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Gygli G. On the reproducibility of enzyme reactions and kinetic modelling. Biol Chem 2022; 403:717-730. [PMID: 35357794 DOI: 10.1515/hsz-2021-0393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/09/2022] [Indexed: 12/20/2022]
Abstract
Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modeling meticulously executed. Furthermore, to enable quality control of enzyme reaction parameters, the experimental conditions, the modeling process as well as the raw data need to be reported comprehensively. By taking these steps, enzyme reaction parameters can be open and FAIR (findable, accessible, interoperable, re-usable) as well as repeatable, replicable and reproducible. This review discusses these requirements and provides a practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and gives an open, FAIR and re-editable example of the kinetic modeling of an enzyme reaction. Both the guide and example are scripted with Python in Jupyter Notebooks and are publicly available (https://fairdomhub.org/investigations/483/snapshots/1). Finally, the prerequisites of automated data analysis and machine learning algorithms are briefly discussed to provide further motivation for the comprehensive, open and FAIR reporting of enzyme reaction parameters.
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Affiliation(s)
- Gudrun Gygli
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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2
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Ferreira P, Hernández-Ortega A, Lucas F, Carro J, Herguedas B, Borrelli KW, Guallar V, Martínez AT, Medina M. Aromatic stacking interactions govern catalysis in aryl-alcohol oxidase. FEBS J 2015; 282:3091-106. [PMID: 25639975 DOI: 10.1111/febs.13221] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/10/2015] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Aryl-alcohol oxidase (AAO, EC 1.1.3.7) generates H2 O2 for lignin degradation at the expense of benzylic and other π system-containing primary alcohols, which are oxidized to the corresponding aldehydes. Ligand diffusion studies on Pleurotus eryngii AAO showed a T-shaped stacking interaction between the Tyr92 side chain and the alcohol substrate at the catalytically competent position for concerted hydride and proton transfers. Bi-substrate kinetics analysis revealed that reactions with 3-chloro- or 3-fluorobenzyl alcohols (halogen substituents) proceed via a ping-pong mechanism. However, mono- and dimethoxylated substituents (in 4-methoxybenzyl and 3,4-dimethoxybenzyl alcohols) altered the mechanism and a ternary complex was formed. Electron-withdrawing substituents resulted in lower quantum mechanics stacking energies between aldehyde and the tyrosine side chain, contributing to product release, in agreement with the ping-pong mechanism observed in 3-chloro- and 3-fluorobenzyl alcohol kinetics analysis. In contrast, the higher stacking energies when electron donor substituents are present result in reaction of O2 with the flavin through a ternary complex, in agreement with the kinetics of methoxylated alcohols. The contribution of Tyr92 to the AAO reaction mechanism was investigated by calculation of stacking interaction energies and site-directed mutagenesis. Replacement of Tyr92 by phenylalanine does not alter the AAO kinetic constants (on 4-methoxybenzyl alcohol), most probably because the stacking interaction is still possible. However, introduction of a tryptophan residue at this position strongly reduced the affinity for the substrate (i.e. the pre-steady state Kd and steady-state Km increase by 150-fold and 75-fold, respectively), and therefore the steady-state catalytic efficiency, suggesting that proper stacking is impossible with this bulky residue. The above results confirm the role of Tyr92 in substrate binding, thus governing the kinetic mechanism in AAO.
