1
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Zhang Y, Chen M, Lu J, Li W, Wolynes PG, Wang W. Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. J Phys Chem B 2022; 126:6792-6801. [PMID: 36044985 PMCID: PMC9483917 DOI: 10.1021/acs.jpcb.2c03832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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Substrate inhibition, whereby enzymatic activity decreases
with
excess substrate after reaching a maximum turnover rate, is among
the most elusive phenomena in enzymatic catalysis. Here, based on
a dynamic energy landscape model, we investigate the underlying mechanism
by performing molecular simulations and frustration analysis for a
model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl
transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these
reveal a kinetic repartitioning mechanism of substrate inhibition,
whereby excess substrate AMP suppresses the population of an energetically
frustrated, but kinetically activated, catalytic pathway going through
a substrate (ATP)-product (ADP) cobound complex with steric incompatibility.
Such a frustrated pathway plays a crucial role in facilitating the
bottleneck product ADP release, and its suppression by excess substrate
AMP leads to a slow down of product release and overall turnover.
The simulation results directly demonstrate that substrate inhibition
arises from the rate-limiting product-release step, instead of the
steps for populating the catalytically competent complex as often
suggested in previous works. Furthermore, there is a tight interplay
between the enzyme conformational equilibrium and the extent of substrate
inhibition. Mutations biasing to more closed conformations tend to
enhance substrate inhibition. We also characterized the key features
of single-molecule enzyme kinetics with substrate inhibition effect.
We propose that the above molecular mechanism of substrate inhibition
may be relevant to other multisubstrate enzymes in which product release
is the bottleneck step.
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Affiliation(s)
- Yangyang Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Mingchen Chen
- Department of Research and Development, neoX Biotech, Beijing 102206, China.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jiajun Lu
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Offenbacher AR, Holman TR. Fatty Acid Allosteric Regulation of C-H Activation in Plant and Animal Lipoxygenases. Molecules 2020; 25:molecules25153374. [PMID: 32722330 PMCID: PMC7436259 DOI: 10.3390/molecules25153374] [Citation(s) in RCA: 14] [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: 06/29/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Lipoxygenases (LOXs) catalyze the (per) oxidation of fatty acids that serve as important mediators for cell signaling and inflammation. These reactions are initiated by a C-H activation step that is allosterically regulated in plant and animal enzymes. LOXs from higher eukaryotes are equipped with an N-terminal PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain that has been implicated to bind to small molecule allosteric effectors, which in turn modulate substrate specificity and the rate-limiting steps of catalysis. Herein, the kinetic and structural evidence that describes the allosteric regulation of plant and animal lipoxygenase chemistry by fatty acids and their derivatives are summarized.
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Affiliation(s)
- Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
- Correspondence:
| | - Theodore R. Holman
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
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3
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Gly188Arg substitution eliminates substrate inhibition in arachidonate 11R-lipoxygenase. Biochem Biophys Res Commun 2019; 519:81-85. [PMID: 31477267 DOI: 10.1016/j.bbrc.2019.08.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 08/23/2019] [Indexed: 11/21/2022]
Abstract
Lipoxygenases (LOXs) are dioxygenases that catalyze the oxygenation of polyunsaturated fatty acids to hydroperoxyl derivates. These products are precursors for different lipid mediators which are associated with pathogenesis of various diseases such as asthma, atherosclerosis and cancer. Several LOXs suffer from substrate inhibition, a potential regulatory mechanism, yet it is unclear what is the cause of this phenomenon. One such enzyme is the coral 11R-LOX which displays a significant decrease in turnover rate at arachidonic acid concentrations above 30 μM. In this report, site-directed mutagenesis and inhibition assays were employed to shed light on the mechanism of substrate inhibition in 11R-LOX. We found that introduction of a positive charge to the active site entrance with Gly188Arg substitution completely eliminates the slow-down at higher substrate concentrations. Inhibition of 11R-LOX by its catalysis product, 11(R)-hydroperoxyeicosatetraenoic acid, suggests an uncompetitive mechanism. We reason that substrate inhibition in 11R-LOX is due to additional fatty acid binding by the enzyme:substrate complex at an allosteric site situated in the very vicinity of the active site entrance.
