1
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Dance I. What triggers the coupling of proton transfer and electron transfer at the active site of nitrogenase? Dalton Trans 2024; 53:7996-8004. [PMID: 38651170 DOI: 10.1039/d4dt00474d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e- + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol-1 and the product stabilised by ca. 7 kcal mol-1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Sydney, NSW 2052, Australia.
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2
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Schrader T, Khanifaev J, Perlt E. Koopmans' theorem for acidic protons. Chem Commun (Camb) 2023; 59:13839-13842. [PMID: 37921279 DOI: 10.1039/d3cc04304e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The famous Brønsted acidity, which is relevant in many areas of experimental and synthetic chemistry, but also in biochemistry and other areas, is investigated from a new perspective. Nuclear electronic orbital methods, which explicitly account for the quantum character of selected protons, are applied. The resulting orbital energies of the proton wavefunction are interpreted and related to enthalpies of deprotonation and acid strength in analogy to the Koopmans' theorem for electrons. For a set of organic acids, we observe a correlation which indicates the validity of such a NEO-Koopmans' approach and opens up new opportunities for the computational investigation of more complex acidic systems.
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Affiliation(s)
- Tim Schrader
- Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany.
| | | | - Eva Perlt
- Friedrich Schiller University Jena, Löbdergraben 32, 07743, Jena, Germany.
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3
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Uversky VN, Giuliani A. Networks of Networks: An Essay on Multi-Level Biological Organization. Front Genet 2021; 12:706260. [PMID: 34234818 PMCID: PMC8255927 DOI: 10.3389/fgene.2021.706260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/31/2021] [Indexed: 01/01/2023] Open
Abstract
The multi-level organization of nature is self-evident: proteins do interact among them to give rise to an organized metabolism, while in the same time each protein (a single node of such interaction network) is itself a network of interacting amino-acid residues allowing coordinated motion of the macromolecule and systemic effect as allosteric behavior. Similar pictures can be drawn for structure and function of cells, organs, tissues, and ecological systems. The majority of biologists are used to think that causally relevant events originate from the lower level (the molecular one) in the form of perturbations, that “climb up” the hierarchy reaching the ultimate layer of macroscopic behavior (e.g., causing a specific disease). Such causative model, stemming from the usual genotype-phenotype distinction, is not the only one. As a matter of fact, one can observe top-down, bottom-up, as well as middle-out perturbation/control trajectories. The recent complex network studies allow to go further the pure qualitative observation of the existence of both non-linear and non-bottom-up processes and to uncover the deep nature of multi-level organization. Here, taking as paradigm protein structural and interaction networks, we review some of the most relevant results dealing with between networks communication shedding light on the basic principles of complex system control and dynamics and offering a more realistic frame of causation in biology.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
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4
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Abstract
Enzymology is concerned with the study of enzyme structure, function, regulation and kinetics. It is an interdisciplinary subject that can be treated as an exclusive sphere of exhaustive inquiry within mathematical, physico-chemical and biological sciences. Hence, teaching of enzymology, in general, and enzyme kinetics, in particular, should be undertaken in an interdisciplinary manner for a holistic appreciation of this subject. Further, analogous examples from everyday life should form an integral component of the teaching for an intuitive grasp of the subject matter. Furthermore, simulation-based appreciation of enzyme kinetics should be preferred over simplifying assumptions and approximations of traditional enzyme kinetics teaching. In this Words of Advice, I outline the domain depth of enzymology across the various disciplines and provide initial ideas on how appropriate analogies can provide firm insights into the subject. Further, I demonstrate how an intuitive feel for the subject can help not only in grasping abstract concepts but also extending it in experimental design and subsequent interpretation. Use of simulations in grasping complex concepts is also advocated given the advantages this medium offers over traditional approaches involving images and molecular models. Furthermore, I discuss the merits of incorporating the historical backdrop of major discoveries in enzymological teaching. We, at AstraZeneca, have experimented with this approach with the desired outcome of generating interest in the subject from people practising diverse disciplines.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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5
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Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing. Proc Natl Acad Sci U S A 2020; 117:10818-10824. [PMID: 32371483 DOI: 10.1073/pnas.1922538117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent advances in neutron crystallographic studies have provided structural bases for quantum behaviors of protons observed in enzymatic reactions. Thus, we resolved the neutron crystal structure of a bacterial copper (Cu) amine oxidase (CAO), which contains a prosthetic Cu ion and a protein-derived redox cofactor, topa quinone (TPQ). We solved hitherto unknown structures of the active site, including a keto/enolate equilibrium of the cofactor with a nonplanar quinone ring, unusual proton sharing between the cofactor and the catalytic base, and metal-induced deprotonation of a histidine residue that coordinates to the Cu. Our findings show a refined active-site structure that gives detailed information on the protonation state of dissociable groups, such as the quinone cofactor, which are critical for catalytic reactions.
