Large Scale ab Initio Quantum Chemical Calculation of the Intermediates in the Soluble Methane Monooxygenase Catalytic Cycle

Dunietz, Barry D.; Beachy, Michael D.; Cao, Yangsen; Whittington, Douglas A.; Lippard, Stephen J.; Friesner, Richard A.

doi:10.1021/ja9920967

Cited by 183 publications

(227 citation statements)

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“…Recent kinetic studies and theoretical calculations have suggested the presence of additional intermediates (6,9,10). For example, proton transfer steps have been observed in the formation and decay of H peroxo , a result consistent with a protonated peroxo intermediate in the mechanism (9).…”

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confidence: 72%

“…Formation of a superoxide species has also been proposed to be the first irreversible step in the reductive activation in a number of other oxygenactivating enzymes (12,15,16). Recent density functional theory (DFT) calculations have identified a possible superoxo intermediate species with an energy comparable with that of H peroxo (10). Further work is required to characterize the early dioxygen activation intermediates, clarify the relationship between kinetic and equilibrium isotope effects, and gain additional insights into the nature of the first irreversible step in the reaction.…”

Section: Analysis Of the Oxygen-18 Kinetic Isotope Effects: Constrainmentioning

confidence: 99%

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Oxygen Kinetic Isotope Effects in Soluble Methane Monooxygenase

Stahl

Francisco

Merkx

et al. 2001

Journal of Biological Chemistry

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Soluble methane monooxygenase (sMMO) contains a nonheme, carboxylate-bridged diiron site that activates dioxygen in the catalytic oxidation of hydrocarbon substrates. Oxygen kinetic isotope effects (KIEs) have been determined under steady-state conditions for the sMMO-catalyzed oxidation of CH 3 CN, a liquid substrate analog. Kinetic studies of the steady-state sMMO reaction revealed a competition between fully coupled oxygenase activity, which produced glycolonitrile (HOCH 2 CN) and uncoupled oxidase activity that led to water formation. The oxygen KIE was measured independently for both the oxygenase and oxidase reactions, and values of 1.0152 ؎ 0.0007 and 1.0167 ؎ 0.0010 were obtained, respectively. The isotope effects and separate dioxygen binding studies do not support irreversible formation of an enzyme-dioxygen Michaelis complex. Additional mechanistic implications are discussed in the context of previous data obtained from single turnover and steady-state kinetic studies.The soluble methane monooxygenase system (sMMO) 1 found in certain methanotrophic bacteria catalyzes the oxidation of methane to methanol according to Reaction 1 (1, 2).This reaction is the first essential step of a metabolic pathway that allows these bacteria to use methane as their sole source of energy and carbon. The soluble MMO system comprises three protein components: a 251 kDa hydroxylase (MMOH), a reductase (MMOR) that transfers electrons from NADH to MMOH, and a cofactorless regulatory protein (MMOB). Reductive activation of dioxygen and subsequent methane oxidation take place at a carboxylate-bridged diiron cluster in the active site of MMOH. (3,4,6,8). This observation suggests that Q, or a subsequent unobserved intermediate, is responsible for methane oxidation.Recent kinetic studies and theoretical calculations have suggested the presence of additional intermediates (6, 9, 10). For example, proton transfer steps have been observed in the formation and decay of H peroxo , a result consistent with a protonated peroxo intermediate in the mechanism (9). Other kinetic studies provide indirect evidence for one or more intermediates preceding the formation of H peroxo . These may include an enzyme-dioxygen Michaelis complex or a superoxo intermediate (6, 9 -11).Kinetic and equilibrium oxygen isotope effects have been determined recently for several proteins and enzymes that activate dioxygen (12)(13)(14)(15)(16)(17)(18). Such experiments directly probe reaction steps involved in the activation of dioxygen and can provide unique mechanistic information that may not be available by other means. In this study, oxygen-18 kinetic isotope effects determined for sMMO from M. capsulatus (Bath) together with steady-state kinetics and dioxygen binding studies yield further insights into dioxygen activation by this enzyme system. EXPERIMENTAL PROCEDURESGeneral Considerations-Growth of M. capsulatus (Bath) cells and subsequent purification of MMOH were carried out as described previously (19,20). Both MMOB and MMOR were obtained from recombi...