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4
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Kostenko A, Ray K, Iavarone AT, Offenbacher AR. Kinetic Characterization of the C-H Activation Step for the Lipoxygenase from the Pathogenic Fungus Magnaporthe oryzae: Impact of N-Linked Glycosylation. Biochemistry 2019; 58:3193-3203. [PMID: 31264852 DOI: 10.1021/acs.biochem.9b00467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipoxygenases from pathogenic fungi belong to the lipoxygenase family of enzymes, which catalyze C-H activation of polyunsaturated fatty acids to form a diverse set of cell-signaling hydroperoxides. While the lipoxygenase catalytic domains are structurally and functionally similar, these fungal enzymes are decorated with N-linked glycans. The impact of N-linked glycans on the structure and function of these enzymes remains largely unknown. One exemplary system is MoLOX, a lipoxygenase from the fungus Magnaporthe oryzae, that is emerging as an important target for the devastating rice blast disease. Herein, we demonstrate that hydrogen transfer, associated with C-H cleavage of the substrate linoleic acid by MoLOX, is rate-determining and occurs by a hydrogen tunneling mechanism. Using the differential enthalpic barrier for hydrogen and deuterium transfer, ΔEa, as a kinetic reporter of tunneling efficiency, a disproportionate increase in the activation energy for deuterium transfer is observed upon treatment of MoLOX with a peptide:N-glycosidase that cleaves N-linked carbohydrates from the protein. This increased ΔEa is consistent with an impairment of substrate positioning in the enzyme-substrate complex for both the tunneling ready state and the ground state. These results provide new insight into the functional consequences of N-linked glycosylation on lipoxygenase C-H activation and have important implications for MoLOX inhibitor design.
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Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Katherine Ray
- Department of Biology , East Carolina University , Greenville , North Carolina 27858 , United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States
| | - Adam R Offenbacher
- Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States
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5
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Navratil A, Shchepinov MS, Dennis EA. Lipidomics Reveals Dramatic Physiological Kinetic Isotope Effects during the Enzymatic Oxygenation of Polyunsaturated Fatty Acids Ex Vivo. J Am Chem Soc 2018; 140:235-243. [PMID: 29206462 PMCID: PMC5765537 DOI: 10.1021/jacs.7b09493] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Indexed: 12/16/2022]
Abstract
Arachidonic acid (AA, 20:4) is an omega-6 polyunsaturated fatty acid (PUFA) and the main precursor to the class of lipid mediators known as eicosanoids. The enzymes that catalyze the oxygenation of AA begin by abstracting hydrogen from one of three bis-allylic carbons within 1,4-cis,cis-diene units. Substitution of deuterium for hydrogen has been shown to lead to massive kinetic isotope effects (KIE) for soybean lipoxygenase (sLOX) oxygenation of linoleic acid (LA, 18:2). Yet, experimental determination of the KIE during oxygenation of AA and LA by mammalian enzymes including cyclooxygenase (COX) and lipoxygenase (LOX) has revealed far lower values. All prior studies investigating the KIE of PUFA oxygenation have relied on in vitro systems using purified enzymes and were limited by availability of deuterated substrates. Here we demonstrate the use of macrophages as an ex vivo model system to study the physiological KIE (PKIE) during enzymatic AA oxygenation by living cells using a newly synthesized library of deuterated AA isotopologues. By extending lipidomic UPLC-MS/MS approaches to simultaneously quantify native and deuterated lipid products, we were able to demonstrate that the magnitude of the PKIE measured in macrophages for COX and LOX oxygenation of AA is similar to KIEs determined in previous reports using the AA isotopologue deuterated at carbon 13 (C13). However, for the first time we show that increasing the number of deuterated bis-allylic carbons to include both C10 and C13 leads to a massive increase in the PKIE for COX oxygenation of AA. We provide evidence that hydrogen(s) present at C10 of AA play a critical role in the catalysis of prostaglandin and thromboxane synthesis. Furthermore, we discovered that deuteration of C10 promotes the formation of the resolving lipid mediator lipoxin B4, likely by interfering with AA cyclization and shunting AA to the LOX pathway under physiological conditions.
