogenase resembles that of a reduced ferredoxin-type of spectrum with two 4Fe-4S clusters. The spectrum of the oxidized enzyme is similar to that of Chromatium high-potential iron-sulphur protein. No redox potentials can be ascribed to these spectra since the redox system changes upon freezing to liquid helium temperatures.
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19
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Douzou P. The study of enzyme mechanisms by a combination of cosolvent, low-temperature and high-pressure techniques. Q Rev Biophys 1979; 12:78. [PMID: 95127 DOI: 10.1017/s0033583500002808] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is generally assumed that the mechanism of enzyme-catalysed reactions would be defined if all the intermediates, complexes and conformational states of each enzyme could be characterized, and the rate-constants for their inter-conversion recorded. In spite of the introduction during the last decades of methods for rapid data acquisition, which permit detection of the number and sequence of intermediates and complexes, measurement of rate-constants, identification of the types of catalysis involved, etc., at best a semi-quantitative understanding of the mechanism of enzyme-catalysis is obtained. The definition of the exact chemical nature of intermediates and complexes is missing because techniques establishing the structures are restricted to the study of transient states which are stable for periods that exceed the half-life of most of typical intermediates. In such conditions, while conformational changes are obviously an essential feature of enzyme activity, the conformational basis of such activity cannot be understood at the molecular level, and enzyme catalysis is still termed a ‘miracle’ compared to the rate-enhancements and specificity of ordinary chemical catalysts.
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Abstract
The effect of viscosity on the rate of catalysis of carboxypeptidase A has been tested. By use of the tripeptide carbobenzoxy-l-alanyl-l-alanyl-l-alanine [Z(L-Ala)3] as substrate, it was shown that most of the effect on the hydrolysis rate caused by the presence of 30 or 40% methanol or glycerol in aqueous solution can be ascribed to a contribution of viscosity to the catalytic rate constant, kcat. Arrhenius plots of kcat in 30 and 40% glycerol or methanol are linear and almost parallel. When the rate constants are "corrected" for the viscosity of various media, the difference between the various Arrhenius plots is considerably reduced; it vanishes, within experimental error, when the effect of the dielectric constant of the solutions is taken into account as well. It is proposed that the viscosity of the medium can influence the rate-limiting step of the enzymic reaction, which is the rate of transitions over the energy barrier preceding product formation. According to the suggested mechanism, the enzyme--substrate complex can overcome this energy barrier by viscosity-dependent structural fluctuations. The quantitative agreement between the theory and the experimental results suggests that (a) due to the temperature dependence of the viscosity of the solution, the potential energy barrier of the reaction is about 5 kcal/mol lower than the observed activation energy and (b) information about the structural flexibility of the complex can be obtained by kinetic measurements.
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Balny C, Le Doucen C, Douzou P, Bieth JG. Affinity chromatography at sub-zero temperatures. A model study with porcine pancreatic elastase. J Chromatogr A 1979; 168:133-8. [PMID: 762228 DOI: 10.1016/s0021-9673(00)80701-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new variety of affinity chromatography of enzymes is described which consists of building up an affinity adsorbent composed of a real substrate. The chromatography is performed at a sub-zero temperature where the turnover of the enzyme is very low or stopped. As a model system Sepharose-bound L-trialanine p-nitroanilide was for used the affinity binding of porcine pancreatic elastase, which was adsorbed to the column in a hypersaline medium at--14 degrees and eluted from the column at the same temperature using 50% (v/v) ethylene glycol. The affinity adsorbent proved to be vary specific as it did not retain trypsin, chymotrypsin and ovalbumin and retained only 20% of cytochrome c.