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confidence: 72%

Section: Analysis Of the Oxygen-18 Kinetic Isotope Effects: Constrainmentioning

confidence: 99%

Oxygen Kinetic Isotope Effects in Soluble Methane Monooxygenase

Stahl

Francisco

Merkx

et al. 2001

Journal of Biological Chemistry

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“…Ab initio calculations provide a wealth of detail that is not available from experiment and a degree of confidence in the results that is not available from more empirical approaches. In systems such as methane monooxygenase, in which a substantial number of careful calculations have been performed by several groups (81,(91)(92)(93)(94)(95)(96) and close contact with experiment has been achieved for many aspects of the catalytic process, a comprehensive picture of the functioning of the enzyme is beginning to be assembled by means of the interaction of theory and experiment. Last, the coupling of ab initio quantum QM͞MM methods with simulation and protein structure prediction techniques permits investigation of events in which reactive chemistry is coupled to substantial conformational changes, such as the catalytic loop motion in triose phosphate isomerase (82).…”

Section: Applicationsmentioning

confidence: 99%

Ab initioquantum chemistry: Methodology and applications

Friesner

2005

Proc. Natl. Acad. Sci. U.S.A.

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This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical͞molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.coupled cluster ͉ density functional theory ͉ second-order Modler-Plesser perturbation theory ͉ mixed quantum͞molecular mechanics O ver the past three decades, ab initio quantum chemistry has become an essential tool in the study of atoms and molecules and, increasingly, in modeling complex systems such as those arising in biology and materials science. The underlying core technology is computational solution of the electronic Schrodinger equation; given the positions of a collection of atomic nuclei, and the total number of electrons in the system, calculate the electronic energy, electron density, and other properties by means of a well defined, automated approximation (a ''model chemistry''). The ability to obtain ''goodenough'' solutions to the electronic Schrodinger equation for systems containing tens, or even hundreds, of atoms has revolutionized the ability of theoretical chemistry to address important problems in a wide range of disciplines; the Nobel Prize awarded to John Pople and Walter Kohn in 1998 is a reflection of this observation.In its exact form, the electronic Schrodinger equation is a many-body problem, whose computational complexity grows exponentially with the number of electrons, and hence, a brute force solution is intractable. Hartree-Fock theory, a mean field approach, produces reasonable results for many properties but is incapable of providing a robust description of reactive chemical events in which electron correlation has a major role. Thus, a key problem has been the development of treatments of electron correlation that exhibit a tractable scaling in computational effort with the size of the system. The considerable progress that has been made along these lines is outlined below.Given a well defined theoretical framework of approximation, the next requirement is efficient computational implementation. Considerable sophistication is required to achieve acceptable accuracy and efficiency; the leading quantum chemistry programs are millions of lines of computer code, and mathematical algorithms to reduce formal scaling of computational effort with system size have an increasingly crucial role in meeting the challenge of handling complex system relevant to practical applications. Below, the most important comp...

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“…Extended x-ray absorption fine structure (EXAFS) analysis of Q has found a short FeOFe distance of 2.5 Å, which has led us to propose an [Fe IV 2 ( -O) 2 ] diamond core structure (6). Density functional theory (DFT) calculations from a number of groups also support the viability of such an intermediate (7)(8)(9)(10)(11). Although several mononuclear oxoiron(IV) complexes have been structurally characterized (12), thus providing valuable information regarding the catalytic mechanism of mononuclear nonheme iron enzymes (13) 3 [L c , tris(5-ethyl-2-pyridylmethyl)amine] (1c, Scheme 1) (14).…”

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confidence: 97%