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Affiliation(s)
- Aaron
R. Navratil
- Departments
of Chemistry & Biochemistry and Pharmacology, University of California San Diego, School of Medicine, La Jolla, California 92093-0601, United States
| | - Mikhail S. Shchepinov
- Retrotope,
Incorporated, 4300 El
Camino Real, Suite 201, Los Altos, California 94022, United States
| | - Edward A. Dennis
- Departments
of Chemistry & Biochemistry and Pharmacology, University of California San Diego, School of Medicine, La Jolla, California 92093-0601, United States
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6
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Korneenko TV, Pestov NB, Hurski AL, Fedarkevich AM, Shmanai VV, Brenna JT, Shchepinov MS. A strong developmental isotope effect in Caenorhabditis elegans induced by 5,5-deuterated lysine. Amino Acids 2017; 49:887-894. [DOI: 10.1007/s00726-017-2386-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 01/27/2017] [Indexed: 01/17/2023]
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7
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Mittal M, Kumar RB, Balagunaseelan N, Hamberg M, Jegerschöld C, Rådmark O, Haeggström JZ, Rinaldo-Matthis A. Kinetic investigation of human 5-lipoxygenase with arachidonic acid. Bioorg Med Chem Lett 2016; 26:3547-51. [DOI: 10.1016/j.bmcl.2016.06.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 11/16/2022]
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8
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Liu Y, Roth JP. A Revised Mechanism for Human Cyclooxygenase-2. J Biol Chem 2016; 291:948-58. [PMID: 26565028 PMCID: PMC4705412 DOI: 10.1074/jbc.m115.668038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/10/2015] [Indexed: 11/06/2022] Open
Abstract
The mechanism of ω-6 polyunsaturated fatty acid oxidation by wild-type cyclooxygenase 2 and the Y334F variant, lacking a conserved hydrogen bond to the catalytic tyrosyl radical/tyrosine, was examined for the first time under physiologically relevant conditions. The enzymes show apparent bimolecular rate constants and deuterium kinetic isotope effects that increase in proportion to co-substrate concentrations before converging to limiting values. The trends exclude multiple dioxygenase mechanisms as well as the proposal that initial hydrogen atom abstraction from the fatty acid is the first irreversible step in catalysis. Temperature dependent kinetic studies reinforce the novel finding that hydrogen transfer from the reduced catalytic tyrosine to a terminal peroxyl radical is the first irreversible step that controls regio- and stereospecific product formation.
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Affiliation(s)
- Yi Liu
- From the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
| | - Justine P Roth
- From the Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218
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9
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Roginskii VA. Kinetic isotope effect in the oxidation of unsaturated fatty acids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2015. [DOI: 10.1134/s1990793115030094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Neau DB, Bender G, Boeglin WE, Bartlett SG, Brash AR, Newcomer ME. Crystal structure of a lipoxygenase in complex with substrate: the arachidonic acid-binding site of 8R-lipoxygenase. J Biol Chem 2014; 289:31905-31913. [PMID: 25231982 DOI: 10.1074/jbc.m114.599662] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lipoxygenases (LOX) play critical roles in mammalian biology in the generation of potent lipid mediators of the inflammatory response; consequently, they are targets for the development of isoform-specific inhibitors. The regio- and stereo-specificity of the oxygenation of polyunsaturated fatty acids by the enzymes is understood in terms of the chemistry, but structural observation of the enzyme-substrate interactions is lacking. Although several LOX crystal structures are available, heretofore the rapid oxygenation of bound substrate has precluded capture of the enzyme-substrate complex, leaving a gap between chemical and structural insights. In this report, we describe the 2.0 Å resolution structure of 8R-LOX in complex with arachidonic acid obtained under anaerobic conditions. Subtle rearrangements, primarily in the side chains of three amino acids, allow binding of arachidonic acid in a catalytically competent conformation. Accompanying experimental work supports a model in which both substrate tethering and cavity depth contribute to positioning the appropriate carbon at the catalytic machinery.
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Affiliation(s)
- David B Neau
- Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois 60439, and
| | - Gunes Bender
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - William E Boeglin
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Sue G Bartlett
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Alan R Brash
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Marcia E Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803,.