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Makinen M, Kuo L, Dymowski J, Jaffer S. Catalytic role of the metal ion of carboxypeptidase A in ester hydrolysis. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37925-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Tsopanakis C, Leeson E, Tsopanakis A, Shall S. Purification and properties of poly(ADP-ribose) polymerase from pig-thymus nuclei. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 90:337-45. [PMID: 213276 DOI: 10.1111/j.1432-1033.1978.tb12610.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The nuclear enzyme poly(ADP-ribose) polymerase has been purified about 9200-fold from pig thymus nuclei with a 46% yield. An aqueous organic solvent system was used for the isolation of the polymerase from nuclei and for its purification by chromatography at sub-zero temperatures. Electrophoretic analysis under both denaturing and non-denaturing conditions revealed a single protein band suggesting that the preparation was homogeneous and that the enzyme is composed of one polypeptide chain. The molecular weight estimated from sodium dodecyl sulphate-/polyacrylamide gel electrophoresis was 63 500 and from gel filtration through columns of Sephadex G-100, 58 000. The enzyme preparation was free from poly(ADP-ribose)-degrading enzymes and from DNA. The purified polymerase showed an absolute requirement for both DNA and histones. The maximal specific activity of the homogeneous preparation measured by the standardized assay, was 20.7 mu mol NAD+ incorporated x min-1 x mg-1 of protein at 37 degree C. Amino-terminal group analysis with dansyl chloride did not reveal a terminal amino acid suggesting that the amino-terminal group may be blocked. In the presence of histones, the Km for NAD+ was 23 micrometer.
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Andersson K, Benyamin Y, Douzou P, Balny C. Organic solvents and temperature effects on desorption from immunoadsorbents. DNP-BSA anti-DNP as a model. J Immunol Methods 1978; 23:17-21. [PMID: 29930 DOI: 10.1016/0022-1759(78)90105-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conditions for desorbing a DNP carrier from its immunoadsorbent were studied in various hydro-organic media at different pHs and temperatures, including the sub-zero range. It appeared that DNP--anti-DNP interaction is the result of a balance between various bonds and the best result (95% yield) was obtained in hydro-organic solvent at high pH and +30 degrees C.
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Anusiem AC, Oshodi AA. Role of water in protein reactions: binding of azide ion to ferrihemoglobin in water and ethylene glycol mixtures. Arch Biochem Biophys 1978; 189:392-6. [PMID: 708058 DOI: 10.1016/0003-9861(78)90226-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Perrella M, Heyda A, Mosca A, Rossi-Bernardi L. Isoelectric focusing and electrophoresis at subzero temperatures. Anal Biochem 1978; 88:212-24. [PMID: 696997 DOI: 10.1016/0003-2697(78)90413-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Allen KG, Stewart JA, Johnson PE, Wettlaufer DG. Identification of the functional ionic groups of papain by pH/rate profile analysis. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 87:575-82. [PMID: 28228 DOI: 10.1111/j.1432-1033.1978.tb12409.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pH dependence of papain catalysis was analyzed by a scheme which evaluates the kinetic contribution of both protonated and unprotonated species of functional groups involved in catalysis. Kinetic measurements were made at constant pH, without buffers, by automatic titration. The rate-determining step for papain-catalyzed hydrolysis of alpha-N-benzoyl-L-arginine ethyl ester, determined by nucleophile competition, changed from acylation below pH 6.5 to mixed acylation-deacylation above pH 6.5. Kinetic analysis indicated that three prototropic groups governed the pH-specificity of alpha-N-benzoyl-L-arginine ethyl ester hydrolysis. These prototropic groups had pKa values of 4.8, 6.5 to 6.7, and 8.7. Theoretical treatment of the kinetics provided an excellent fit with the experimentally found profile when the contribution of all three prototropic groups was considered. Analysis showed that, in acid, the pathways of papain catalysis were functional with either two or three active-site protons. In base, a single functional ionic pathway is associated with an active site with only one proton. Pathways involving an unprotonated active site are catalytically inoperative in both acid and base. These results indicate that papain exhibits several catalytically functional ionic pathways. The results are discussed in terms of pKa assignments, and the mechanism of papain catalysis.
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Abstract
A water in oil emulsion technique is proposed to investigate enzyme catalyzed reactions at sub-zero temperatures in the supercooled liquid state to avoid some reversible effects of the usual cosolvents on kinetics. Some results are listed: potentialities and technical problems of the procedure are discussed.
