1
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Chen Z, Kang XW, Zhou Y, Zhou Z, Tang S, Zou S, Wang K, Huang J, Ding B, Zhong D. Dissecting the Ultrafast Stepwise Bidirectional Proton Relay in a Blue-Light Photoreceptor. J Am Chem Soc 2023; 145:3394-3400. [PMID: 36722850 DOI: 10.1021/jacs.2c10206] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Proton relays through H-bond networks are essential in realizing the functionality of protein machines such as in photosynthesis and photoreceptors. It has been challenging to dissect the rates and energetics of individual proton-transfer steps during the proton relay. Here, we have designed a proton rocking blue light using a flavin (BLUF) domain with the flavin mononucleotide (FMN)-glutamic acid (E)-tryptophan (W) triad and have resolved the four individual proton-transfer steps kinetically using ultrafast spectroscopy. We have found that after the photo-induced charge separation forming FMN·-/E-COOH/WH·+, the proton first rapidly jumps from the bridging E-COOH to FMN- (τfPT2 = 3.8 ps; KIE = 1.0), followed by a second proton transfer from WH·+ to E-COO- (τfPT1 = 336 ps; KIE = 2.6) which immediately rocks back to W· (τrPT1 = 85 ps; KIE = 6.7), followed by a proton return from FMNH· to E-COO- (τrPT2 = 34 ps; KIE = 3.3) with the final charge recombination between FMN·- and WH·+ to close the reaction cycle. Our results revisited the Grotthuss mechanism on the ultrafast timescale using the BLUF domain as a paradigm protein.
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Affiliation(s)
- Zijing Chen
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiu-Wen Kang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yalin Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zhongneng Zhou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Siwei Tang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Shuhua Zou
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Kailin Wang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiulong Huang
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Bei Ding
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Dongping Zhong
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China.,Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio43210, United States.,School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai200240, China
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2
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Copper monooxygenase reactivity: Do consensus mechanisms accurately reflect experimental observations? J Inorg Biochem 2022; 231:111780. [DOI: 10.1016/j.jinorgbio.2022.111780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 11/21/2022]
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3
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Liu Y, Yan Y, Xing T, Shi Q. Understanding the Large Kinetic Isotope Effect of Hydrogen Tunneling in Condensed Phases by Using Double-Well Model Systems. J Phys Chem B 2021; 125:5959-5970. [PMID: 34033714 DOI: 10.1021/acs.jpcb.1c02851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many experiments have shown large kinetic isotope effects (KIEs) for hydrogen transfer reactions in condensed phases as evidence of strong quantum tunneling effects. Since accurate calculation of the tunneling dynamics in such systems still present significant challenges, previous studies have employed different types of approximations to estimate the tunneling effects and KIEs. In this work, by employing model systems consisting of a double-well coupled to a harmonic bath, we calculate the tunneling effects and KIEs using the numerically exact hierarchical equations of motion (HEOM) method. It is found that hydrogen and deuterium transfer reactions in the same system may show rather different behaviors, where hydrogen transfer is dominated by tunneling between the two lowest vibrational states and deuterium transfer is controlled by excited vibrational states close to the barrier top. The simulation results are also used to test the validity of various approximate methods. It is shown that the Wolynes theory of dissipative tunneling gives a good estimation of rate constants in the over-the-barrier regime, while the nonadiabatic reaction rate theory based on the Landau-Zener formula is more suitable for deep tunneling reactions.
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Affiliation(s)
- Yanying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Yaming Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Tao Xing
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
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4
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Abstract
This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.
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5
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Das A, Hessin C, Ren Y, Desage-El Murr M. Biological concepts for catalysis and reactivity: empowering bioinspiration. Chem Soc Rev 2020; 49:8840-8867. [PMID: 33107878 DOI: 10.1039/d0cs00914h] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biological systems provide attractive reactivity blueprints for the design of challenging chemical transformations. Emulating the operating mode of natural systems may however not be so easy and direct translation of structural observations does not always afford the anticipated efficiency. Metalloenzymes rely on earth-abundant metals to perform an incredibly wide range of chemical transformations. To do so, enzymes in general have evolved tools and tricks to enable control of such reactivity. The underlying concepts related to these tools are usually well-known to enzymologists and bio(inorganic) chemists but may be a little less familiar to organometallic chemists. So far, the field of bioinspired catalysis has greatly focused on the coordination sphere and electronic effects for the design of functional enzyme models but might benefit from a paradigm shift related to recent findings in biological systems. The goal of this review is to bring these fields closer together as this could likely result in the development of a new generation of highly efficient bioinspired systems. This contribution covers the fields of redox-active ligands, entatic state reactivity, energy conservation through electron bifurcation, and quantum tunneling for C-H activation.
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Affiliation(s)
- Agnideep Das
- Université de Strasbourg, Institut de Chimie, UMR CNRS 7177, 67000 Strasbourg, France.