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11
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Kinetic Isotope Effect of Prostaglandin H Synthase Exhibits Inverted Temperature Dependence. Catalysts 2014. [DOI: 10.3390/catal4020174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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12
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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13
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Affiliation(s)
- Katarzyna Swiderek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology , Zeromskiego 116, 90-924 Lodz, Poland
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14
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Cyclooxygenase reaction mechanism of prostaglandin H synthase from deuterium kinetic isotope effects. J Inorg Biochem 2011; 105:382-90. [PMID: 21394223 DOI: 10.1016/j.jinorgbio.2010.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cyclooxygenase catalysis by prostaglandin H synthase (PGHS) is thought to involve a multistep mechanism with several radical intermediates. The proposed mechanism begins with transfer of the C13 pro-(S) hydrogen atom from the substrate arachidonic acid (AA) to the Tyr385 radical in PGHS, followed by oxygen insertion and several bond rearrangements. The importance of the hydrogen-transfer step to controlling the overall kinetics of cyclooxygenase catalysis has not been directly examined. We quantified the non-competitive primary kinetic isotope effect (KIE) for both PGHS-1 and -2 using unlabeled AA and several deuterated AAs, including 13-pro-(S) d-AA, 13,13-d(2)-AA and 10, 10, 13,13-d(4)-AA. The primary KIE for steady-state cyclooxygenase catalysis, (D)k(cat), ranged between 1.8 and 2.3 in oxygen electrode measurements. The intrinsic KIE of AA radical formation by C13 pro-(S) hydrogen abstraction in PGHS-1 was estimated to be 1.9-2.3 using rapid freeze-quench EPR kinetic analysis of anaerobic reactions and computer modeling to a mechanism that includes slow formation of a pentadienyl AA radical and rapid equilibration of the AA radical with a tyrosyl radical, NS1c. The observation of similar values for steady-state and pre-steady state KIEs suggests that hydrogen abstraction is a rate-limiting step in cyclooxygenase catalysis. The large difference of the observed KIE from that of lipoxygenase indicates very different mechanism of hydrogen transfer.
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15
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Wecksler AT, Jacquot C, van der Donk WA, Holman TR. Mechanistic investigations of human reticulocyte 15- and platelet 12-lipoxygenases with arachidonic acid. Biochemistry 2009; 48:6259-67. [PMID: 19469483 DOI: 10.1021/bi802332j] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human reticulocyte 15-lipoxygenase-1 (15-hLO-1) and human platelet 12-lipoxygenase (12-hLO) have been implicated in a number of diseases, with differences in their relative activity potentially playing a central role. In this work, we characterize the catalytic mechanism of these two enzymes with arachidonic acid (AA) as the substrate. Using variable-temperature kinetic isotope effects (KIE) and solvent isotope effects (SIE), we demonstrate that both k(cat)/K(M) and k(cat) for 15-hLO-1 and 12-hLO involve multiple rate-limiting steps that include a solvent-dependent step and hydrogen atom abstraction. A relatively low k(cat)/K(M) KIE of 8 was determined for 15-hLO-1, which increases to 18 upon the addition of the allosteric effector molecule, 12-hydroxyeicosatetraenoic acid (12-HETE), indicating a tunneling mechanism. Furthermore, the addition of 12-HETE lowers the observed k(cat)/K(M) SIE from 2.2 to 1.4, indicating that the rate-limiting contribution from a solvent sensitive step in the reaction mechanism of 15-hLO-1 has decreased, with a concomitant increase in the C-H bond abstraction contribution. Finally, the allosteric binding of 12-HETE to 15-hLO-1 decreases the K(M)[O(2)] for AA to 15 microM but increases the K(M)[O(2)] for linoleic acid (LA) to 22 microM, such that the k(cat)/K(M)[O(2)] values become similar for both substrates (approximately 0.3 s(-1) microM(-1)). Considering that the oxygen concentration in cancerous tissue can be less than 5 microM, this result may have cellular implications with respect to the substrate specificity of 15-hLO-1.
