1
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Zhang LY, Geng JB, Wang NX, Wu YH, Yan Z, Xu BC, Xing Y. The Efficient Synthesis of 2-(3-Carbamoylpyridine-2-yl) Nicotinamide Pyridine
Salts. LETT ORG CHEM 2022. [DOI: 10.2174/1570178618666210706112141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
The synthesis of axially chiral compounds has attracted a great deal of attention in
recent years. Herein, an efficient and economical synthetic route has been developed for 2-(3-
carbamoylpyridin-2-yl) nicotinamide pyridine salts, axially chiral compounds. The starting material
1,10-phenanthroline is readily available. In this study, 2-(3-carbamoylpyridin-2-yl) nicotinamide
pyridine salts are obtained in moderate to good yields. This protocol includes simple
operations and has easy scalability. In addition, the axial chirality of the products is also preliminary
studied.
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Affiliation(s)
- Lei-Yang Zhang
- Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Beijing, 100190, China
| | - Jing-Bo Geng
- Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Beijing, 100190, China
| | - Nai-Xing Wang
- Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Beijing, 100190, China
| | - Yue-Hua Wu
- Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Beijing, 100190, China
| | - Zhan Yan
- Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences,
Beijing, 100190, China
| | - Bao-Cai Xu
- School of Food and Chemical Engineering, Beijing Technology and Business University,
Beijing, 100048, China
| | - Yalan Xing
- Department of Chemistry, William Paterson University of New Jersey, New Jersey, 07470,
United States
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2
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Rowbotham JS, Reeve HA, Vincent KA. Hybrid Chemo-, Bio-, and Electrocatalysis for Atom-Efficient Deuteration of Cofactors in Heavy Water. ACS Catal 2021; 11:2596-2604. [PMID: 33842020 PMCID: PMC8025731 DOI: 10.1021/acscatal.0c03437] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/31/2021] [Indexed: 11/29/2022]
Abstract
Deuterium-labeled nicotinamide cofactors such as [4-2H]-NADH can be used as mechanistic probes in biological redox processes and offer a route to the synthesis of selectively [2H] labeled chemicals via biocatalytic reductive deuteration. Atom-efficient routes to the formation and recycling of [4-2H]-NADH are therefore highly desirable but require careful design in order to alleviate the requirement for [2H]-labeled reducing agents. In this work, we explore a suite of electrode or hydrogen gas driven catalyst systems for the generation of [4-2H]-NADH and consider their use for driving reductive deuteration reactions. Catalysts are evaluated for their chemoselectivity, stereoselectivity, and isotopic selectivity, and it is shown that inclusion of an electronically coupled NAD+-reducing enzyme delivers considerable advantages over purely metal based systems, yielding exclusively [4S-2H]-NADH. We further demonstrate the applicability of these types of [4S-2H]-NADH recycling systems for driving reductive deuteration reactions, regardless of the facioselectivity of the coupled enzyme.
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Affiliation(s)
- Jack S. Rowbotham
- Department of Chemistry,
Inorganic Chemistry Laboratory, University
of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Holly A. Reeve
- Department of Chemistry,
Inorganic Chemistry Laboratory, University
of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Kylie A. Vincent
- Department of Chemistry,
Inorganic Chemistry Laboratory, University
of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
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3
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Iyer A, Reis RAG, Gannavaram S, Momin M, Spring-Connell AM, Orozco-Gonzalez Y, Agniswamy J, Hamelberg D, Weber IT, Gozem S, Wang S, Germann MW, Gadda G. A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Biochemistry 2021; 60:711-724. [PMID: 33630571 DOI: 10.1021/acs.biochem.1c00054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme's reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.