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6
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Howe GW, van der Donk WA. Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase. Biochemistry 2019; 58:4260-4268. [PMID: 31535852 PMCID: PMC6852621 DOI: 10.1021/acs.biochem.9b00732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase catalyzes the transfer of a hydride from phosphite to NAD+, producing phosphate and NADH. We have evaluated the role of hydride tunneling in a thermostable variant of this enzyme (17X-PTDH) by measuring the temperature dependence of the primary 2H kinetic isotope effects (KIEs) between 5 and 45 °C. Pre-steady-state kinetic measurements were used to demonstrate that the hydride transfer is rate-determining across this temperature range and that the observed KIEs are equal to the intrinsic isotope effect on the chemical step. The KIEs on the pre-exponential factor (AH/AD) and the activation energy (ΔEa) were 1.6 ± 0.1 and 0.21 ± 0.05 kcal/mol, respectively, suggesting that 17X-PTDH facilitates extensive tunneling of both isotopes via a Marcus-like model. Site-directed mutagenesis was used to evaluate the role of an active site threonine (Thr104) found on the back face of the nicotinamide in promoting the close packing of the substrates. In mutants with reduced steric bulk at this position, values of AH/AD and ΔEa fall within the range describing semiclassical "over the barrier" reactivity, suggesting that Thr104 acts as a steric backstop to promote tunneling in 17X-PTDH. Whereas hydrogen tunneling is now a widely appreciated feature of C-H activating enzymes, these observations with a P-H activating system are consistent with the proposal that tunneling is likely to be a common feature on all enzymes that catalyze hydrogen transfers.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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7
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Ehudin MA, Quist DA, Karlin KD. Enhanced Rates of C-H Bond Cleavage by a Hydrogen-Bonded Synthetic Heme High-Valent Iron(IV) Oxo Complex. J Am Chem Soc 2019; 141:12558-12569. [PMID: 31318198 PMCID: PMC6734939 DOI: 10.1021/jacs.9b01253] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Secondary coordination sphere interactions are critical in facilitating the formation, stabilization, and enhanced reactivity of high-valent oxidants required for essential biochemical processes. Herein, we compare the C-H bond oxidizing capabilities of spectroscopically characterized synthetic heme iron(IV) oxo complexes, F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a 2,6-lutidinium triflate (LutH+) Lewis acid adduct involving ferryl O-atom hydrogen-bonding, F8Cmpd-II(LutH+). Second-order rate constants utilizing C-H and C-D substrates were obtained by UV-vis spectroscopic monitoring, while products were characterized and quantified by EPR spectroscopy and gas chromatography (GC). With xanthene, F8Cmpd-II(LutH+) reacts 40 times faster (k2 = 14.2 M-1 s-1; -90 °C) than does F8Cmpd-II, giving bixanthene plus xanthone and the heme product [F8FeIIIOH2]+. For substrates with greater C-H bond dissociation energies (BDEs) F8Cmpd-II(LutH+) reacts with the second order rate constants k2(9,10-dihydroanthracene; DHA) = 0.485 M-1 s-1 and k2(fluorene) = 0.102 M-1 s-1 (-90 °C); by contrast, F8Cmpd-II is unreactive toward these substrates. For xanthene vs xanthene-(d2), large, nonclassical deuterium kinetic isotope effects are roughly estimated for both F8Cmpd-II and F8Cmpd-II(LutH+). The deuterated H-bonded analog, F8Cmpd-II(LutD+), was also prepared; for the reaction with DHA, an inverse KIE (compared to F8Cmpd-II(LutH+)) was observed. This work originates/inaugurates experimental investigation of the reactivity of authentic H-bonded heme-based FeIV═O compounds, critically establishing the importance of oxo H-bonding (or protonation) in heme complexes and enzyme active sites.
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Affiliation(s)
- Melanie A. Ehudin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - David A. Quist
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D. Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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8
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Abstract
Aerobic life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O2 activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O2 activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
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9
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Xu Y, Bao P, Song K, Shi Q. Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor. J Comput Chem 2018; 40:1005-1014. [PMID: 30341953 DOI: 10.1002/jcc.25561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 07/01/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022]
Abstract
The BLUF (blue light sensor using flavin adenine dinucleotide) domain is widely studied as a prototype for proton coupled electron transfer (PCET) reactions in biological systems. In this work, the photo-induced concerted PCET reaction from the light state of the AppA BLUF domain is investigated. To model the simultaneous transfer of two protons in the reaction, two-dimensional potential energy surfaces for the double proton transfer are first calculated for the locally excited and charge transfer states, which are then used to obtain the vibrational wave function overlaps and the vibrational energy levels. Contributions to the PCET rate constant from each pair of vibronic states are then analyzed using the theory based on the Fermi's golden rule. We show that, the recently proposed light state structure of the BLUF domain with a tautomerized Gln63 residue is consistent with the concerted transfer of one electron and two protons. It is also found that, thermal fluctuations of the protein structure, especially the proton donor-acceptor distances, play an important role in determining the PCET reaction rate. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Yang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Bao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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11
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Schramm VL, Schwartz SD. Promoting Vibrations and the Function of Enzymes. Emerging Theoretical and Experimental Convergence. Biochemistry 2018; 57:3299-3308. [PMID: 29608286 DOI: 10.1021/acs.biochem.8b00201] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A complete understanding of enzyme catalysis requires knowledge of both transition state features and the detailed motions of atoms that cause reactant molecules to form and traverse the transition state. The seeming intractability of the problem arises from the femtosecond lifetime of chemical transition states, preventing most experimental access. Computational chemistry is admirably suited to short time scale analysis but can be misled by inappropriate starting points or by biased assumptions. Kinetic isotope effects provide an experimental approach to transition state structure and a method for obtaining transition state analogues but, alone, do not inform how that transition state is reached. Enzyme structures with transition state analogues provide computational starting points near the transition state geometry. These well-conditioned starting points, combined with the unbiased computational method of transition path sampling, provide realistic atomistic motions involved in transition state formation and passage. In many, but not all, enzymatic systems, femtosecond local protein motions near the catalytic site are linked to transition state formation. These motions are not inherently revealed by most approaches of transition state theory, because transition state theory replaces dynamics with the statistics of the transition state. Experimental and theoretical convergence of the link between local catalytic site vibrational modes and catalysis comes from heavy atom ("Born-Oppenheimer") enzymes. Fully labeled and catalytic site local heavy atom labels perturb the probability of finding enzymatic transition states in ways that can be analyzed and predicted by transition path sampling. Recent applications of these experimental and computational approaches reveal how subpicosecond local catalytic site protein modes play important roles in creating the transition state.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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12