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Affiliation(s)
- Aaron T Wecksler
- Chemistry and Biochemistry Department, University of California, Santa Cruz, California 95064, USA
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16
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Jacquot C, McGinley CM, Plata E, Holman TR, van der Donk WA. Synthesis of 11-thialinoleic acid and 14-thialinoleic acid, inhibitors of soybean and human lipoxygenases. Org Biomol Chem 2008; 6:4242-52. [PMID: 18972057 PMCID: PMC2883171 DOI: 10.1039/b808003h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipoxygenases catalyse the oxidation of polyunsaturated fatty acids and have been invoked in many diseases including cancer, atherosclerosis and Alzheimer's disease. Currently, no X-ray structures are available with substrate or substrate analogues bound in a productive conformation. Such structures would be very useful for examining interactions between substrate and active site residues. Reported here are the syntheses of linoleic acid analogues containing a sulfur atom at the 11 or 14 positions. The key steps in the syntheses were the incorporation of sulfur using nucleophilic attack of metallated alkynes on electrophilic sulfur compounds and the subsequent stereospecific tantalum-mediated reduction of the alkynylsulfide to the cis-alkenylsulfide. Kinetic assays performed with soybean lipoxygenase-1 showed that both 11-thialinoleic acid and 14-thialinoleic acid were competitive inhibitors with respect to linoleic acid with K(i) values of 22 and 35 microM, respectively. On the other hand, 11-thialinoleic acid was a noncompetitive inhibitor with respect to arachidonic acid with K(is) and K(ii) values of 48 and 36 microM, respectively. 11-Thialinoleic acid was also a noncompetitive inhibitor of human 15-lipoxygenase-1 with arachidonic acid (K(is) = 11.4 microM, K(ii) = 18.1 microM) or linoleic acid as substrate (K(is) = 20.1 microM, K(ii) = 20.0 microM), and a competitive inhibitor of human 12-lipoxygenase with arachidonic acid as substrate (K(i) = 2.5 microM). The presence of inhibitor did not change the regioselectivity of soybean lipoxygenase-1, human 12- or 15-lipoxygenase-1.
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Affiliation(s)
- Cyril Jacquot
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801. Fax: (217) 244-8533; Tel: (217) 244-5360;
| | - Chris M. McGinley
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801. Fax: (217) 244-8533; Tel: (217) 244-5360;
| | - Erik Plata
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801. Fax: (217) 244-8533; Tel: (217) 244-5360;
| | - Theodore R. Holman
- Chemistry and Biochemistry Department, University of California, Santa Cruz, Santa Cruz, CA 95064. Fax: (831) 459-2935; Tel: (831) 459-5884;
| | - Wilfred A. van der Donk
- Department of Chemistry, Roger Adams Laboratory, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801. Fax: (217) 244-8533; Tel: (217) 244-5360;
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17
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Jacquot C, Peng S, van der Donk WA. Kinetic isotope effects in the oxidation of arachidonic acid by soybean lipoxygenase-1. Bioorg Med Chem Lett 2008; 18:5959-62. [PMID: 18793849 PMCID: PMC2652760 DOI: 10.1016/j.bmcl.2008.08.108] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 08/23/2008] [Accepted: 08/26/2008] [Indexed: 11/22/2022]
Abstract
The reaction of soybean lipoxygenase-1 with linoleic acid has been extensively studied and displays very large kinetic isotope effects. In this work, substrate and solvent kinetic isotope effects as well as the viscosity dependence of the oxidation of arachidonic acid were investigated. The hydrogen atom abstraction step was rate-determining at all temperatures, but was partially masked by a viscosity-dependent step at ambient temperatures. The observed KIEs on k(cat) were large ( approximately 100 at 25 degrees C).
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Affiliation(s)
- Cyril Jacquot
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, 600 S. Mathews Avenue, Urbana, IL 61801, USA
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18
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Fukuzumi S. Proton-Coupled Electron Transfer of Unsaturated Fatty Acids and Mechanistic Insight into Lipoxygenase. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690223] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Kitaguchi H, Ohkubo K, Ogo S, Fukuzumi S. Additivity rule holds in the hydrogen transfer reactivity of unsaturated fatty acids with a peroxyl radical: mechanistic insight into lipoxygenase. Chem Commun (Camb) 2006:979-81. [PMID: 16491182 DOI: 10.1039/b515004c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple additivity rule holds in the hydrogen transfer reactivity of unsaturated fatty acids with cumylperoxyl radical, which is expressed by the additive contributions of the reactivity of active hydrogens from the 1,4-pentadiene subunit and those of the allylic subunit; the kinetic isotope effect on the hydrogen transfer reactions (KIE = 6.1) is significantly smaller than that observed for lipoxygenase (KIE = 81).