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6
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Dance I. Computational Investigations of the Chemical Mechanism of the Enzyme Nitrogenase. Chembiochem 2020; 21:1671-1709. [DOI: 10.1002/cbic.201900636] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ian Dance
- School of Chemistry UNSW Sydney Sydney 2052 Australia
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7
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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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8
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Ulpiani P, Romanelli G, Onorati D, Parmentier A, Festa G, Schooneveld E, Cazzaniga C, Arcidiacono L, Andreani C, Senesi R. Optimization of detection strategies for epithermal neutron spectroscopy using photon-sensitive detectors. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:073901. [PMID: 31370488 DOI: 10.1063/1.5091084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/15/2019] [Indexed: 06/10/2023]
Abstract
In this work, we discuss an improved detection procedure for the photon-sensitive yttrium-aluminum-perovskite detectors installed on the VESUVIO spectrometer at the ISIS pulsed neutron and muon source. By decreasing the low-level energy threshold of detected photons, we observe an increased count rate up to a factor ∼3, and a decrease of relative error bars and noise of ∼40% and 35%, respectively, for deep inelastic neutron scattering measurements. In addition, we demonstrate how the reported optimization may increase the accuracy in the line shape analysis of neutron Compton profiles, as well as in the application of the mean-force approach to detect the anisotropy and anharmonicity in the single-particle local potential. We envisage that such an upgrade of the detection procedure would have a substantial impact on the VESUVIO scientific programme based on deep inelastic neutron scattering investigations.
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Affiliation(s)
- Pierfrancesco Ulpiani
- Università degli studi di Roma "Tor Vergata", Dipartimento di Scienze e Tecnologie Chimiche, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Giovanni Romanelli
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Dalila Onorati
- Università degli studi di Roma "Tor Vergata", Centro NAST, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Alexandra Parmentier
- INFN Sezione di Roma Tor Vergata, Via della Ricerca Scientifica 1, I-00133 Rome, Italy
| | - Giulia Festa
- Centro Fermi - Museo Storico della Fisica e Centro Studi e Ricerche "Enrico Fermi", Piazza del Viminale 1, Rome, 00184, Italy
| | - Erik Schooneveld
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Carlo Cazzaniga
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, Oxfordshire OX11 OQX, United Kingdom
| | - Laura Arcidiacono
- Università degli studi di Roma "Tor Vergata", Centro NAST, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Carla Andreani
- Università degli studi di Roma "Tor Vergata", Centro NAST, Via della Ricerca Scientifica 1, Rome, 00133, Italy
| | - Roberto Senesi
- Università degli studi di Roma "Tor Vergata", Centro NAST, Via della Ricerca Scientifica 1, Rome, 00133, Italy
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9
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Kohen A. Kinetic Isotope Effects as Probes for Hydrogen Tunneling, Coupled Motion and Dynamics Contributions to Enzyme Catalysis. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967403103165486] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since the early days of enzymology attempts have been made to deconvolute the various contributions of physical phenomena to enzyme catalysis. Here we present experimental and theoretical studies that examine the possible role of hydrogen tunneling, coupled motion, and enzyme dynamics in catalysis. In this review, we first introduce basic concepts of enzyme catalysis from a physical chemistry point of view. Then, we present several recent developments in the application of experimental tools that can probe tunneling, coupled motion, dynamic effects and other possible physical phenomena that may contribute to catalysis. These tools include kinetic isotope effects (KIEs), their temperature dependency and H/D/T mutual relations (the Swain–Schaad relationship). Several theories and models that assist in understanding those phenomena are also described. The possibility that these models invoke a direct role for the enzyme's dynamics (environmental fluctuations and rearrangements) is discussed. Finally, the need to compare the enzymatic reaction to the uncatalyzed one while investigating contributions to catalysis is emphasised.