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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13
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Xu Y, Song K, Shi Q. Mixed quantum-classical simulation of the hydride transfer reaction catalyzed by dihydrofolate reductase based on a mapped system-harmonic bath model. J Chem Phys 2018; 148:102322. [DOI: 10.1063/1.4990515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Song
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China and University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Abstract
An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry & Physics, Graduate Center, City University of New York , 365 Fifth Ave, New York, New York 10016, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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15
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Markle TF, Zhang MT, Santoni MP, Johannissen LO, Hammarström L. Proton-Coupled Electron Transfer in a Series of Ruthenium-Linked Tyrosines with Internal Bases: Evaluation of a Tunneling Model for Experimental Temperature-Dependent Kinetics. J Phys Chem B 2016; 120:9308-21. [DOI: 10.1021/acs.jpcb.6b05885] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Todd F. Markle
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Ming-Tian Zhang
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Marie-Pierre Santoni
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Linus O. Johannissen
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
| | - Leif Hammarström
- Department of Chemistry − Ångström
Laboratory, Uppsala University, P.O. Box 523, S-75120 Uppsala, Sweden
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16
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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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17
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Amorati R, Baschieri A, Morroni G, Gambino R, Valgimigli L. Peroxyl Radical Reactions in Water Solution: A Gym for Proton-Coupled Electron-Transfer Theories. Chemistry 2016; 22:7924-34. [DOI: 10.1002/chem.201504492] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Riccardo Amorati
- Department of Chemistry “G. Ciamician”; University of Bologna; Via S. Giacomo 11 40126 Bologna Italy
| | - Andrea Baschieri
- Department of Chemistry “G. Ciamician”; University of Bologna; Via S. Giacomo 11 40126 Bologna Italy
| | - Gloria Morroni
- Department of Chemistry “G. Ciamician”; University of Bologna; Via S. Giacomo 11 40126 Bologna Italy
| | - Rossana Gambino
- Department of Chemistry “G. Ciamician”; University of Bologna; Via S. Giacomo 11 40126 Bologna Italy
| | - Luca Valgimigli
- Department of Chemistry “G. Ciamician”; University of Bologna; Via S. Giacomo 11 40126 Bologna Italy
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18
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Pagba CV, McCaslin TG, Chi SH, Perry JW, Barry BA. Proton-Coupled Electron Transfer and a Tyrosine-Histidine Pair in a Photosystem II-Inspired β-Hairpin Maquette: Kinetics on the Picosecond Time Scale. J Phys Chem B 2016; 120:1259-72. [PMID: 26886811 DOI: 10.1021/acs.jpcb.6b00560] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosystem II (PSII) and ribonucleotide reductase employ oxidation and reduction of the tyrosine aromatic ring in radical transport pathways. Tyrosine-based reactions involve either proton-coupled electron transfer (PCET) or electron transfer (ET) alone, depending on the pH and the pKa of tyrosine's phenolic oxygen. In PSII, a subset of the PCET reactions are mediated by a tyrosine-histidine redox-driven proton relay, YD-His189. Peptide A is a PSII-inspired β-hairpin, which contains a single tyrosine (Y5) and histidine (H14). Previous electrochemical characterization indicated that Peptide A conducts a net PCET reaction between Y5 and H14, which have a cross-strand π-π interaction. The kinetic impact of H14 has not yet been explored. Here, we address this question through time-resolved absorption spectroscopy and 280-nm photolysis, which generates a neutral tyrosyl radical. The formation and decay of the neutral tyrosyl radical at 410 nm were monitored in Peptide A and its variant, Peptide C, in which H14 is replaced by cyclohexylalanine (Cha14). Significantly, both electron transfer (ET, pL 11, L = lyonium) and PCET (pL 9) were accelerated in Peptide A and C, compared to model tyrosinate or tyrosine at the same pL. Increased electronic coupling, mediated by the peptide backbone, can account for this rate acceleration. Deuterium exchange gave no significant solvent isotope effect in the peptides. At pL 9, but not at pL 11, the reaction rate decreased when H14 was mutated to Cha14. This decrease in rate is attributed to an increase in reorganization energy in the Cha14 mutant. The Y5-H14 mechanism in Peptide A is reminiscent of proton- and electron-transfer events involving YD-H189 in PSII. These results document a mechanism by which proton donors and acceptors can regulate the rate of PCET reactions.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - San-Hui Chi
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Joseph W Perry
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, the Petit Institute for Bioengineering and Bioscience, and the ‡Center for Organic Photonics and Electronics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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19
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Maiuri M, Delfino I, Cerullo G, Manzoni C, Pelmenschikov V, Guo Y, Wang H, Gee LB, Dapper CH, Newton WE, Cramer SP. Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration. J Inorg Biochem 2015; 153:128-135. [PMID: 26343576 DOI: 10.1016/j.jinorgbio.2015.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/18/2015] [Accepted: 07/09/2015] [Indexed: 11/28/2022]
Abstract
We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.
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Affiliation(s)
- Margherita Maiuri
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Ines Delfino
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Largo dell'Università, I-01100 Viterbo, Italy
| | - Giulio Cerullo
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Cristian Manzoni
- IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano, Italy
| | - Vladimir Pelmenschikov
- Institut für Chemie, Technische Universität Berlin, Strasse des 17 Juni 135, 10623 Berlin, Germany
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, United States
| | - Hongxin Wang
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Leland B Gee
- Department of Chemistry, University of California, Davis, CA 95616, United States
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, United States
| | - Stephen P Cramer
- Department of Chemistry, University of California, Davis, CA 95616, United States; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States.