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Affiliation(s)
- Hironori Kitaguchi
- Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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20
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Kitaguchi H, Ohkubo K, Ogo S, Fukuzumi S. Electron-Transfer Oxidation Properties of Unsaturated Fatty Acids and Mechanistic Insight into Lipoxygenases. J Phys Chem A 2006; 110:1718-25. [PMID: 16451000 DOI: 10.1021/jp054648f] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rate constants of photoinduced electron-transfer oxidation of unsaturated fatty acids with a series of singlet excited states of oxidants in acetonitrile at 298 K were examined and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of unsaturated fatty acids and the intrinsic barrier of electron transfer. The k(et) values of linoleic acid with a series of oxidants are the same as the corresponding k(et) values of methyl linoleate, linolenic acid, and arachidonic acid, leading to the same E(ox) value of linoleic acid, methyl linoleate, linolenic acid, and arachidonic acid (1.76 V vs SCE), which is significantly lower than that of oleic acid (2.03 V vs SCE) as indicated by the smaller k(et) values of oleic acid than those of other unsaturated fatty acids. The radical cation of linoleic acid produced in photoinduced electron transfer from linoleic acid to the singlet excited state of 10-methylacridinium ion as well as that of 9,10-dicyanoanthracene was detected by laser flash photolysis experiments. The apparent rate constant of deprotonation of the radical cation of linoleic acid was determined as 8.1 x 10(3) s(-1). In the presence of oxygen, the addition of oxygen to the deprotonated radical produces the peroxyl radical, which has successfully been detected by ESR. No thermal electron transfer or proton-coupled electron transfer has occurred from linoleic acid to a strong one-electron oxidant, Ru(bpy)3(3+) (bpy = 2,2'-bipyridine) or Fe(bpy)3(3+). The present results on the electron-transfer and proton-transfer properties of unsaturated fatty acids provide valuable mechanistic insight into lipoxygenases to clarify the proton-coupled electron-transfer process in the catalytic function.
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Affiliation(s)
- Hironori Kitaguchi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, SORST, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871, Japan
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Kitaguchi H, Ohkubo K, Ogo S, Fukuzumi S. Direct ESR Detection of Pentadienyl Radicals and Peroxyl Radicals in Lipid Peroxidation: Mechanistic Insight into Regioselective Oxygenation in Lipoxygenases. J Am Chem Soc 2005; 127:6605-9. [PMID: 15869281 DOI: 10.1021/ja044345j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Well-resolved ESR spectra of free pentadienyl radicals have been observed under photoirradiation of di-tert-butylperoxide (Bu(t)OOBu(t)) and polyunsaturated fatty acids in the absence of O(2), allowing us to determine the hfc values. The hfc values of linoleyl radical indicate that the spin density is the largest at the C-11 position. The linoleyl radical is readily trapped by O(2) to produce the peroxyl radical (11-HPO.) in which O(2) is added mainly at the C-11 position of the pentadienyl radical as indicated by the comparison of the ESR spectra of peroxyl radicals derived from linoleic acid and [11,11-(2)H(2)]linoleic acid. The peroxyl radical (13-HPO.), which is initially formed by the hydrogen abstraction from 13-(S)-hydroperoxy-9(Z),11(E)-octadecadienoic acid (13-HPOD) by Bu(t)O., is found to isomerize to 11-HPO. via removal of O(2) from 13-HPO. and addition of O(2) to linoleyl radical to produce 11-HPO. . This finding supports an idea of O(2) entering via a specific protein channel, which determines the stereo- and regiochemistry of the biradical combination between O(2) and linoleyl radical in lipoxygenases.
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Affiliation(s)
- Hironori Kitaguchi
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, SORST, Japan Science and Technology Agency (JST), Suita, Osaka 565-0871, Japan
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