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Affiliation(s)
- Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
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10
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Uversky VN. Protein intrinsic disorder and structure-function continuum. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:1-17. [DOI: 10.1016/bs.pmbts.2019.05.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Uversky VN. Flexibility of the "rigid" classics or rugged bottom of the folding funnels of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1. INTRINSICALLY DISORDERED PROTEINS 2018; 5:e1355205. [PMID: 30250772 DOI: 10.1080/21690707.2017.1355205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 10/18/2022]
Abstract
The abilities to crystalize of a globular protein and to solve its crystal structure seem to represent triumph of the lock-and-key model of protein functionality, where the presence of unique 3D structure resembling aperiodic crystal is considered as a prerequisite for a given protein to possess specific biologic activity. The history of protein crystallography has its roots in first crystal structures of myoglobin, lysozyme, RNase A, chymotrypsin, cytochrome c, and carboxypeptidase A1 solved more than 50 y ago. This article briefly considers extensive structural information currently available for these proteins and shows that the bottoms of their folding funnels (i.e., the lowest parts of their potential energy landscapes) are not smoothed but rugged. In other words, these crystallization classics are characterized by significant conformational flexibility and are not rigid (immobile) crystal-like entities.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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13
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14
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Romero E, Gómez Castellanos JR, Gadda G, Fraaije MW, Mattevi A. Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes. Chem Rev 2018; 118:1742-1769. [DOI: 10.1021/acs.chemrev.7b00650] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Elvira Romero
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - J. Rubén Gómez Castellanos
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanni Gadda
- Departments of Chemistry and Biology, Center for Diagnostics and Therapeutics, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
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15
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Offenbacher AR, Hu S, Poss EM, Carr CAM, Scouras AD, Prigozhin DM, Iavarone AT, Palla A, Alber T, Fraser JS, Klinman JP. Hydrogen-Deuterium Exchange of Lipoxygenase Uncovers a Relationship between Distal, Solvent Exposed Protein Motions and the Thermal Activation Barrier for Catalytic Proton-Coupled Electron Tunneling. ACS CENTRAL SCIENCE 2017; 3:570-579. [PMID: 28691068 PMCID: PMC5492416 DOI: 10.1021/acscentsci.7b00142] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 05/11/2023]
Abstract
Defining specific pathways for efficient heat transfer from protein-solvent interfaces to their active sites represents one of the compelling and timely challenges in our quest for a physical description of the origins of enzyme catalysis. Enzymatic hydrogen tunneling reactions constitute excellent systems in which to validate experimental approaches to this important question, given the inherent temperature independence of quantum mechanical wave function overlap. Herein, we present the application of hydrogen-deuterium exchange coupled to mass spectrometry toward the spatial resolution of protein motions that can be related to an enzyme's catalytic parameters. Employing the proton-coupled electron transfer reaction of soybean lipoxygenase as proof of principle, we first corroborate the impact of active site mutations on increased local flexibility and, second, uncover a solvent-exposed loop, 15-34 Å from the reactive ferric center whose temperature-dependent motions are demonstrated to mirror the enthalpic barrier for catalytic C-H bond cleavage. A network that connects this surface loop to the active site is structurally identified and supported by changes in kinetic parameters that result from site-specific mutations.
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Affiliation(s)
- Adam R. Offenbacher
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Shenshen Hu
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Erin M. Poss
- Department
of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California 94158, United States
| | - Cody A. M. Carr
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Alexander D. Scouras
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Daniil M. Prigozhin
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
| | - Ali Palla
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Tom Alber
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - James S. Fraser
- Department
of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California 94158, United States
| | - Judith P. Klinman
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- California
Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- E-mail:
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16
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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept. Int J Mol Sci 2016; 17:ijms17111874. [PMID: 27834926 PMCID: PMC5133874 DOI: 10.3390/ijms17111874] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/10/2023] Open
Abstract
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based hetero-tetramers, and is able to interact with many binding partners. It contains numerous posttranslational modifications, has several isoforms generated by alternative splicing, alternative promoter usage or alternative initiation of translation, and is commonly mutated in different cancers. Therefore, p53 serves as an important illustration of the protein structure–function continuum concept, where the generation of multiple proteoforms by various mechanisms defines the ability of this protein to have a multitude of structurally and functionally different states. Considering p53 in the light of a proteoform-based structure–function continuum represents a non-canonical and conceptually new contemplation of structure, regulation, and functionality of this important protein.
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17
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Pairas GN, Tsoungas PG. H-Bond: Τhe Chemistry-Biology H-Bridge. ChemistrySelect 2016; 1:4520-4532. [PMID: 32328512 PMCID: PMC7169486 DOI: 10.1002/slct.201600770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
H-bonding, as a non covalent stabilizing interaction of diverse nature, has a central role in the structure, function and dynamics of chemical and biological processes, pivotal to molecular recognition and eventually to drug design. Types of conventional and non conventional (H-H, dihydrogen, H- π, CH- π, anti- , proton coordination and H-S) H-bonding interactions are discussed as well as features emerging from their interplay, such as cooperativity (σ- and π-) effects and allostery. Its utility in many applications is described. Catalysis, proton and electron transfer processes in various materials or supramolecular architectures of preorganized hosts for guest binding, are front-line technology. The H-bond-related concept of proton transfer (PT) addresses energy issues or deciphering the mechanism of many natural and synthetic processes. PT is also of paramount importance in the functions of cells and is assisted by large complex proteins embedded in membranes. Both intermolecular and intramolecular PT in H-bonded systems has received attention, theoretically and experimentally, using prototype molecules. It is found in rearrangement reactions, protein functions, and enzyme reactions or across proton channels and pumps. Investigations on the competition between intra- and intermolecular H bonding are discussed. Of particular interest is the H-bond furcation, a common phenomenon in protein-ligand binding. Multiple H-bonding (H-bond furcation) is observed in supramolecular structures.