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20
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Liu Y, Liu H, Song K, Xu Y, Shi Q. Theoretical Study of Proton Coupled Electron Transfer Reactions: The Effect of Hydrogen Bond Bending Motion. J Phys Chem B 2015; 119:8104-14. [DOI: 10.1021/acs.jpcb.5b02927] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yang Liu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Hao Liu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Kai Song
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Yang Xu
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
| | - Qiang Shi
- Beijing
National Laboratory
for Molecular Sciences, State Key Laboratory for Structural Chemistry
of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China
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21
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Liu X, Salahub DR. Molybdenum Carbide Nanocatalysts at Work in the in Situ Environment: A Density Functional Tight-Binding and Quantum Mechanical/Molecular Mechanical Study. J Am Chem Soc 2015; 137:4249-59. [DOI: 10.1021/jacs.5b01494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Xingchen Liu
- Department of Chemistry,
Institute for Quantum Science and Technology, and Centre for Molecular
Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Dennis R. Salahub
- Department of Chemistry,
Institute for Quantum Science and Technology, and Centre for Molecular
Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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22
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Cong Z, Kinemuchi H, Kurahashi T, Fujii H. Factors affecting hydrogen-tunneling contribution in hydroxylation reactions promoted by oxoiron(IV) porphyrin π-cation radical complexes. Inorg Chem 2014; 53:10632-41. [PMID: 25222493 DOI: 10.1021/ic501737j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hydrogen atom transfer with a tunneling effect (H-tunneling) has been proposed to be involved in aliphatic hydroxylation reactions catalyzed by cytochrome P450 and synthetic heme complexes as a result of the observation of large hydrogen/deuterium kinetic isotope effects (KIEs). In the present work, we investigate the factors controlling the H-tunneling contribution to the H-transfer process in hydroxylation reaction by examining the kinetics of hydroxylation reactions at the benzylic positions of xanthene and 1,2,3,4-tetrahydronaphthalene by oxoiron(IV) 5,10,15,20-tetramesitylporphyrin π-cation radical complexes ((TMP(+•))Fe(IV)O(L)) under single-turnover conditions. The Arrhenius plots for these hydroxylation reactions of H-isotopomers have upwardly concave profiles. The Arrhenius plots of D-isotopomers, clear isosbestic points, and product analysis rule out the participation of thermally dependent other reaction processes in the concave profiles. These results provide evidence for the involvement of H-tunneling in the rate-limiting H-transfer process. These profiles are simulated using an equation derived from Bell's tunneling model. The temperature dependence of the KIE values (k(H)/k(D)) determined for these reactions indicates that the KIE value increases as the reaction temperature becomes lower, the bond dissociation energy (BDE) of the C-H bond of a substrate becomes higher, and the reactivity of (TMP(+•))Fe(IV)O(L) decreases. In addition, we found correlation of the slope of the ln(k(H)/k(D)) - 1/T plot and the bond strengths of the Fe═O bond of (TMP(+•))Fe(IV)O(L) estimated from resonance Raman spectroscopy. These observations indicate that these factors modulate the extent of the H-tunneling contribution by modulating the ratio of the height and thickness of the reaction barrier.
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Affiliation(s)
- Zhiqi Cong
- Department of Chemistry, Biology and Environmental Science, Faculty of Science, Nara Women's University , Kitauoyanishi, Nara 830-8506, Japan
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23
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Affiliation(s)
- Joshua P. Layfield
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 600 South Mathews Avenue, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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24
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Park J, Morimoto Y, Lee YM, Nam W, Fukuzumi S. Unified view of oxidative C-H bond cleavage and sulfoxidation by a nonheme iron(IV)-oxo complex via Lewis acid-promoted electron transfer. Inorg Chem 2014; 53:3618-28. [PMID: 24605985 DOI: 10.1021/ic403124u] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by a nonheme iron(IV)-oxo complex, [(N4Py)Fe(IV)(O)](2+) (N4Py = N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine), were remarkably enhanced by the presence of triflic acid (HOTf) and Sc(OTf)3 in acetonitrile at 298 K. All the logarithms of the observed second-order rate constants of both the oxidative C-H bond cleavage and sulfoxidation reactions exhibit remarkably unified correlations with the driving forces of proton-coupled electron transfer (PCET) and metal ion-coupled electron transfer (MCET) in light of the Marcus theory of electron transfer when the differences in the formation constants of precursor complexes between PCET and MCET were taken into account, respectively. Thus, the mechanisms of both the oxidative C-H bond cleavage of toluene derivatives and sulfoxidation of thioanisole derivatives by [(N4Py)Fe(IV)(O)](2+) in the presence of HOTf and Sc(OTf)3 have been unified as the rate-determining electron transfer, which is coupled with binding of [(N4Py)Fe(IV)(O)](2+) by proton (PCET) and Sc(OTf)3 (MCET). There was no deuterium kinetic isotope effect (KIE) on the oxidative C-H bond cleavage of toluene via the PCET pathway, whereas a large KIE value was observed with Sc(OTf)3, which exhibited no acceleration of the oxidative C-H bond cleavage of toluene. When HOTf was replaced by DOTf, an inverse KIE (0.4) was observed for PCET from both toluene and [Ru(II)(bpy)3](2+) (bpy =2,2'-bipyridine) to [(N4Py)Fe(IV)(O)](2+). The PCET and MCET reactivities of [(N4Py)Fe(IV)(O)](2+) with Brønsted acids and various metal triflates have also been unified as a single correlation with a quantitative measure of the Lewis acidity.
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Affiliation(s)
- Jiyun Park
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, ALCA , Japan Science and Technology Agency (JST) , Suita, Osaka 565-0871, Japan
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25
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Wiebe H, Prachnau M, Weinberg N. Hydrogen transfer reactions in viscous media — Potential and free energy surfaces in solvent–solute coordinates and their kinetic implications. CAN J CHEM 2013. [DOI: 10.1139/cjc-2012-0554] [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
Two-dimensional potential energy and free energy surfaces are obtained using quantum mechanical and molecular dynamics calculations for four hydrogen transfer reactions in n-hexane solvent: the methyl–methane, n-propyl–n-propane, n-pentyl–n-pentane, and t-butyl–isobutane systems. The resultant surfaces have similar landscapes despite the fact the equilibrated solvent cavities for these systems are notably different in size and shape. The kinetic implications of these landscapes are discussed. The Arrhenius and tunneling kinetics of hydrogen transfer in nonpolar hydrocarbon solute–solvent systems are not expected to show any significant viscosity dependence.
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Affiliation(s)
- Heather Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Melissa Prachnau
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
| | - Noham Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada
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26
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Kline CD, Mayfield M, Blackburn NJ. HHM motif at the CuH-site of peptidylglycine monooxygenase is a pH-dependent conformational switch. Biochemistry 2013; 52:2586-96. [PMID: 23530865 DOI: 10.1021/bi4002248] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylglycine monooxygenase is a copper-containing enzyme that catalyzes the amidation of neuropeptides hormones, the first step of which is the conversion of a glycine-extended pro-peptide to its α-hydroxyglcine intermediate. The enzyme contains two mononuclear Cu centers termed CuM (ligated to imidazole nitrogens of H242, H244 and the thioether S of M314) and CuH (ligated to imidazole nitrogens of H107, H108, and H172) with a Cu-Cu separation of 11 Å. During catalysis, the M site binds oxygen and substrate, and the H site donates the second electron required for hydroxylation. The WT enzyme shows maximum catalytic activity at pH 5.8 and undergoes loss of activity at lower pHs due to a protonation event with a pKA of 4.6. Low pH also causes a unique structural transition in which a new S ligand coordinates to copper with an identical pKA, manifest by a large increase in Cu-S intensity in the X- ray absorption spectroscopy. In previous work (Bauman, A. T., Broers, B. A., Kline, C. D., and Blackburn, N. J. (2011) Biochemistry 50, 10819-10828), we tentatively assigned the new Cu-S interaction to binding of M109 to the H-site (part of an HHM conserved motif common to all but one member of the family). Here we follow up on these findings via studies on the catalytic activity, pH-activity profiles, and spectroscopic (electron paramagnetic resonance, XAS, and Fourier transform infrared) properties of a number of H-site variants, including H107A, H108A, H172A, and M109I. Our results establish that M109 is indeed the coordinating ligand and confirm the prediction that the low pH structural transition with associated loss of activity is abrogated when the M109 thioether is absent. The histidine mutants show more complex behavior, but the almost complete lack of activity in all three variants coupled with only minor differences in their spectroscopic properties suggests that unique structural elements at H are critical for functionality. The data suggest a more general utility for the HHM motif as a copper- and pH-dependent conformational switch.
