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Karakhim SO. Kinetics of the enzyme titration process by reversible modifiers. Biochimie 2023; 214:11-26. [PMID: 37279802 DOI: 10.1016/j.biochi.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/22/2023] [Accepted: 06/03/2023] [Indexed: 06/08/2023]
Abstract
The effect of reversible modifiers on the initial rate of enzyme catalysed reactions has been investigated in a quasi-equilibrium approximation using the general modifier mechanism of Botts and Morales. It has been shown that, when investigating the dependence of the initial rate on the modifier concentration at a fixed substrate concentration, the kinetics of enzyme titration by reversible modifiers can generally be described using two kinetic constants. Just as the dependence of the initial rate on the substrate concentration (at a fixed modifier concentration) is described using two kinetic constants: the Michaelis constant Km and the limiting rate Vm. Only one constant M50 is needed to describe the kinetics of linear inhibition, and in the case of nonlinear inhibition and activation, along with M50 the constant QM is also needed. Knowing the values of the constants M50 and QM, it is possible to unambiguously determine the modification efficiency, that is, to calculate how many times the initial rate of the enzyme catalysed reaction will change when a certain modifier concentration is added to the incubation medium. The properties of these fundamental constants have been analysed in detail and the dependence of these constants on other parameters of the Botts-Morales model have been shown. Equations describing the dependence of relative reaction rates on the modifier concentration using these kinetic constants are presented. Various ways of linearising these equations for calculating the kinetic constants M50 and QM from experimental data are also presented.
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Affiliation(s)
- S O Karakhim
- Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, 9 Leontovicha Street, Kyiv, 01054, Ukraine.
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Liu F, Chen HM, Armstrong Z, Withers SG. Azido Groups Hamper Glycan Acceptance by Carbohydrate Processing Enzymes. ACS CENTRAL SCIENCE 2022; 8:656-662. [PMID: 35647280 PMCID: PMC9136970 DOI: 10.1021/acscentsci.1c01172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Indexed: 06/15/2023]
Abstract
Azido sugars have found frequent use as probes of biological systems in approaches ranging from cell surface metabolic labeling to activity-based proteomic profiling of glycosidases. However, little attention is typically paid to how well azide-substituted sugars represent the parent molecule, despite the substantial difference in size and structure of an azide compared to a hydroxyl. To quantitatively assess how well azides are accommodated, we have used glycosidases as tractable model enzyme systems reflecting what would also be expected for glycosyltransferases and other sugar binding/modifying proteins. In this vein, specificity constants have been measured for the hydrolysis of a series of azidodeoxy glucosides and N-acetylhexosaminides by a large number of glycosidases produced from expressed synthetic gene and metagenomic libraries. Azides at secondary carbons are not significantly accommodated, and thus, associated substrates are not processed, while those at primary carbons are productively recognized by only a small subset of the enzymes and often then only very poorly. Accordingly, in the absence of careful controls, results obtained with azide-modified sugars may not be representative of the situation with the natural sugar and should be interpreted with considerable caution. Azide incorporation can indeed provide a useful tool to monitor and detect glycosylation, but careful consideration should go into the selection of sites of azide substitution; such studies should not be used to quantitate glycosylation or to infer the absence of glycosylation activity.
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McDonald AG, Tipton KF. Parameter Reliability and Understanding Enzyme Function. Molecules 2022; 27:263. [PMID: 35011495 PMCID: PMC8746786 DOI: 10.3390/molecules27010263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/21/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge of the Michaelis-Menten parameters and their meaning in different circumstances is an essential prerequisite to understanding enzyme function and behaviour. The published literature contains an abundance of values reported for many enzymes. The problem concerns assessing the appropriateness and validity of such material for the purpose to which it is to be applied. This review considers the evaluation of such data with particular emphasis on the assessment of its fitness for purpose.