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Affiliation(s)
- George N. Pairas
- Department of PharmacyLaboratory of Medicinal ChemistryUniversity of PatrasGR-265 04PatrasGreece
| | - Petros G. Tsoungas
- Laboratory of BiochemistryHellenic Pasteur Institute127 Vas. Sofias Ave.GR-115 21AthensGreece
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18
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Luk LYP, Loveridge EJ, Allemann RK. Protein motions and dynamic effects in enzyme catalysis. Phys Chem Chem Phys 2016; 17:30817-27. [PMID: 25854702 DOI: 10.1039/c5cp00794a] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The role of protein motions in promoting the chemical step of enzyme catalysed reactions remains a subject of considerable debate. Here, a unified view of the role of protein dynamics in dihydrofolate reductase catalysis is described. Recently the role of such motions has been investigated by characterising the biophysical properties of isotopically substituted enzymes through a combination of experimental and computational analyses. Together with previous work, these results suggest that dynamic coupling to the chemical coordinate is detrimental to catalysis and may have been selected against during DHFR evolution. The full catalytic power of Nature's catalysts appears to depend on finely tuning protein motions in each step of the catalytic cycle.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
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19
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Shirmovsky SE. Quantum dynamics of a hole migration through DNA: A single strand DNA model. Biophys Chem 2016; 217:42-57. [PMID: 27497061 DOI: 10.1016/j.bpc.2016.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/05/2016] [Accepted: 07/17/2016] [Indexed: 11/24/2022]
Abstract
A model predicting the behavior of a hole acting on the DNA strand was investigated. The hole-DNA interaction on the basis of a quantum-classical, non-linear DNA single strand model was described. The fact that a DNA molecule is formed by a furanose ring as its sugar, phosphate group and bases was taken into consideration. Based on the model, results were obtained for the probability of a hole location on the DNA base sequences, such as GTTGGG, GATGTGGG, GTTGTTGGG as well as on the sugar-phosphate groups mated with them.
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Affiliation(s)
- S Eh Shirmovsky
- Far Eastern Federal University, 8 Sukhanov St., Vladivostok 690950, Russia.
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20
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21
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015; 54:9016-20. [PMID: 26079622 PMCID: PMC4985705 DOI: 10.1002/anie.201503968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 11/21/2022]
Abstract
Chemical ligation has been used to alter motions in specific regions of dihydrofolate reductase from E. coli and to investigate the effects of localized motional changes on enzyme catalysis. Two isotopic hybrids were prepared; one with the mobile N-terminal segment containing heavy isotopes ((2) H, (13) C, (15) N) and the remainder of the protein with natural isotopic abundance, and the other one with only the C-terminal segment isotopically labeled. Kinetic investigations indicated that isotopic substitution of the N-terminal segment affected only a physical step of catalysis, whereas the enzyme chemistry was affected by protein motions from the C-terminal segment. QM/MM studies support the idea that dynamic effects on catalysis mostly originate from the C-terminal segment. The use of isotope hybrids provides insights into the microscopic mechanism of dynamic coupling, which is difficult to obtain with other studies, and helps define the dynamic networks of intramolecular interactions central to enzyme catalysis.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - J Javier Ruiz-Pernía
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain)
| | | | - E Joel Loveridge
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot (Spain).
| | - Vincent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló (Spain).
| | - Rudolf K Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff, CF10 3AT (UK).
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22
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Luk LYP, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503968] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site. Proc Natl Acad Sci U S A 2014; 111:18454-9. [PMID: 25503367 DOI: 10.1073/pnas.1417923111] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.
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24
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Luk LYP, Ruiz-Pernía JJ, Dawson WM, Loveridge EJ, Tuñón I, Moliner V, Allemann RK. Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant. J Am Chem Soc 2014; 136:17317-23. [PMID: 25396728 DOI: 10.1021/ja5102536] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Catalysis by dihydrofolate reductase from the moderately thermophilic bacterium Geobacillus stearothermophilus (BsDHFR) was investigated by isotope substitution of the enzyme. The enzyme kinetic isotope effect for hydride transfer was close to unity at physiological temperatures but increased with decreasing temperatures to a value of 1.65 at 5 °C. This behavior is opposite to that observed for DHFR from Escherichia coli (EcDHFR), where the enzyme kinetic isotope effect increased slightly with increasing temperature. These experimental results were reproduced in the framework of variational transition-state theory that includes a dynamical recrossing coefficient that varies with the mass of the protein. Our simulations indicate that BsDHFR has greater flexibility than EcDHFR on the ps-ns time scale, which affects the coupling of the environmental motions of the protein to the chemical coordinate and consequently to the recrossing trajectories on the reaction barrier. The intensity of the dynamic coupling in DHFRs is influenced by compensatory temperature-dependent factors, namely the enthalpic barrier needed to achieve an ideal transition-state configuration with minimal nonproductive trajectories and the protein disorder that disrupts the electrostatic preorganization required to stabilize the transition state. Together with our previous studies of other DHFRs, the results presented here provide a general explanation why protein dynamic effects vary between enzymes. Our theoretical treatment demonstrates that these effects can be satisfactorily reproduced by including a transmission coefficient in the rate constant calculation, whose dependence on temperature is affected by the protein flexibility.