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Affiliation(s)
- Chelsey D Kline
- Institute of Environmental, Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, USA
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27
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Park J, Lee YM, Nam W, Fukuzumi S. Brønsted Acid-Promoted C–H Bond Cleavage via Electron Transfer from Toluene Derivatives to a Protonated Nonheme Iron(IV)-Oxo Complex with No Kinetic Isotope Effect. J Am Chem Soc 2013; 135:5052-61. [DOI: 10.1021/ja311662w] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiyun Park
- Department
of Material and Life
Science, Graduate School of Engineering, ALCA, Japan Science and Technology
Agency, Osaka University, Suita, Osaka
565-0871, Japan
| | - Yong-Min Lee
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
| | - Wonwoo Nam
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
| | - Shunichi Fukuzumi
- Department
of Material and Life
Science, Graduate School of Engineering, ALCA, Japan Science and Technology
Agency, Osaka University, Suita, Osaka
565-0871, Japan
- Department
of Bioinspired Science, Ewha Womans University, Seoul 120-750, Korea
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28
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Markle TF, Tronic TA, DiPasquale AG, Kaminsky W, Mayer JM. Effect of basic site substituents on concerted proton-electron transfer in hydrogen-bonded pyridyl-phenols. J Phys Chem A 2012; 116:12249-59. [PMID: 23176252 PMCID: PMC3926939 DOI: 10.1021/jp311388n] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Separated concerted proton-electron transfer (sCPET) reactions of two series of phenols with pendent substituted pyridyl moieties are described. The pyridine is either attached directly to the phenol (HOAr-pyX) or connected through a methylene linker (HOArCH(2)pyX) (X = 4-NO(2), 5-CF(3), 4-CH(3), and 4-NMe(2)). Electron-donating and -withdrawing substituents have a substantial effect on the chemical environment of the transferring proton, as indicated by IR and (1)H NMR spectra, X-ray structures, and computational studies. One-electron oxidation of the phenols occurs concomitantly with proton transfer from the phenolic oxygen to the pyridyl nitrogen. The oxidation potentials vary linearly with the pK(a) of the free pyridine (pyX), with slopes slightly below the Nerstian value of 59 mV/pK(a). For the HOArCH(2)pyX series, the rate constants k(sCPET) for oxidation by NAr(3)(•+) or [Fe(diimine)(3)](3+) vary primarily with the thermodynamic driving force (ΔG°(sCPET)), whether ΔG° is changed by varying the potential of the oxidant or the substituent on the pyridine, indicating a constant intrinsic barrier λ. In contrast, the substituents in the HOAr-pyX series affect λ as well as ΔG°(sCPET), and compounds with electron-withdrawing substituents have significantly lower reactivity. The relationship between the structural and spectroscopic properties of the phenols and their CPET reactivity is discussed.
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Affiliation(s)
| | - Tristan A. Tronic
- Department of Chemistry, Campus Box 351700, University of Washington, Seattle, Washington 98195-1700
| | | | - Werner Kaminsky
- Department of Chemistry, Campus Box 351700, University of Washington, Seattle, Washington 98195-1700
| | - James M. Mayer
- Department of Chemistry, Campus Box 351700, University of Washington, Seattle, Washington 98195-1700
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29
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Chan SI, Chien CYC, Yu CSC, Nagababu P, Maji S, Chen PPY. Efficient catalytic oxidation of hydrocarbons mediated by tricopper clusters under mild conditions. J Catal 2012. [DOI: 10.1016/j.jcat.2012.06.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Nagel ZD, Meadows CW, Dong M, Bahnson BJ, Klinman JP. Active site hydrophobic residues impact hydrogen tunneling differently in a thermophilic alcohol dehydrogenase at optimal versus nonoptimal temperatures. Biochemistry 2012; 51:4147-56. [PMID: 22568562 DOI: 10.1021/bi3001352] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A growing body of data suggests that protein motion plays an important role in enzyme catalysis. Two highly conserved hydrophobic active site residues in the cofactor-binding pocket of ht-ADH (Leu176 and V260) have been mutated to a series of hydrophobic side chains of smaller size, as well as one deletion mutant, L176Δ. Mutations decrease k(cat) and increase K(M)(NAD(+)). Most of the observed decreases in effects on k(cat) at pH 7.0 are due to an upward shift in the optimal pH for catalysis; a simple electrostatic model is invoked that relates the change in pK(a) to the distance between the positively charged nicotinamide ring and bound substrate. Structural modeling of the L176Δ and V260A variants indicates the development of a cavity behind the nicotinamide ring without any significant perturbation of the secondary structure of the enzyme relative to that of the wild type. Primary kinetic isotope effects (KIEs) are modestly increased for all mutants. Above the dynamical transition at 30 °C for ht-ADH [Kohen, A., et al. (1999) Nature 399, 496], the temperature dependence of the KIE is seen to increase with a decrease in side chain volume at positions 176 and 260. Additionally, the relative trends in the temperature dependence of the KIE above and below 30 °C appear to be reversed for the cofactor-binding pocket mutants in relation to wild-type protein. The aggregate results are interpreted in the context of a full tunneling model of enzymatic hydride transfer that incorporates both protein conformational sampling (preorganization) and active site optimization of tunneling (reorganization). The reduced temperature dependence of the KIE in the mutants below 30 °C indicates that at low temperatures, the enzyme adopts conformations refractory to donor-acceptor distance sampling.