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Maurel P. Relevance of dielectric constant and solvent hydrophobicity to the organic solvent effect in enzymology. J Biol Chem 1978. [DOI: 10.1016/s0021-9258(17)34918-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Larroque C, Maurel P, Douzou P. Redox potentials in hydro-organic media at normal and subzero temperatures. Ferro-ferricyanide and cytochrome c as models. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 501:20-32. [PMID: 202313 DOI: 10.1016/0005-2728(78)90092-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Redox potentials of ferro-ferricyanide and cytochrome c were measured in water/ethylene glycol and water/dimethylsulfoxide (volume ratio from 100/0 to 50/50) between 25 and -25 degrees C. For both systems, the midpoint potential decreases in the presence of organic solvents and increases by cooling. The magnitude of these variations is larger in dimethylsulfoxide than in ethylene glycol; moreover in the same solvent mixture it is larger with ferro-ferricyanide than with cytochrome c, so that the difference between the redox potentials of these two systems can be strongly affected and even reversed. While in pure water (cacodylate buffer pH 7.0, NaCl 0.1 M) they are respectively +388 and +265 mV, in 50% dimethylsulfoxide at 25 degrees C they decrease to +112 and +208 mV. Reduction of cytochrome c by ferro-ferricyanide, in this mixture, is then expected and was indeed observed. On the other hand, as (deltaE/deltaT)T, (E being the redox potential) is higher for ferro-ferricyanide than for cytochrome c, the oxidative power of the former for the latter is expected to increase as temperature decreases. This effect was observed in 50% ethylene glycol at -16 degrees C. Organic solvents and large temperature variations appear then as powerful perturbants of redox reactions. Their effects should be taken into account in studies of redox reactions carried out in cooled hydro-organic media.
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Douzou P, Balny C. Protein fractionation at subzero temperatures. ADVANCES IN PROTEIN CHEMISTRY 1978; 32:77-189. [PMID: 362872 DOI: 10.1016/s0065-3233(08)60575-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bercot M, Morales F, De Mendonca M, Appel M, Bidault J, Masson-Pierre D, Ribalet B, Paillette D. Acidosis protection during 24-hour ischemic heart preservation. Cryobiology 1977; 14:435-42. [PMID: 19204 DOI: 10.1016/0011-2240(77)90005-0] [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: 12/12/2022]
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Fink AL, Ahmed AI. Formation of stable crystalline enzyme-substrate intermediates at sub-zero temperatures. Nature 1976; 263:294-7. [PMID: 8732 DOI: 10.1038/263294a0] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sub-zero temperatures can be used to trap intermediates in enzyme-catalysed reactions using suitable cryosolvents. The feasibility of obtaining such intermediates in the crystalline state for X-ray diffraction studies has been demonstrated with several proteases, using specific substrates and optimal pH.
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Larroque C, Maurel P, Balny C, Douzou P. Practical potentiometric determinations of proton activity in hydro organic solvents at subzero temperatures. Anal Biochem 1976; 73:9-19. [PMID: 7974 DOI: 10.1016/0003-2697(76)90136-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Fink AL. Cryoenzymology of chymotrypsin: the detection of intermediates in the catalysis of a specific anilide substrate. Biochemistry 1976; 15:1580-6. [PMID: 944050 DOI: 10.1021/bi00652a031] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The reaction between chymotrypsin and N-acetyl-L-phenylalanine p-nitroanilide has been studied at subzero temperatures in fluid aqueous dimethyl sulfoxide solvent. Following initiation of the reaction at temperatures as low as -90 degrees C, a series of four reactions prior to the normal rate-limiting step (acylation) was detected spectrophotometrically. Various experimental observations have led to the following interpretation of these reactions. Reaction 1 corresponds to the binding of substrate yielding the initial Michaelis complex. Reactions 2 and 3 are two pH-independent reactions, ascribed to substrate-induced changes in the positions of active-site groups. Reaction 4 is a pH-dependent reaction (pK = 5.9) which involves the imidazole of His-57 but which is not the formation of a tetrahedral intermediate, oxazolinone, or acyl enzyme. The slowest detected step corresponded to the acylation reaction. No evidence for the accumulation of a tetrahedral intermediate was obtained. Spectral, kinetic, and thermodynamic data for these reactions are presented, as is justification for the relevance of these findings to the reaction under physiological conditions. These results demonstrate the utility of subzero temperatures in enzyme mechanism studies, especially with regard to allowing the accumulation of intermediates which may be quite stable at appropriate values of pH and low temperature.
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Maurel P, Douzou P. Catalytic implications of electrostatic potentials: the lytic activity of lysozymes as a model. J Mol Biol 1976; 102:253-64. [PMID: 5609 DOI: 10.1016/s0022-2836(76)80052-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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