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Affiliation(s)
- Louis Y P Luk
- School of Chemistry and ∥Cardiff Catalysis Institute, School of Chemistry, Cardiff University , Park Place, Cardiff, CF10 3AT, United Kingdom
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25
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Mazzuca JW, Garashchuk S, Jakowski J. The effect of local substrate motion on quantum hydrogen transfer in soybean lipoxygenase-1 modeled with QTES-DFTB dynamics. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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26
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Homayoon Z, Bowman JM, Evangelista FA. Calculations of Mode-Specific Tunneling of Double-Hydrogen Transfer in Porphycene Agree with and Illuminate Experiment. J Phys Chem Lett 2014; 5:2723-2727. [PMID: 26277970 DOI: 10.1021/jz501482v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a theoretical study of mode-specific tunneling splittings in double-hydrogen transfer in trans-porphycene. We use a novel, mode-specific "Qim path method", in which the reaction coordinate is the imaginary-frequency normal mode of the saddle point separating the equivalent minima. The model considers all 108 normal modes and uses no adjustable parameters. The method gives the ground vibrational-state tunneling splitting, as well the increase in the splitting upon excitation of certain modes, in good agreement with experiment. Interpretation of these results is also transparent with this method. In addition, predictions are made for mode excitations not investigated experimentally. Results for d1 and d2 isotopolgues are also in agreement with experiment.
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Affiliation(s)
- Zahra Homayoon
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M Bowman
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Francesco A Evangelista
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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27
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Krasilnikov PM. Two-dimensional model of a double-well potential: Proton transfer upon hydrogen bond deformation. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914020158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Francis K, Kohen A. Standards for the reporting of kinetic isotope effects in enzymology. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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Yahashiri A, Rubach JK, Plapp BV. Effects of cavities at the nicotinamide binding site of liver alcohol dehydrogenase on structure, dynamics and catalysis. Biochemistry 2014; 53:881-94. [PMID: 24437493 PMCID: PMC3969020 DOI: 10.1021/bi401583f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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A role
for protein dynamics in enzymatic catalysis of hydrogen
transfer has received substantial scientific support, but the connections
between protein structure and catalysis remain to be established.
Valine residues 203 and 207 are at the binding site for the nicotinamide
ring of the coenzyme in liver alcohol dehydrogenase and have been
suggested to facilitate catalysis with “protein-promoting vibrations”
(PPV). We find that the V207A substitution has small effects on steady-state
kinetic constants and the rate of hydrogen transfer; the introduced
cavity is empty and is tolerated with minimal effects on structure
(determined at 1.2 Å for the complex with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol). Thus, no evidence is found to
support a role for Val-207 in the dynamics of catalysis. The protein
structures and ligand geometries (including donor–acceptor
distances) in the V203A enzyme complexed with NAD+ and
2,3,4,5,6-pentafluorobenzyl alcohol or 2,2,2-trifluoroethanol (determined
at 1.1 Å) are very similar to those for the wild-type enzyme,
except that the introduced cavity accommodates a new water molecule
that contacts the nicotinamide ring. The structures of the V203A enzyme
complexes suggest, in contrast to previous studies, that the diminished
tunneling and decreased rate of hydride transfer (16-fold, relative
to that of the wild-type enzyme) are not due to differences in ground-state
ligand geometries. The V203A substitution may alter the PPV and the
reorganization energy for hydrogen transfer, but the protein scaffold
and equilibrium thermal motions within the Michaelis complex may be
more significant for enzyme catalysis.
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Affiliation(s)
- Atsushi Yahashiri
- Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242-1109, United States
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30
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Álvarez-Barcia S, Flores JR, Kästner J. Tunneling Above the Crossover Temperature. J Phys Chem A 2013; 118:78-82. [DOI: 10.1021/jp411189m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Jesús R. Flores
- Facultade
de Química, Universidade de Vigo, E-36310 Vigo (Pontevedra), Spain
| | - Johannes Kästner
- Computational
Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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31
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Grover M, Grover R, Singh R, Kumar R, Kumar S. Quantum combinatorial model of gene expression. Bioinformation 2013; 9:141-4. [PMID: 23422839 PMCID: PMC3569601 DOI: 10.6026/97320630009141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 01/05/2013] [Indexed: 11/23/2022] Open
Abstract
We propose that the DNA within the chromatin behaves as a dynamic combinatorial library capable of forming novel structures by
reversible processes. We also hypothesize that states within the library may be linked via quantum tunneling. RNA polymerase
then could scan these states and the system decoheres to the “appropriate” state. Two ways of sustaining quantum coherence at
relevant time scales could be possible, first, screening: the quantum system can be kept isolated from its decohering environment,
second, the existence of decoherence free subspaces .We discuss the role of superconductivity in context of avoiding decoherence in
context of our hypothesis.
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Affiliation(s)
- Monendra Grover
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India ; Amity Institute of Biotechnology, Amity University, NOIDA, India
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32
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33
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Unusual biophysics of intrinsically disordered proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:932-51. [PMID: 23269364 DOI: 10.1016/j.bbapap.2012.12.008] [Citation(s) in RCA: 413] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/21/2012] [Accepted: 12/12/2012] [Indexed: 02/08/2023]
Abstract
Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.