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Affiliation(s)
- Andrew G. McDonald
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland;
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Koshkin V, Kochmann S, Sorupanathan A, Peng C, Ailles LE, Liu G, Krylov SN. Cytometry of Reaction Rate Constant: Measuring Reaction Rate Constant in Individual Cells To Facilitate Robust and Accurate Analysis of Cell-Population Heterogeneity. Anal Chem 2019; 91:4186-4194. [PMID: 30829484 DOI: 10.1021/acs.analchem.9b00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Robust and accurate analysis of cell-population heterogeneity is challenging but required in many areas of biology and medicine. In particular, it is pivotal to the development of reliable cancer biomarkers. Here, we prove that cytometry of reaction rate constant (CRRC) can facilitate such analysis when the kinetic mechanism of a reaction associated with the heterogeneity is known. In CRRC, the cells are loaded with a reaction substrate, and its conversion into a product is followed by time-lapse fluorescence microscopy at the single-cell level. A reaction rate constant is determined for every cell, and a kinetic histogram "number of cells versus the rate constant" is used to determine quantitative parameters of reaction-based cell-population heterogeneity. Such parameters include, for example, the number and sizes of subpopulations. In this work, we applied CRRC to a reaction of substrate extrusion from cells by ATP-binding cassette (ABC) transporters. This reaction is viewed as a potential basis for predictive biomarkers of chemoresistance in cancer. CRRC proved to be robust (insensitive to variations in experimental settings) and accurate for finding quantitative parameters of cell-population heterogeneity. In contrast, a typical nonkinetic analysis, performed on the same data sets, proved to be both nonrobust and inaccurate. Our results suggest that CRRC can potentially facilitate the development of reliable cancer biomarkers on the basis of quantitative parameters of cell-population heterogeneity. A plausible implementation scenario of CRRC-based development, validation, and clinical use of a predictor of ovarian cancer chemoresistance to its frontline therapy is presented.
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Affiliation(s)
| | | | | | | | - Laurie E Ailles
- Department of Medical Biophysics , University of Toronto , Toronto , Ontario N5G 1L7 , Canada
| | - Geoffrey Liu
- Department of Medicine, Medical Oncology , Princess Margaret Cancer Centre , Toronto , Ontario M5G 2M9 , Canada
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Ortiz GE, Noseda DG, Ponce Mora MC, Recupero MN, Blasco M, Albertó E. A Comparative Study of New Aspergillus Strains for Proteolytic Enzymes Production by Solid State Fermentation. Enzyme Res 2016; 2016:3016149. [PMID: 26989505 PMCID: PMC4771904 DOI: 10.1155/2016/3016149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/28/2015] [Accepted: 01/10/2016] [Indexed: 11/18/2022] Open
Abstract
A comparative study of the proteolytic enzymes production using twelve Aspergillus strains previously unused for this purpose was performed by solid state fermentation. A semiquantitative and quantitative evaluation of proteolytic activity were carried out using crude enzymatic extracts obtained from the fermentation cultures, finding seven strains with high and intermediate level of protease activity. Biochemical, thermodynamics, and kinetics features such as optimum pH and temperature values, thermal stability, activation energy (E a), quotient energy (Q 10), K m , and V max were studied in four enzymatic extracts from the selected strains that showed the highest productivity. Additionally, these strains were evaluated by zymogram analysis obtaining protease profiles with a wide range of molecular weight for each sample. From these four strains with the highest productivity, the proteolytic extract of A. sojae ATCC 20235 was shown to be an appropriate biocatalyst for hydrolysis of casein and gelatin substrates, increasing its antioxidant activities in 35% and 125%, respectively.
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Affiliation(s)
- Gastón Ezequiel Ortiz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
| | - Diego Gabriel Noseda
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
| | - María Clara Ponce Mora
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
| | - Matías Nicolás Recupero
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
| | - Martín Blasco
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
| | - Edgardo Albertó
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM) and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, 1650 Buenos Aires, Argentina
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Rodríguez-Contreras A, Calafell-Monfort M, Marqués-Calvo MS. Enzymatic degradation of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) by commercial lipases. Polym Degrad Stab 2012. [DOI: 10.1016/j.polymdegradstab.2012.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Mancini F, De Simone A, Andrisano V. Beta-secretase as a target for Alzheimer’s disease drug discovery: an overview of in vitro methods for characterization of inhibitors. Anal Bioanal Chem 2011; 400:1979-96. [DOI: 10.1007/s00216-011-4963-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/09/2011] [Accepted: 03/26/2011] [Indexed: 10/18/2022]
