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Ramos-Figueroa JS, Palmer DRJ, Horsman GP. Phosphoenolpyruvate mutase-catalyzed C-P bond formation: mechanistic ambiguities and opportunities. Chembiochem 2022; 23:e202200285. [PMID: 35943842 DOI: 10.1002/cbic.202200285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/05/2022] [Indexed: 11/06/2022]
Abstract
Phosphonates are produced across all domains of life and used widely in medicine and agriculture. Biosynthesis almost universally originates from the enzyme phosphoenolpyruvate mutase (Ppm), EC 5.4.2.9, which catalyzes O-P bond cleavage in phosphoenolpyruvate (PEP) and forms a high energy C-P bond in phosphonopyruvate (PnPy). Mechanistic scrutiny of this unusual intramolecular O-to-C phosphoryl transfer began with the discovery of Ppm in 1988 and concluded in 2008 with computational evidence supporting a concerted phosphoryl transfer via a dissociative metaphosphatelike transition state. This mechanism deviates from the standard 'in-line attack' paradigm for enzymatic phosphoryl transfer that typically involves a phosphoryl-enzyme intermediate, but definitive evidence is sparse. Here we review the experimental evidence leading to our current mechanistic understanding and highlight the roles of previously underappreciated conserved active site residues. We then identify remaining opportunities to evaluate overlooked residues and unexamined substrates/inhibitors.
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Affiliation(s)
| | | | - Geoff P Horsman
- Wilfrid Laurier University, Chemistry & Biochemistry, 75 University Ave W, N2L 3C5, Waterloo, CANADA
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2
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Kalu GI, Ubochi CI, Onyido I. MAPPING TRANSITION STATE STRUCTURES FOR THIOPHOSPHINOYL GROUP TRANSFER BETWEEN OXYANIONIC NUCLEOPHILES IN WATER AND AQUEOUS ETHANOL SOLVENTS. NEW J CHEM 2022. [DOI: 10.1039/d2nj02008d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Second-order rate constants were measured for thiophosphinoyl group transfer from the substrates 3a-g to oxygen nucleophiles in 50% water-50% ethanol and 30% water-70% ethanol mixtures, to obtain solvent-independent Brønsted coefficients...
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Kalu GI, Ubochi CI, Onyido I. Reactions of aryl dimethylphosphinothioate esters with anionic oxygen nucleophiles: transition state structure in 70% water-30% ethanol. RSC Adv 2021; 11:8833-8845. [PMID: 35423373 PMCID: PMC8695247 DOI: 10.1039/d0ra10759j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/03/2021] [Indexed: 11/21/2022] Open
Abstract
Aryl dimethylphosphinates, 2, react with anionic oxygen nucleophiles in water via a concerted (ANDN) mechanism. With EtO- in anhydrous ethanol, the mechanism is associative (AN + DN), with rate-limiting pentacoordinate intermediate formation. This change in mechanism with solvent change has been ascribed to changes in the nucleophile and leaving group basicities accompanying solvent change. This paper reports on a kinetic analysis of the reactions of the aryl dimethylphosphinothioates, 3a-g, with oxygen nucleophiles in 70% water-30% ethanol (v/v) solvent at 25 °C, reactions known to proceed by a concerted mechanism in water, to test the rationalization stated above, since the nucleophiles and LGs of interest are more basic in aqueous ethanol than in water. The change in solvent causes an ca. 14 to 320-fold decrease in rate. Hammett and Brønsted-type correlations characterize a concerted TS with less P-LG bonding in aqueous ethanol than in water. Two opposing consequences are associated with the solvent change: (a) increased basicity of nucleophiles and LGs, which lead to a modest tightening of the TS; and (b) better stabilization of the IS relative to the TS in aqueous ethanol, which results in a slower reaction with a more product-like TS. Hammond and anti-Hammond effects on the TS arising from better stabilization of the IS over the TS dominate over the effects of increased nucleophile and LG basicity in determining the looser TS structure in aqueous ethanol. An altered TS structure is consistent with an altered reaction potential energy surface, in this case caused by a change in solvent polarity.
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Affiliation(s)
- Georgina I Kalu
- Department of Chemistry, Imo State University Owerri Nigeria
| | | | - Ikenna Onyido
- Department of Pure and Industrial Chemistry, Nnamdi Azikiwe University Awka Nigeria +234-806-268-5122
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Bordes I, Ruiz-Pernía JJ, Castillo R, Moliner V. A computational study of the phosphoryl transfer reaction between ATP and Dha in aqueous solution. Org Biomol Chem 2015; 13:10179-90. [PMID: 26303076 DOI: 10.1039/c5ob01079a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate of the synthesis of pyruvate and a very important building block in nature, can be generated by converting free dihydroxyacetone (Dha) through the action of the dihydroxyacetone kinase enzyme. In this paper the reference uncatalyzed reaction in solution has been studied in order to define the foundations of the chemical reaction and to determine the most adequate computational method to describe this electronically complex reaction. In particular, the phosphorylation reaction mechanism between adenosine triphosphate (ATP) and Dha in aqueous solution has been studied by means of quantum mechanics/molecular mechanics (QM/MM) Molecular Dynamics (MD) simulations with the QM subset of atoms described with semi-empirical and DFT methods. The results appear to be strongly dependent on the level of calculation, which will have to be taken into account for future studies of the reaction catalyzed by enzymes. In particular, PM3/MM renders lower free energy barriers and a less endergonic process than AM1d/MM and PM6/MM methods. Nevertheless, the concerted pathway was not located with the former combination of potentials.