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34
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Stojković V, Perissinotti LL, Willmer D, Benkovic SJ, Kohen A. Effects of the donor-acceptor distance and dynamics on hydride tunneling in the dihydrofolate reductase catalyzed reaction. J Am Chem Soc 2012; 134:1738-45. [PMID: 22171795 DOI: 10.1021/ja209425w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A significant contemporary question in enzymology involves the role of protein dynamics and hydrogen tunneling in enhancing enzyme catalyzed reactions. Here, we report a correlation between the donor-acceptor distance (DAD) distribution and intrinsic kinetic isotope effects (KIEs) for the dihydrofolate reductase (DHFR) catalyzed reaction. This study compares the nature of the hydride-transfer step for a series of active-site mutants, where the size of a side chain that modulates the DAD (I14 in E. coli DHFR) is systematically reduced (I14V, I14A, and I14G). The contributions of the DAD and its dynamics to the hydride-transfer step were examined by the temperature dependence of intrinsic KIEs, hydride-transfer rates, activation parameters, and classical molecular dynamics (MD) simulations. Results are interpreted within the framework of the Marcus-like model where the increase in the temperature dependence of KIEs arises as a direct consequence of the deviation of the DAD from its distribution in the wild type enzyme. Classical MD simulations suggest new populations with larger average DADs, as well as broader distributions, and a reduction in the population of the reactive conformers correlated with the decrease in the size of the hydrophobic residue. The more flexible active site in the mutants required more substantial thermally activated motions for effective H-tunneling, consistent with the hypothesis that the role of the hydrophobic side chain of I14 is to restrict the distribution and dynamics of the DAD and thus assist the hydride-transfer. These studies establish relationships between the distribution of DADs, the hydride-transfer rates, and the DAD's rearrangement toward tunneling-ready states. This structure-function correlation shall assist in the interpretation of the temperature dependence of KIEs caused by mutants far from the active site in this and other enzymes, and may apply generally to C-H→C transfer reactions.
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Affiliation(s)
- Vanja Stojković
- Department of Chemistry, The University of Iowa, Iowa City, Iowa 52242, USA
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35
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MINCER JOSHUAS, NUÑEZ SARA, SCHWARTZ STEVEND. COUPLING PROTEIN DYNAMICS TO REACTION CENTER ELECTRON DENSITY IN ENZYMES: AN ELECTRONIC PROTEIN PROMOTING VIBRATION IN HUMAN PURINE NUCLEOSIDE PHOSPHORYLASE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633604001215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The notable three oxygen stacking that occurs upon binding of ribonucleoside substrate and phosphate nucleophile by human purine nucleoside phosphorylase (hPNP) enables the coupling of protein dynamic modes to compress this stack, squeezing the ribosyl O4' between ribosyl O5' and the nuclophilic O P . Created primarily by the motion of active site residue H257, this compression dynamically lowers the barrier height for N9–C1' ribosidic bond cleavage by as much as 20%. As such, this compression constitutes a protein promoting vibration (PPV) (S. Nuñez et al.). Presently, we demonstrate charge fluctuations in the ribose and purine components of the ribonucleoside substrate, as well as specifically across the N9–C1' ribosidic bond, that are correlated with the PPV and can explain the decrease in reaction barrier height due to their facilitating cleavage of the ribosidic bond. hPNP apparently employs protein dynamics to push electrons, a finding that suggests that this coupling may be found more generally in enzymes that catalyze substitution and elimination reactions.
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Affiliation(s)
- JOSHUA S. MINCER
- Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - SARA NUÑEZ
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - STEVEN D. SCHWARTZ
- Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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36
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Şerb MD, Wang R, Meven M, Englert U. The whole range of hydrogen bonds in one crystal structure: neutron diffraction and charge-density studies of N,N-dimethylbiguanidinium bis(hydrogensquarate). ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2011; 67:552-9. [DOI: 10.1107/s0108768111043138] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/18/2011] [Indexed: 11/10/2022]
Abstract
N,N-Dimethylbiguanidinium bis(hydrogensquarate) features an impressive range of hydrogen bonds within the same crystal structure: neighbouring anions aggregate to a dianionic pair through two strong O—H...O interactions; one of these can be classified among the shortest hydrogen bonds ever studied. Cations and anions in this organic salt further interact via conventional N—H...O and nonclassical C—H...O contacts to an extended structure. As all these interactions occur in the same sample, the title compound is particularly suitable to monitor even subtle trends in hydrogen bonds. Neutron and high-resolution X-ray diffraction experiments have enabled us to determine the electron density precisely and to address its properties with an emphasis on the nature of the X—H...O interactions. Sensitive criteria such as the Laplacian of the electron density and energy densities in the bond-critical points reveal the incipient covalent character of the shortest O—H...O bond. These findings are in agreement with the precise geometry from neutron diffraction: the shortest hydrogen bond is also significantly more symmetric than the longer interactions.