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Affiliation(s)
- Zachary D Nagel
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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31
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Markle TF, Tenderholt AL, Mayer JM. Probing quantum and dynamic effects in concerted proton-electron transfer reactions of phenol-base compounds. J Phys Chem B 2012; 116:571-84. [PMID: 22148459 PMCID: PMC3974916 DOI: 10.1021/jp2091736] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton-electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer's multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework. The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor-acceptor (i.e., O-N) distances to assess the importance of heavy atom "gating". Such changes in d(ON) dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor-acceptor distances despite the large (~0.2 Å) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative 1 versus the CH(2)-pyridyl 2, but the computed factor of 5 is smaller than the experimental 10(2). The amine derivative is calculated to react similarly to 1, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results.
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Affiliation(s)
| | - Adam L. Tenderholt
- Department of Chemistry, University of Washington, Box 351700 Seattle, WA 98195-1700
| | - James M. Mayer
- Department of Chemistry, University of Washington, Box 351700 Seattle, WA 98195-1700
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32
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Markle TF, Rhile IJ, Mayer JM. Kinetic effects of increased proton transfer distance on proton-coupled oxidations of phenol-amines. J Am Chem Soc 2011; 133:17341-52. [PMID: 21919508 PMCID: PMC3228417 DOI: 10.1021/ja2056853] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh(2)NH(2) substituent (1). Spectroscopic, structural, thermochemical, and computational studies show that the two amino-phenols are very similar, except that the O···N distance (d(ON)) is >0.1 Å longer in 2 than in 1. The difference in d(ON) is 0.13 ± 0.03 Å from X-ray crystallography and 0.165 Å from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations (•)OAr-NH(3)(+) by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. 2 orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C(6)H(4)OMe)(3)(•+) (3a(+)) occurs at (1.4 ± 0.1) × 10(4) M(-1) s(-1), only a factor of 2 slower than the closely related reaction of 1 with N(C(6)H(4)OMe)(2)(C(6)H(4)Br)(•+) (3b(+)). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG° (2 + 3a(+)) = +0.078 V versus ΔG° (1 + 3b(+)) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Brønsted α, Δ ln(k)/Δ ln(K(eq))). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the two phenols emphasizes the importance of the highly anharmonic O···H···N potential energy surface and the influence of proton vibrational excited states.
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Affiliation(s)
- Todd F Markle
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
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Brala CJ, Pilepić V, Sajenko I, Karković A, Uršić S. Ions Can Move a Proton-Coupled Electron-Transfer Reaction into Tunneling Regime. Helv Chim Acta 2011. [DOI: 10.1002/hlca.201100035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Barry BA. Proton coupled electron transfer and redox active tyrosines in Photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2011; 104:60-71. [PMID: 21419640 PMCID: PMC3164834 DOI: 10.1016/j.jphotobiol.2011.01.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 01/25/2011] [Accepted: 01/31/2011] [Indexed: 11/30/2022]
Abstract
In this article, progress in understanding proton coupled electron transfer (PCET) in Photosystem II is reviewed. Changes in acidity/basicity may accompany oxidation/reduction reactions in biological catalysis. Alterations in the proton transfer pathway can then be used to alter the rates of the electron transfer reactions. Studies of the bioenergetic complexes have played a central role in advancing our understanding of PCET. Because oxidation of the tyrosine results in deprotonation of the phenolic oxygen, redox active tyrosines are involved in PCET reactions in several enzymes. This review focuses on PCET involving the redox active tyrosines in Photosystem II. Photosystem II catalyzes the light-driven oxidation of water and reduction of plastoquinone. Photosystem II provides a paradigm for the study of redox active tyrosines, because this photosynthetic reaction center contains two tyrosines with different roles in catalysis. The tyrosines, YZ and YD, exhibit differences in kinetics and midpoint potentials, and these differences may be due to noncovalent interactions with the protein environment. Here, studies of YD and YZ and relevant model compounds are described.
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Affiliation(s)
- Bridgette A Barry
- School of Chemistry and Biochemistry and The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Karković A, Brala CJ, Pilepić V, Uršić S. Solvent-induced hydrogen tunnelling in ascorbate proton-coupled electron transfers. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.01.142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Theory of proton coupled electron transfer reactions: Assessing the Born–Oppenheimer approximation for the proton motion using an analytically solvable model. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2010.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nagel ZD, Klinman JP. Update 1 of: Tunneling and dynamics in enzymatic hydride transfer. Chem Rev 2010; 110:PR41-67. [PMID: 21141912 PMCID: PMC4067601 DOI: 10.1021/cr1001035] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Zachary D. Nagel
- Departments of Chemistry and of Molecular and Cell Biology and the
California Institute for Quantitative Biosciences, University of California,
Berkeley, California 94720
| | - Judith P. Klinman
- Departments of Chemistry and of Molecular and Cell Biology and the
California Institute for Quantitative Biosciences, University of California,
Berkeley, California 94720
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The copper centers of tyramine β-monooxygenase and its catalytic-site methionine variants: an X-ray absorption study. J Biol Inorg Chem 2010; 15:1195-207. [PMID: 20544364 PMCID: PMC2988203 DOI: 10.1007/s00775-010-0677-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 05/12/2010] [Indexed: 10/31/2022]
Abstract
Tyramine β-monooxygenase (TBM) is a member of a family of copper monooxygenases containing two noncoupled copper centers, and includes peptidylglycine monooxygenase and dopamine β-monooxygenase. In its Cu(II) form, TBM is coordinated by two to three His residues and one to two non-His O/N ligands consistent with a [Cu(M)(His)(2)(OH(2))(2)-Cu(H)(His)(3)(OH(2))] formulation. Reduction to the Cu(I) state causes a change in the X-ray absorption spectroscopy (XAS) spectrum, consistent with a change to a [Cu(M)(His)(2)S(Met)-Cu(H)(His)(3)] environment. Lowering the pH to 4.0 results in a large increase in the intensity of the Cu(I)-S extended X-ray absorption fine structure (EXAFS) component, suggesting a tighter Cu-S bond or the coordination of an additional sulfur donor. The XAS spectra of three variants, where the Cu(M) Met471 residue had been mutated to His, Cys, and Asp, were examined. Significant differences from the wild-type enzyme are evident in the spectra of the reduced mutants. Although the side chains of His, Cys, and Asp are expected to substitute for Met at the Cu(M) site, the data showed identical spectra for all three reduced variants, with no evidence for coordination of residue 471. Rather, the K-edge data suggested a modest decrease in coordination number, whereas the EXAFS indicated an average of two His residues at each Cu(I) center. These data highlight the unique role of the Met residue at the Cu(M) center, and pose interesting questions as to why replacement by the cuprophilic thiolate ligand leads to detectable activity whereas replacement by imidazole generates inactive TBM.