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Mancini F, Andrisano V. Development of a liquid chromatographic system with fluorescent detection for β-secretase immobilized enzyme reactor on-line enzymatic studies. J Pharm Biomed Anal 2010; 52:355-61. [DOI: 10.1016/j.jpba.2009.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 07/04/2009] [Accepted: 07/09/2009] [Indexed: 11/24/2022]
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Methanogenesis from methanol at low temperatures by a novel psychrophilic methanogen, "Methanolobus psychrophilus" sp. nov., prevalent in Zoige wetland of the Tibetan plateau. Appl Environ Microbiol 2008; 74:6114-20. [PMID: 18676698 DOI: 10.1128/aem.01146-08] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Zoige wetland of the Tibetan plateau is at permanent low temperatures and is a methane emission heartland of the plateau; however, cold-adaptive methanogens in the soil are poorly understood. In this study, a variety of methanogenic enrichments at 15 degrees C and 30 degrees C were obtained from the wetland soil. It was demonstrated that hydrogenotrophic methanogenesis was the most efficient type at 30 degrees C, while methanol supported the highest methanogenesis rate at 15 degrees C. Moreover, methanol was the only substrate to produce methane more efficiently at 15 degrees C than at 30 degrees C. A novel psychrophilic methanogen, strain R15, was isolated from the methanol enrichment at 15 degrees C. Phylogenetic analysis placed strain R15 within the genus Methanolobus, loosely clustered with Methanolobus taylorii (96.7% 16S rRNA similarity). R15 produced methane from methanol, trimethylamine, and methyl sulfide and differed from other Methanolobus species by growing and producing methane optimally at 18 degrees C (specific growth rate of 0.063 +/- 0.001 h(-1)) and even at 0 degrees C. Based on these characteristics, R15 was proposed to be a new species and named "Methanolobus psychrophilus" sp. nov. The K(m) and V(max) of R15 for methanol conversion were determined to be 87.5 +/- 0.4 microM and 0.39 +/- 0.04 mM h(-1) at 18 degrees C, respectively, indicating a high affinity and conversion efficiency for methanol. The proportion of R15 in the soil was determined by quantitative PCR, and it accounted for 17.2% +/- 2.1% of the total archaea, enumerated as 10(7) per gram of soil; the proportion was increased to 42.4% +/- 2.3% in the methanol enrichment at 15 degrees C. This study suggests that the psychrophilic methanogens in the Zoige wetland are likely to be methylotrophic and to play a role in methane emission of the wetland.
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Paschalidou K, Neumann U, Gerhartz B, Tzougraki C. Highly sensitive intramolecularly quenched fluorogenic substrates for renin based on the combination of L-2-amino-3-(7-methoxy-4-coumaryl)propionic acid with 2,4-dinitrophenyl groups at various positions. Biochem J 2005; 382:1031-8. [PMID: 15233625 PMCID: PMC1133981 DOI: 10.1042/bj20040729] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 06/10/2004] [Accepted: 07/02/2004] [Indexed: 11/17/2022]
Abstract
The development of renin inhibitors for the treatment of hypertension requires highly sensitive substrates to evaluate potency and to characterize the mechanism of tight-binding inhibitors. A series of intramolecularly quenched fluorogenic renin substrates, based on the N-terminal tetradecapeptide sequence of human angiotensinogen (hTDP), was synthesized using a solid-phase technique. Incorporation of the fluorescent amino acid L-Amp [L-2-amino-3-(7-methoxy-4-coumaryl)propionic acid] and the DNP (2,4-dinitrophenyl) group at various positions resulted in >90% quenching efficiency and strong product fluorescence. Shortening the hTDP sequence to an octapeptide from histidine in P5 to histidine in P3' (substrate 3) resulted in an acceptable k(cat)/K(m) (41000 M(-1).s(-1)) and further systematic variation gave substrate 9, DNP-Lys-His-Pro-Phe-His-Leu-Val-Ile-His-L-Amp, with a k(cat)/K(m) value of 350000 M(-1).s(-1) and 94% quenching efficiency. The free side chain of lysine, replacing the isoleucine residue at P6 position in the angiotensinogen sequence, contributed to the increased value for k(cat). The pH dependence of k(cat)/K(m) for renin and substrate 9 showed that the optimal pH is at pH 6-7. It also showed two titrating groups on the acidic side of the pH optimum, and one titrating group with a pK(a) of 7.8 on the alkaline side. The combination of good kinetic and spectroscopic properties resulted in a >20-fold improvement in the sensitivity of renin assay, compared with the commercial substrate Arg-Glu(EDANS)-Ile-His-Pro-Phe-His-Leu-Val-Ile-His-Thr-Lys(DABCYL)-Arg [where EDANS is 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid and DABCYL is 4-(4-dimethylaminophenylazo)benzoic acid] (k(cat)/K(m)=268000 M(-1) x s(-1), quenching efficiency <80%). The detection limit in a microplate renin assay was 60 pM, making substrate 9 well suited for the evaluation of inhibitors at picomolar concentrations.