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37
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Meisner J, Rommel JB, Kästner J. Kinetic isotope effects calculated with the instanton method. J Comput Chem 2011; 32:3456-63. [DOI: 10.1002/jcc.21930] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 07/30/2011] [Accepted: 08/01/2011] [Indexed: 01/18/2023]
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38
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Rommel JB, Goumans TPM, Kästner J. Locating Instantons in Many Degrees of Freedom. J Chem Theory Comput 2011; 7:690-8. [DOI: 10.1021/ct100658y] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judith B. Rommel
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
| | - T. P. M. Goumans
- Gorlaeus Laboratories, LIC, Leiden University, Leiden, The Netherlands
| | - Johannes Kästner
- Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Stuttgart, Germany
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39
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Loveridge EJ, Allemann RK. The temperature dependence of the kinetic isotope effects of dihydrofolate reductase from Thermotoga maritima is influenced by intersubunit interactions. Biochemistry 2010; 49:5390-6. [PMID: 20515024 DOI: 10.1021/bi100761x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) is unique among structurally characterized chromosomal DHFRs in that it forms a stable homodimer. Dimerization is believed to play a key role in the high thermal stability of TmDHFR, which is reflected in a melting temperature in excess of 85 degrees C. The dimer interface of TmDHFR is composed of a hydrophobic core with charged residues around the periphery. In particular, Lys129 of each subunit forms three-membered salt bridges with Glu136 and Glu138 of the other subunit. To probe the role of these salt bridges in the dimerization and thermal stability of TmDHFR, we generated a series of variants (TmDHFR-K129E, TmDHFR-E136K, TmDHFR-E138K, and TmDHFR-E136K/E138K) in which these residues were exchanged for residues whose side chains bear the opposite charge. Our results indicate that these salt bridges are key for the high thermal stability of TmDHFR but are not a requirement for dimerization. Although the rate of dihydrofolate reduction by TmDHFR is not significantly affected by the loss of the K129-E136-E138 salt bridges, changes to the temperature dependence of the kinetic isotope effect on hydride transfer are observed. These changes are in agreement with the proposal that DHFR catalysis may be affected by changes to the conformational ensemble of the enzyme rather than only to the coupling of protein motions to the reaction coordinate.
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Affiliation(s)
- E Joel Loveridge
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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40
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Peregrina JR, Sánchez-Azqueta A, Herguedas B, Martínez-Júlvez M, Medina M. Role of specific residues in coenzyme binding, charge-transfer complex formation, and catalysis in Anabaena ferredoxin NADP+-reductase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1638-46. [PMID: 20471952 DOI: 10.1016/j.bbabio.2010.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 05/04/2010] [Accepted: 05/06/2010] [Indexed: 10/19/2022]
Abstract
Two transient charge-transfer complexes (CTC) form prior and upon hydride transfer (HT) in the reversible reaction of the FAD-dependent ferredoxin-NADP+ reductase (FNR) with NADP+/H, FNR(ox)-NADPH (CTC-1), and FNR(rd)-NADP+ (CTC-2). Spectral properties of both CTCs, as well as the corresponding interconversion HT rates, are here reported for several Anabaena FNR site-directed mutants. The need for an adequate initial interaction between the 2'P-AMP portion of NADP+/H and FNR that provides subsequent conformational changes leading to CTC formation is further confirmed. Stronger interactions between the isoalloxazine and nicotinamide rings might relate with faster HT processes, but exceptions are found upon distortion of the active centre. Thus, within the analyzed FNR variants, there is no strict correlation between the stability of the transient CTCs formation and the rate of the subsequent HT. Kinetic isotope effects suggest that, while in the WT, vibrational enhanced modulation of the active site contributes to the tunnel probability of HT; complexes of some of the active site mutants with the coenzyme hardly allow the relative movement of isoalloxazine and nicotinamide rings along the HT reaction. The architecture of the WT FNR active site precisely contributes to reduce the stacking probability between the isoalloxazine and nicotinamide rings in the catalytically competent complex, modulating the angle and distance between the N5 of the FAD isoalloxazine and the C4 of the coenzyme nicotinamide to values that ensure efficient HT processes.
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Affiliation(s)
- José Ramón Peregrina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, and Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, E-50009 Zaragoza, Spain
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41
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Williams IH. Quantum catalysis? A comment on tunnelling contributions for catalysed and uncatalysed reactions. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1658] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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42
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Sen A, Kohen A. Enzymatic tunneling and kinetic isotope effects: chemistry at the crossroads. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1633] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Stojković V, Kohen A. Enzymatic H Transfers: Quantum Tunneling and Coupled Motion from Kinetic Isotope Effect Studies. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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44
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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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45
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Abstract
Much work has gone into understanding the physical basis of the enormous catalytic power of enzymes over the last 50 years or so. Nevertheless, the detailed mechanism used by Nature's catalysts to speed chemical transformations remains elusive. DHFR (dihydrofolate reductase) has served as a paradigm to study the relationship between the structure, function and dynamics of enzymatic transformations. A complex reaction cascade, which involves rearrangements and movements of loops and domains of the enzyme, is used to orientate cofactor and substrate in a reactive configuration from which hydride is transferred by quantum mechanical tunnelling. In the present paper, we review results from experiments that probe the influence of protein dynamics on the chemical step of the reaction catalysed by TmDHFR (DHFR from Thermotoga maritima). This enzyme appears to have evolved an optimal structure that can maintain a catalytically competent conformation under extreme conditions.