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Affiliation(s)
- Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Swathi Gannavaram
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Mohamed Momin
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | | | | | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Irene T Weber
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Samer Gozem
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States.,Department of Biology, Georgia State University, Atlanta, Georgia 30302, United States.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, United States
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4
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Arcus VL, van der Kamp MW, Pudney CR, Mulholland AJ. Enzyme evolution and the temperature dependence of enzyme catalysis. Curr Opin Struct Biol 2020; 65:96-101. [DOI: 10.1016/j.sbi.2020.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 10/23/2022]
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5
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Gao S, Thompson EJ, Barrow SL, Zhang W, Iavarone AT, Klinman JP. Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis. J Am Chem Soc 2020; 142:19936-19949. [PMID: 33181018 DOI: 10.1021/jacs.0c07866] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are intrinsically flexible macromolecules that undergo internal motions with time scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the optimization of reaction barriers for enzyme catalyzed reactions. Time, temperature, and mutation dependent hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has been previously employed to identify spatially resolved, catalysis-linked dynamical regions of enzymes. We now extend this technique to pursue the correlation of protein flexibility and chemical reactivity within the diverse and widespread TIM barrel proteins, targeting murine adenosine deaminase (mADA) that catalyzes the irreversible deamination of adenosine to inosine and ammonia. Following a structure-function analysis of rate and activation energy for a series of mutations at a second sphere phenylalanine positioned in proximity to the bound substrate, the catalytically impaired Phe61Ala with an elevated activation energy (Ea = 7.5 kcal/mol) and the wild type (WT) mADA (Ea = 5.0 kcal/mol) were selected for HDX-MS experiments. The rate constants and activation energies of HDX for peptide segments are quantified and used to assess mutation-dependent changes in local and distal motions. Analyses reveal that approximately 50% of the protein sequence of Phe61Ala displays significant changes in the temperature dependence of HDX behaviors, with the dominant change being an increase in protein flexibility. Utilizing Phe61Ile, which displays the same activation energy for kcat as WT, as a control, we were able to further refine the HDX analysis, highlighting the regions of mADA that are altered in a functionally relevant manner. A map is constructed that illustrates the regions of protein that are proposed to be essential for the thermal optimization of active site configurations that dominate reaction barrier crossings in the native enzyme.
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Affiliation(s)
| | | | | | - Wenju Zhang
- David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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6
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Johannissen LO, Iorgu AI, Scrutton NS, Hay S. What are the signatures of tunnelling in enzyme-catalysed reactions? Faraday Discuss 2020; 221:367-378. [DOI: 10.1039/c9fd00044e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computed tunnelling contributions and correlations between apparent activation enthalpy and entropy are explored for the interpretation of enzyme-catalysed H-transfer reactions.
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Affiliation(s)
- Linus O. Johannissen
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Andreea I. Iorgu
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
| | - Sam Hay
- Manchester Institute of Biotechnology (MIB)
- School of Chemistry
- University of Manchester
- Manchester
- UK
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7
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Laciak AR, Korasick DA, Wyatt JW, Gates KS, Tanner JJ. Structural and biochemical consequences of pyridoxine-dependent epilepsy mutations that target the aldehyde binding site of aldehyde dehydrogenase ALDH7A1. FEBS J 2019; 287:173-189. [PMID: 31302938 DOI: 10.1111/febs.14997] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023]
Abstract
In humans, certain mutations in the gene encoding aldehyde dehydrogenase 7A1 are associated with pyridoxine-dependent epilepsy (PDE). Understanding the impact of PDE-causing mutations on the structure and activity of ALDH7A1 could allow for the prediction of symptom-severity and aid the development of patient-specific medical treatments. Herein, we investigate the biochemical and structural consequences of PDE missense mutations targeting residues in the aldehyde substrate binding site: N167S, P169S, A171V, G174V, and W175G. All but G174V could be purified for biochemical and X-ray crystallographic analysis. W175G has a relatively mild kinetic defect, exhibiting a fivefold decrease in kcat with no change in Km . P169S and N167S have moderate defects, characterized by catalytic efficiencies of 20- and 100-times lower than wild-type, respectively. A171V has a profound functional defect, with catalytic efficiency 2000-times lower than wild-type. The crystal structures of the variants are the first for any PDE-associated mutant of ALDH7A1. The structures show that missense mutations that decrease the steric bulk of the side chain tend to create a cavity in the active site. The protein responds by relaxing into the vacant space, and this structural perturbation appears to cause misalignment of the aldehyde substrate in W175G and N167S. The P169S structure is nearly identical to that of the wild-type enzyme; however, analysis of B-factors suggests the catalytic defect may result from altered protein dynamics. The A171V structure suggests that the potential for steric clash with Val171 prevents Glu121 from ion pairing with the amino group of the aldehyde substrate. ENZYMES: Aldehyde dehydrogenase 7A1 (EC1.2.1.31). DATABASES: Coordinates have been deposited in the Protein Data Bank under the following accession codes: 6O4B, 6O4C, 6O4D, 6O4E, 6O4F, 6O4G, 6O4H.