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Murdock D, Burns LA, Vaccaro PH. Vibrational specificity of proton-transfer dynamics in ground-state tropolone. Phys Chem Chem Phys 2010; 12:8285-99. [DOI: 10.1039/c003140b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wecksler AT, Kenyon V, Garcia NK, Deschamps JD, van der Donk WA, Holman TR. Kinetic and structural investigations of the allosteric site in human epithelial 15-lipoxygenase-2. Biochemistry 2009; 48:8721-30. [PMID: 19645454 DOI: 10.1021/bi9009242] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allosteric regulation of human lipoxygenase (hLO) activity has recently been implicated in the cellular biology of prostate cancer. In the current work, we present isotope effect, pH, and substrate inhibitor data of epithelial 15-hLO-2, which probe the allosteric effects on its mechanistic behavior. The Dk(cat)/KM for 15-hLO-2, with AA and LA as substrate, is large indicating hydrogen atom abstraction is the principle rate-determining step, involving a tunneling mechanism for both substrates. For AA, there are multiple rate determining steps (RDS) at both high and low temperatures, with both diffusion and hydrogen bonding rearrangements contributing at high temperature, but only hydrogen bonding rearrangements contributing at low temperature. The observed kinetic dependency on the hydrogen bonding rearrangement is eliminated upon addition of the allosteric effector, 13-(S)-hydroxyoctadecadienoic acid (13-HODE), and no allosteric effects were seen on diffusion or hydrogen atom abstraction. The (k(cat)/KM)AA/(k(cat)/KM)LA ratio was observed to have a pH dependence, which was fit with a titration curve (pKa = 7.7), suggesting the protonation of a histidine residue, which could hydrogen bond with the carboxylate of 13-HODE. Assuming this interaction, 13-HODE was docked to the solvent exposed histidines of a 15-hLO-2 homology model and found to bind well with H627, suggesting a potential location for the allosteric site. Utilizing d31-LA as an inhibitor, it was demonstrated that the binding of d31-LA to the allosteric site changes the conformation of 15-hLO-2 such that the affinity for substrate increases. This result suggests that allosteric binding locks the enzyme into a catalytically competent state, which facilitates binding of LA and decreases the (k(cat)/KM)AA/(k(cat)/KM)LA ratio. Finally, the magnitude of the 13-HODE KD for 15-hLO-2 is over 200-fold lower than that of 13-HODE for 15-hLO-1, changing the substrate specificity of 15-hLO-2 to 1.9. This would alter the LO product distribution and increase the production of the pro-tumorigenic, 13-HODE, possibly representing a pro-tumorigenic feedback loop for 13-HODE and 15-hLO-2.
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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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Thiabaud G, Guillemot G, Schmitz-Afonso I, Colasson B, Reinaud O. Solid-State Chemistry at an Isolated Copper(I) Center with O2. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Thiabaud G, Guillemot G, Schmitz-Afonso I, Colasson B, Reinaud O. Solid-State Chemistry at an Isolated Copper(I) Center with O2. Angew Chem Int Ed Engl 2009; 48:7383-6. [DOI: 10.1002/anie.200902691] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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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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Reece SY, Nocera DG. Proton-coupled electron transfer in biology: results from synergistic studies in natural and model systems. Annu Rev Biochem 2009; 78:673-99. [PMID: 19344235 DOI: 10.1146/annurev.biochem.78.080207.092132] [Citation(s) in RCA: 361] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proton-coupled electron transfer (PCET) underpins energy conversion in biology. PCET may occur with the unidirectional or bidirectional transfer of a proton and electron and may proceed synchronously or asynchronously. To illustrate the role of PCET in biology, this review presents complementary biological and model systems that explore PCET in electron transfer (ET) through hydrogen bonds [azurin as compared to donor-acceptor (D-A) hydrogen-bonded networks], the activation of C-H bonds [alcohol dehydrogenase and soybean lipoxygenase (SLO) as compared to Fe(III) metal complexes], and the generation and transport of amino acid radicals [photosystem II (PSII) and ribonucleotide reductase (RNR) as compared to tyrosine-modified photoactive Re(I) and Ru(II) complexes]. In providing these comparisons, the fundamental principles of PCET in biology are illustrated in a tangible way.