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Affiliation(s)
- Katherine Paschalidou
- *Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 157 71 Athens, Greece
| | - Ulf Neumann
- †Novartis Institute of BioMedical Research, CH-4002 Basel, Switzerland
| | - Bernd Gerhartz
- †Novartis Institute of BioMedical Research, CH-4002 Basel, Switzerland
| | - Chryssa Tzougraki
- *Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Zografou, 157 71 Athens, Greece
- To whom correspondence should be addressed (email )
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Hidaka K, Caffrey JJ, Hua L, Zhang T, Falck JR, Nickel GC, Carrel L, Barnes LD, Shears SB. An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase. J Biol Chem 2002; 277:32730-8. [PMID: 12105228 DOI: 10.1074/jbc.m205476200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Combinatorial expression of the various isoforms of diphosphoinositol synthases and phosphohydrolases determines the rates of phosphorylation/dephosphorylation cycles that have been functionally linked to vesicle trafficking, stress responses, DNA repair, and apoptosis. We now describe two new 19-kDa diphosphoinositol polyphosphate phosphohydrolases (DIPPs), named types 3alpha and 3beta, which possess the canonical Nudix-type catalytic motif flanked on either side by short Gly-rich sequences. The two enzymes differ only in that Pro-89 in the alpha form is replaced by Arg-89 in the beta form, making the latter approximately 2-fold more active in vitro. Another Nudix substrate, diadenosine hexaphosphate, was hydrolyzed less efficiently (k(cat)/K(m) = 0.2 x 10(5) m(-1) s(-1)) compared with diphosphoinositol polyphosphates (k(cat)/K(m) = 2-40 x 10(5) m(-1) s(-1)). Catalytic activity in vivo was established by individual overexpression of the human (h) DIPP3 isoforms in HEK293 cells, which reduced cellular levels of diphosphoinositol polyphosphates by 40-50%. The hDIPP3 mRNA is preferentially expressed in testis, accompanied by relatively weak expression in the brain, contrasting with hDIPP1 and hDIPP2 which are widely expressed. The hDIPP3 genes (NUDT10 encodes hDIPP3alpha; NUDT11 encodes hDIPP3beta) are only 152 kbp apart at p11.22 on chromosome X and probably arose by duplication. Transcription of both genes is inactivated on one of the X chromosomes of human females to maintain appropriate gene dosage. The hDIPP3 pair add tissue-specific diversity to the molecular mechanisms regulating diphosphoinositol polyphosphate turnover.
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Affiliation(s)
- Kiyoshi Hidaka
- Inositide Signaling Section, Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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Jongejan A, Machado SS, Jongejan JA. The enantioselectivity of quinohaemoprotein alcohol dehydrogenases: mechanistic and structural aspects. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1381-1177(99)00063-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Neuenschwander P, Morrissey J. Roles of the membrane-interactive regions of factor VIIa and tissue factor. The factor VIIa Gla domain is dispensable for binding to tissue factor but important for activation of factor X. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37152-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Mulgrave L, Attwood PV. Characterization of an SHV-5 related extended broad-spectrum beta-lactamase in Enterobacteriaceae from Western Australia. Pathology 1993; 25:71-5. [PMID: 8316504 DOI: 10.3109/00313029309068906] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Among 209 isolates of aminoglycoside resistant Enterobacteriaceae isolated from patients attending the Sir Charles Gairdner Hospital in Perth, Western Australia between January 1985 and June 1991, 41 strains demonstrated additional resistance to cefotaxime, ceftriaxone, ceftazidime and aztreonam. Significant synergy was demonstrable between these beta-lactams and clavulanic acid against resistant strains. The beta-lactamase was mediated by a 170 Kb self-transferring plasmid and identified as the SHV-5 type in isoelectric focusing (pl 8.2) and substrate hydrolysis kinetic studies. The findings record the introduction of extended broad-spectrum beta-lactamases to Australia.
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Affiliation(s)
- L Mulgrave
- Department of Microbiology, University of Western Australia, Nedlands
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Prats M, Rodriguez F. A michaelis—menten enzyme: Time correction introduced for computing kinetic parameters at low values of [S]/Km. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0307-4412(92)90067-v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Extrapolation procedures are shown to be useful for obtaining kinetic parameters from irreversible enzymic reactions in which there are two intermediates, under both single-turnover and steady-state conditions. Small excesses of one component are treated as if they were large excesses, which is convenient in practice. The method has also been applied to a non-enzymic reversible bimolecular reaction.
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Affiliation(s)
- I E Crompton
- Sir William Dunn School of Pathology, University of Oxford, U.K
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Cornish-Bowden A. The time dimension in steady-state kinetic: A simplified representation of control coefficients. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0307-4412(87)90048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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