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46
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Hothi P, Hay S, Roujeinikova A, Sutcliffe MJ, Lee M, Leys D, Cullis PM, Scrutton NS. Driving Force Analysis of Proton Tunnelling Across a Reactivity Series for an Enzyme-Substrate Complex. Chembiochem 2008; 9:2839-45. [DOI: 10.1002/cbic.200800408] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Panay AJ, Fitzpatrick PF. Kinetic isotope effects on aromatic and benzylic hydroxylation by Chromobacterium violaceum phenylalanine hydroxylase as probes of chemical mechanism and reactivity. Biochemistry 2008; 47:11118-24. [PMID: 18817418 DOI: 10.1021/bi801295w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phenylalanine hydroxylase from Chromobacterium violaceum (CvPheH) is a non-heme iron monooxygenase that catalyzes the hydroxylation of phenylalanine to tyrosine. In this study, we used deuterium kinetic isotope effects to probe the chemical mechanisms of aromatic and benzylic hydroxylation to compare the reactivities of bacterial and eukaryotic aromatic amino acid hydroxylases. The (D) k cat value for the reaction of CvPheH with [(2)H 5]phenylalanine is 1.2 with 6-methyltetrahydropterin and 1.4 with 6,7-dimethyltetrahydropterin. With the mutant enzyme I234D, the (D) k cat value decreases to 0.9 with the latter pterin; this is likely to be the intrinsic effect for addition of oxygen to the amino acid. The isotope effect on the subsequent tautomerization of a dienone intermediate was determined to be 5.1 by measuring the retention of deuterium in tyrosine produced from partially deuterated phenylalanine; this large isotope effect is responsible for the normal effect on k cat. The isotope effect for hydroxylation of the methyl group of 4-CH 3-phenylalanine, obtained from the partitioning of benzylic and aromatic hydroxylation products, is 10. The temperature dependence of this isotope effect establishes the contribution of hydrogen tunneling to benzylic hydroxylation by this enzyme. The results presented here provide evidence that the reactivities of the prokaryotic and eukaryotic hydroxylases are similar and further define the reactivity of the iron center for the family of aromatic amino acid hydroxylases.
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Affiliation(s)
- Aram J Panay
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, USA
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48
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Dance I. The chemical mechanism of nitrogenase: hydrogen tunneling and further aspects of the intramolecular mechanism for hydrogenation of eta(2)-N(2) on FeMo-co to NH(3). Dalton Trans 2008:5992-8. [PMID: 19082055 DOI: 10.1039/b806103c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preceding paper (Dalton Trans., 2008, DOI: 10.1039/b806100a) describes the logical development of a chemical mechanism for the catalysis of hydrogenation of N(2) to 2NH(3) that occurs at the Fe(7)MoS(9)N(c)(homocitrate) cofactor (FeMo-co) of the enzyme nitrogenase. The mechanism uses a single replenishable path for serial supply of protons which become H atoms on FeMo-co, migrating to become S-H and Fe-H donors to N(2) and to the intermediates that follow. This chemical catalysis at FeMo-co is distinctly intramolecular: transition states and reaction profiles for the preferred 21 step pathway were presented. This paper describes a number of alternative intermediates and pathways that were considered in developing the mechanism. These results reveal further relevant principles of the reactivity of hydrogenated FeMo-co, and the reasons why these pathways are less likely to be part of the mechanism. The intramolecular character of the mechanism, and the relatively small distances over which H atoms transfer, lead to expectations of extensive quantum mechanical hydrogen tunneling as part of the catalytic rate enhancement. This possibility is supported by comparisons of reaction profiles with those for enzyme reactions for which tunneling is established.
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Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.
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49
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Starikov EB, Panas I, Nordén B. Chemical-to-Mechanical Energy Conversion in Biomacromolecular Machines: A Plasmon and Optimum Control Theory for Directional Work. 1. General Considerations. J Phys Chem B 2008; 112:8319-29. [DOI: 10.1021/jp801580d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evgeni B. Starikov
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Itai Panas
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Bengt Nordén
- Institute for Nanotechnology, Research Center Karlsruhe, Post Box 3640, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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50
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Backstrom N, Burton NA, Turega S, Watt CIF. The primary kinetic hydrogen isotope effect in the deprotonation of a nitroalkane by an intramolecular carboxylate group. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1330] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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