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Affiliation(s)
- Steven Y Reece
- Department of Chemistry, Massachusetts Institutes of Technology, Cambridge, MA 02139-4307, USA
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Hay S, Sutcliffe MJ, Scrutton NS. Probing Coupled Motions in Enzymatic Hydrogen Tunnelling Reactions: Beyond Temperature-Dependence Studies of Kinetic Isotope Effects. QUANTUM TUNNELLING IN ENZYME-CATALYSED REACTIONS 2009. [DOI: 10.1039/9781847559975-00199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sam Hay
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Michael J. Sutcliffe
- School of Chemical Engineering and Analytical Science, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Nigel S. Scrutton
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester 131 Princess Street Manchester M1 7DN UK
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Nauser T, Casi G, Koppenol WH, Schöneich C. Reversible intramolecular hydrogen transfer between cysteine thiyl radicals and glycine and alanine in model peptides: absolute rate constants derived from pulse radiolysis and laser flash photolysis. J Phys Chem B 2009; 112:15034-44. [PMID: 18973367 DOI: 10.1021/jp805133u] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intramolecular reaction of cysteine thiyl radicals with peptide and protein alphaC-H bonds represents a potential mechanism for irreversible protein oxidation. Here, we have measured absolute rate constants for these reversible hydrogen transfer reactions by means of pulse radiolysis and laser flash photolysis of model peptides. For N-Ac-CysGly6 and N-Ac-CysGly2AspGly3, Cys thiyl radicals abstract hydrogen atoms from Gly with k(f) = (1.0-1.1 x 10(5) s(-1), generating carbon-centered radicals, while the reverse reaction proceeds with k(r) = (8.0-8.9) x 10(5) s(-1). The forward reaction shows a normal kinetic isotope effect of k(H)/k(D) = 6.9, while the reverse reaction shows a significantly higher normal kinetic isotope effect of 17.6, suggesting a contribution of tunneling. For N-Ac-CysAla2AspAla3, cysteine thiyl radicals abstract hydrogen atoms from Ala with k(f) = (0.9-1.0) x 10(4) s(-1), while the reverse reaction proceeds with k(r) = 1.0 x 10(5) s(-1). The order of reactivity, Gly > Ala, is in accord with previous studies on intermolecular reactions of thiyl radicals with these amino acids. The fact that k(f) < k(r) suggests some secondary structure of the model peptides, which prevents the adoption of extended conformations, for which calculations of homolytic bond dissociation energies would have predicted k(f) > k(r). Despite k(f) < k(r), model calculations show that intramolecular hydrogen abstraction by Cys thiyl radicals can lead to significant oxidation of other amino acids in the presence of physiologic oxygen concentrations.
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Affiliation(s)
- Thomas Nauser
- Institute of Inorganic Chemistry and Institute of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
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Hay S, Pang J, Monaghan PJ, Wang X, Evans RM, Sutcliffe MJ, Allemann RK, Scrutton NS. Secondary kinetic isotope effects as probes of environmentally-coupled enzymatic hydrogen tunneling reactions. Chemphyschem 2008; 9:1536-9. [PMID: 18613201 DOI: 10.1002/cphc.200800291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Hay S, Scrutton NS. H-transfers in Photosystem II: what can we learn from recent lessons in the enzyme community? PHOTOSYNTHESIS RESEARCH 2008; 98:169-177. [PMID: 18766465 DOI: 10.1007/s11120-008-9326-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Accepted: 06/28/2008] [Indexed: 05/26/2023]
Abstract
Over the last 10 years, studies of enzyme systems have demonstrated that, in many cases, H-transfers occur by a quantum mechanical tunneling mechanism analogous to long-range electron transfer. H-transfer reactions can be described by an extension of Marcus theory and, by substituting hydrogen with deuterium (or even tritium), it is possible to explore this theory in new ways by employing kinetic isotope effects. Because hydrogen has a relatively short deBroglie wavelength, H-transfers are controlled by the width of the reaction barrier. By coupling protein dynamics to the reaction coordinate, enzymes have the potential ability to facilitate more efficient H-tunneling by modulating barrier properties. In this review, we describe recent advances in both experimental and theoretical studies of enzymatic H-transfer, in particular the role of protein dynamics or promoting motions. We then discuss possible consequences with regard to tyrosine oxidation/reduction kinetics in Photosystem II.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester, UK.
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Meyer MP, Tomchick DR, Klinman JP. Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (I553) in soybean lipoxygenase-1. Proc Natl Acad Sci U S A 2008; 105:1146-51. [PMID: 18216254 PMCID: PMC2234106 DOI: 10.1073/pnas.0710643105] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Indexed: 11/18/2022] Open
Abstract
This study examines the impact of a series of mutations at position 553 on the kinetic and structural properties of soybean lipoxygenase-1 (SLO-1). The previously uncharacterized mutants reported herein are I553L, I553V, and I553G. High-resolution x-ray studies of these mutants, together with the earlier studied I553A, show almost no structural change in relation to the WT-enzyme. By contrast, a progression in kinetic behavior occurs in which the decrease in the size of the side chain at position 553 leads to an increased importance of donor-acceptor distance sampling in the course of the hydrogen transfer process. These dynamical changes in behavior are interpreted in the context of two general classes of protein motions, preorganization and reorganization, with the latter including the distance sampling modes [Klinman JP (2006) Philos Trans R Soc London Ser B 361:1323-1331; Nagel Z, Klinman JP (2006) Chem Rev 106:3095-3118]. The aggregate data for SLO-1 show how judicious placement of hydrophobic side chains can influence enzyme catalysis via enhanced donor-acceptor hydrogenic wave function overlap.
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Affiliation(s)
- Matthew P. Meyer
- *Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, CA 94720-1460; and
| | - Diana R. Tomchick
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Judith P. Klinman
- *Departments of Chemistry and of Molecular and Cell Biology, University of California, Berkeley, CA 94720-1460; and
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Abstract
A series of seven substituted 4,6-di-tert-butyl-2-(4,5-diarylimidazolyl)-phenols have been prepared and characterized, along with two related benzimidazole compounds. X-ray crystal structures of all of the compounds show that the phenol and imidazole rings are close to coplanar and are connected by an intramolecular ArOHN hydrogen bond. One-electron oxidation of these compounds occurs with movement of the phenolic proton to the imidazole base by concerted proton-electron transfer (CPET) to yield fairly stable distonic radical cations. These phenol-base compounds are a valuable system in which to examine the key features of CPET. Kinetic measurements of bimolecular CPET oxidations, with E(rxn) between +0.04 and -0.33 V, give rate constants from (6.3 +/- 0.6) x 10(2) to (3.0 +/- 0.6) x 10(6) M(-1) s(-1). There is a good correlation of log(k) with DeltaG degrees , with only one of the 15 rate constants falling more than a factor of 5.2 from the correlation line. Substituents on the imidazole affect the (O-HN) hydrogen bond, as marked by variations in the (1)H NMR and calculated vibrational spectra and geometries. Crystallographic d(ON) values appear to be more strongly affected by crystal packing forces. However, there is almost no correlation of rate constants with any of these measured or computed parameters. Over this range of compounds from the same structural family, the dominant contributor to the differences in rate constant is the driving force DeltaG degrees .
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