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Affiliation(s)
- Patricia Ferreira
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
| | - Aitor Hernández-Ortega
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Fátima Lucas
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Juan Carro
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Beatriz Herguedas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
| | - Kenneth W Borrelli
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain
| | - Victor Guallar
- Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Angel T Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, and Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
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Prongjit M, Sucharitakul J, Palfey BA, Chaiyen P. Oxidation mode of pyranose 2-oxidase is controlled by pH. Biochemistry 2013; 52:1437-45. [PMID: 23356577 DOI: 10.1021/bi301442x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoenzyme that catalyzes the oxidation of d-glucose and other aldopyranose sugars at the C2 position by using O₂ as an electron acceptor to form the corresponding 2-keto-sugars and H₂O₂. In this study, the effects of pH on the oxidative half-reaction of P2O were investigated using stopped-flow spectrophotometry. The results showed that flavin oxidation occurred via different pathways depending on the pH of the environment. At pH values lower than 8.0, reduced P2O reacts with O₂ to form a C4a-hydroperoxyflavin intermediate, leading to elimination of H₂O₂. At pH 8.0 and higher, the majority of the reduced P2O reacts with O₂ via a pathway that does not allow detection of the C4a-hydroperoxyflavin, and flavin oxidation occurs with decreased rate constants upon the rise in pH. The switching between the two modes of P2O oxidation is controlled by protonation of a group which has a pK(a) of 7.6 ± 0.1. Oxidation reactions of reduced P2O under rapid pH change as performed by stopped-flow mixing were different from the same reactions performed with enzyme pre-equilibrated at the same specified pH values, implying that the protonation of the group which controls the mode of flavin oxidation cannot be rapidly equilibrated with outside solvent. Using a double-mixing stopped-flow experiment, a rate constant for proton dissociation from the reaction site was determined to be 21.0 ± 0.4 s⁻¹.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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4
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Gadda G. Oxygen Activation in Flavoprotein Oxidases: The Importance of Being Positive. Biochemistry 2012; 51:2662-9. [DOI: 10.1021/bi300227d] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, and §The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia
30302-4098, United States
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Yuan H, Fu G, Brooks PT, Weber I, Gadda G. Steady-State Kinetic Mechanism and Reductive Half-Reaction of d-Arginine Dehydrogenase from Pseudomonas aeruginosa. Biochemistry 2010; 49:9542-50. [DOI: 10.1021/bi101420w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Irene Weber
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
| | - Giovanni Gadda
- Departments of Chemistry
- Biology
- The Center for Biotechnology and Drug Design
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Pitsawong W, Sucharitakul J, Prongjit M, Tan TC, Spadiut O, Haltrich D, Divne C, Chaiyen P. A conserved active-site threonine is important for both sugar and flavin oxidations of pyranose 2-oxidase. J Biol Chem 2010; 285:9697-9705. [PMID: 20089849 DOI: 10.1074/jbc.m109.073247] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pyranose 2-oxidase (P2O) catalyzes the oxidation by O(2) of d-glucose and several aldopyranoses to yield the 2-ketoaldoses and H(2)O(2). Based on crystal structures, in one rotamer conformation, the threonine hydroxyl of Thr(169) forms H-bonds to the flavin-N5/O4 locus, whereas, in a different rotamer, it may interact with either sugar or other parts of the P2O.sugar complex. Transient kinetics of wild-type (WT) and Thr(169) --> S/N/G/A replacement variants show that D-Glc binds to T169S, T169N, and WT with the same K(d) (45-47 mm), and the hydride transfer rate constants (k(red)) are similar (15.3-9.7 s(-1) at 4 degrees C). k(red) of T169G with D-glucose (0.7 s(-1), 4 degrees C) is significantly less than that of WT but not as severely affected as in T169A (k(red) of 0.03 s(-1) at 25 degrees C). Transient kinetics of WT and mutants using d-galactose show that P2O binds d-galactose with a one-step binding process, different from binding of d-glucose. In T169S, T169N, and T169G, the overall turnover with d-Gal is faster than that of WT due to an increase of k(red). In the crystal structure of T169S, Ser(169) O gamma assumes a position identical to that of O gamma 1 in Thr(169); in T169G, solvent molecules may be able to rescue H-bonding. Our data suggest that a competent reductive half-reaction requires a side chain at position 169 that is able to form an H-bond within the ES complex. During the oxidative half-reaction, all mutants failed to stabilize a C4a-hydroperoxyflavin intermediate, thus suggesting that the precise position and geometry of the Thr(169) side chain are required for intermediate stabilization.