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Affiliation(s)
- Adrian R Laciak
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - David A Korasick
- Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Jesse W Wyatt
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA
| | - John J Tanner
- Department of Chemistry, University of Missouri, Columbia, MO, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, USA
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8
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Role of introduced surface cysteine of NADH oxidase from Lactobacillus rhamnosus. Int J Biol Macromol 2019; 132:150-156. [DOI: 10.1016/j.ijbiomac.2019.03.168] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/10/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022]
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9
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Iorgu AI, Hedison TM, Hay S, Scrutton NS. Selectivity through discriminatory induced fit enables switching of NAD(P)H coenzyme specificity in Old Yellow Enzyme ene-reductases. FEBS J 2019; 286:3117-3128. [PMID: 31033202 PMCID: PMC6767020 DOI: 10.1111/febs.14862] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/22/2019] [Accepted: 04/24/2019] [Indexed: 11/30/2022]
Abstract
Most ene‐reductases belong to the Old Yellow Enzyme (OYE) family of flavin‐dependent oxidoreductases. OYEs use nicotinamide coenzymes as hydride donors to catalyze the reduction of alkenes that contain an electron‐withdrawing group. There have been many investigations of the structures and catalytic mechanisms of OYEs. However, the origin of coenzyme specificity in the OYE family is unknown. Structural NMR and X‐ray crystallographic data were used to rationally design variants of two OYEs, pentaerythritol tetranitrate reductase (PETNR) and morphinone reductase (MR), to discover the basis of coenzyme selectivity. PETNR has dual‐specificity and reacts with NADH and NADPH; MR accepts only NADH as hydride donor. Variants of a β‐hairpin motif in an active site loop of both these enzymes were studied using stopped‐flow spectroscopy. Specific attention was placed on the potential role of arginine residues within the β‐hairpin motif. Mutagenesis demonstrated that Arg130 governs the preference of PETNR for NADPH, and that Arg142 interacts with the coenzyme pyrophosphate group. These observations were used to switch coenzyme specificity in MR by replacing either Glu134 or Leu146 with arginine residues. These variants had increased (~15‐fold) affinity for NADH. Mutagenesis enabled MR to accept NADPH as a hydride donor, with E134R MR showing a significant (55‐fold) increase in efficiency in the reductive half‐reaction, when compared to the essentially unreactive wild‐type enzyme. Insight into the question of coenzyme selectivity in OYEs has therefore been addressed through rational redesign. This should enable coenzyme selectivity to be improved and switched in other OYEs.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, UK
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10
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Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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11
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Hedison TM, Scrutton NS. Tripping the light fantastic in membrane redox biology: linking dynamic structures to function in ER electron transfer chains. FEBS J 2019; 286:2004-2017. [PMID: 30657259 PMCID: PMC6563164 DOI: 10.1111/febs.14757] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/16/2018] [Accepted: 01/15/2019] [Indexed: 12/19/2022]
Abstract
How the dynamics of proteins assist catalysis is a contemporary issue in enzymology. In particular, this holds true for membrane‐bound enzymes, where multiple structural, spectroscopic and biochemical approaches are needed to build up a comprehensive picture of how dynamics influence enzyme reaction cycles. Of note are the recent studies of cytochrome P450 reductases (CPR)–P450 (CYP) endoplasmic reticulum redox chains, showing the relationship between dynamics and electron flow through flavin and haem redox centres and the impact this has on monooxygenation chemistry. These studies have led to deeper understanding of mechanisms of electron flow, including the timing and control of electron delivery to protein‐bound cofactors needed to facilitate CYP‐catalysed reactions. Individual and multiple component systems have been used to capture biochemical behaviour and these have led to the emergence of more integrated models of catalysis. Crucially, the effects of membrane environment and composition on reaction cycle chemistry have also been probed, including effects on coenzyme binding/release, thermodynamic control of electron transfer, conformational coupling between partner proteins and vectorial versus ‘off pathway’ electron flow. Here, we review these studies and discuss evidence for the emergence of dynamic structural models of electron flow along human microsomal CPR–P450 redox chains.
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Affiliation(s)
- Tobias M Hedison
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, UK
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