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Affiliation(s)
- Warintra Pitsawong
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Faculty of Dentistry, Chulalongkorn University, Henri-Dunant Road, Patumwan, Bangkok 10300, Thailand
| | - Methinee Prongjit
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tien-Chye Tan
- Division of Glycoscience, Kungliga Tekniska Högskolan Biotechnology, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Oliver Spadiut
- Division of Glycoscience, Kungliga Tekniska Högskolan Biotechnology, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Dietmar Haltrich
- Department of Food Science and Technology, Bodenkultur-University of Natural Resource and Applied Life Sciences, A-1190 Vienna, Austria
| | - Christina Divne
- Division of Glycoscience, Kungliga Tekniska Högskolan Biotechnology, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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Pennati A, Gadda G. Involvement of ionizable groups in catalysis of human liver glycolate oxidase. J Biol Chem 2009; 284:31214-22. [PMID: 19758989 PMCID: PMC2781520 DOI: 10.1074/jbc.m109.040063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 09/04/2009] [Indexed: 11/06/2022] Open
Abstract
Glycolate oxidase is a flavin-dependent, peroxisomal enzyme that oxidizes alpha-hydroxy acids to the corresponding alpha-keto acids, with reduction of oxygen to H(2)O(2). In plants, the enzyme participates in photorespiration. In humans, it is a potential drug target for treatment of primary hyperoxaluria, a genetic disorder where overproduction of oxalate results in the formation of kidney stones. In this study, steady-state and pre-steady-state kinetic approaches have been used to determine how pH affects the kinetic steps of the catalytic mechanism of human glycolate oxidase. The enzyme showed a Ping-Pong Bi-Bi kinetic mechanism between pH 6.0 and 10.0. Both the overall turnover of the enzyme (k(cat)) and the rate constant for anaerobic substrate reduction of the flavin were pH-independent at pH values above 7.0 and decreased slightly at lower pH, suggesting the involvement of an unprotonated group acting as a base in the chemical step of glycolate oxidation. The second-order rate constant for capture of glycolate (k(cat)/K(glycolate)) and the K(d)((app)) for the formation of the enzyme-substrate complex suggested the presence of a protonated group with apparent pK(a) of 8.5 participating in substrate binding. The k(cat)/K(oxygen) values were an order of magnitude faster when a group with pK(a) of 6.8 was unprotonated. These results are discussed in the context of the available three-dimensional structure of GOX.
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Affiliation(s)
| | - Giovanni Gadda
- From the Departments of Chemistry and
- Biologyand
- Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098
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Prongjit M, Sucharitakul J, Wongnate T, Haltrich D, Chaiyen P. Kinetic mechanism of pyranose 2-oxidase from trametes multicolor. Biochemistry 2009; 48:4170-80. [PMID: 19317444 DOI: 10.1021/bi802331r] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyranose 2-oxidase (P2O) from Trametes multicolor is a flavoprotein oxidase that catalyzes the oxidation of aldopyranoses by molecular oxygen to yield the corresponding 2-keto-aldoses and hydrogen peroxide. P2O is the first enzyme in the class of flavoprotein oxidases, for which a C4a-hydroperoxy-flavin adenine dinucleotide (FAD) intermediate has been detected during the oxidative half-reaction. In this study, the reduction kinetics of P2O by d-glucose and 2-d-d-glucose at pH 7.0 was investigated using stopped-flow techniques. The results indicate that d-glucose binds to the enzyme with a two-step binding process; the first step is the initial complex formation, while the second step is the isomerization to form an active Michaelis complex (E-Fl(ox):G). Interestingly, the complex (E-Fl(ox):G) showed greater absorbance at 395 nm than the oxidized enzyme, and the isomerization process showed a significant inverse isotope effect, implying that the C2-H bond of d-glucose is more rigid in the E-Fl(ox):G complex than in the free form. A large normal primary isotope effect (k(H)/k(D) = 8.84) was detected in the flavin reduction step. Steady-state kinetics at pH 7.0 shows a series of parallel lines. Kinetics of formation and decay of C-4a-hydroperoxy-FAD is the same in absence and presence of 2-keto-d-glucose, implying that the sugar does not bind to P2O during the oxidative half-reaction. This suggests that the kinetic mechanism of P2O is likely to be the ping-pong-type where the sugar product leaves prior to the oxygen reaction. The movement of the active site loop when oxygen is present is proposed to facilitate the release of the sugar product. Correlation between data from pre-steady-state and steady-state kinetics has shown that the overall turnover of the reaction is limited by the steps of flavin reduction and decay of C4a-hydroperoxy-FAD.
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Affiliation(s)
- Methinee Prongjit
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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