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Affiliation(s)
- I Bordes
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain.
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Quantum mechanical modeling: a tool for the understanding of enzyme reactions. Biomolecules 2013; 3:662-702. [PMID: 24970187 PMCID: PMC4030948 DOI: 10.3390/biom3030662] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 01/16/2023] Open
Abstract
Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.
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6
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Benchmark calculations on models of the phosphoryl transfer reaction catalyzed by protein kinase A. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0600-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Xu D, Guo H. Ab initio QM/MM studies of the phosphoryl transfer reaction catalyzed by PEP mutase suggest a dissociative metaphosphate transition state. J Phys Chem B 2008; 112:4102-8. [PMID: 18331021 DOI: 10.1021/jp0776816] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interconversion between phosphoenolpyruvate (PEP) and phosphonopyruvate (P-pyr) catalyzed by PEP mutase is investigated using an ab initio QM/MM method with the QM region treated at the B3LYP/6-31G* level of theory. Two-dimensional minimum energy path calculations were carried out for both the wild-type enzyme and the N122A mutant. The calculations suggest a dissociative transition state featuring metaphosphate and Mg(2+)-coordinating pyruvate enolate, stabilized by an extensive hydrogen bond network involving Asn122, Ser123, Arg159, His190, Ser46, and Leu48. It is also found that a substantial conformational change in the pyruvyl group is required for the interconversion.
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Affiliation(s)
- Dingguo Xu
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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Yang Y, Yu H, York D, Elstner M, Cui Q. Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization. J Chem Theory Comput 2008; 4:2067-2084. [PMID: 19352441 PMCID: PMC2665970 DOI: 10.1021/ct800330d] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphate chemistry is involved in many key biological processes yet the underlying mechanism often remains unclear. For theoretical analysis to effectively complement experimental mechanistic analysis, it is essential to develop computational methods that can capture the complexity of the underlying potential energy surface and allow for sufficient sampling of the configurational space. To this end, we report the parameterization of an approximate density functional theory, Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) method for systems containing phosphorus. Compared to high-level density functional theory and ab initio (MP2 and G3B3) results, the standard second-order parameterization is shown to give reliable structures for a diverse set of phosphate compounds but inaccurate energetics. With the on-site third-order terms included, referred to as SCC-DFTBPA, calculated proton affinities of phosphate compounds are substantially improved, although it remains difficult to obtain reliable proton affinity for both phosphates and compounds that do not contain phosphorus, indicating that further improvement in the formulation of SCC-DFTB is still a challenge to meet. To make SCC-DFTB applicable to phosphate reactions in the current (on-site-third-order-only) formulation, a "reaction-specific" parameterization, referred to as SCC-DFTBPR, is developed based on hydrolysis reactions of model phosphate species. Benchmark calculations in both the gas-phase and solution-phase indicate that SCC-DFTBPR gives reliable structural properties and semi-quantitative energetics for phosphate hydrolysis reactions. Since the number of reaction-specific parameters is small, it is likely that SCC-DFTBPR is applicable to a broad set of phosphate species. Indeed, for 56 reaction exothermicities and 47 energy barriers related to RNA catalysis model reactions collected from the QCRNA database, which involve molecules rather different from those used to parameterize SCC-DFTBPR, the corresponding root-mean-square difference between SCC-DFTBPR and high-level DFT results is only 5.3 kcal/mol. We hope that the parameterized SCC-DFTB models will complement NDDO based reaction-specific models (e.g., AM1-d/PhoT) and high-level ab initio QM/MM methods in better understanding the mechanism of phosphate chemistry in condensed phase, particularly biological systems.
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Affiliation(s)
- Yang Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
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Zhang L, Xie D, Xu D, Guo H. Supermolecule density functional calculations suggest a key role for solvent in alkaline hydrolysis of p-nitrophenyl phosphate. Chem Commun (Camb) 2007:1638-40. [PMID: 17530085 DOI: 10.1039/b617946k] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Supermolecule density functional theory calculations show that solvent is responsible for the concerted transition state in alkaline hydrolysis of p-nitrophenyl phosphate suggested by heavy atom kinetic isotope effects.
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Affiliation(s)
- Lidong Zhang
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, People's Republic of China
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Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, de Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM. QCRNA 1.0: a database of quantum calculations for RNA catalysis. J Mol Graph Model 2006; 25:423-33. [PMID: 16580853 DOI: 10.1016/j.jmgm.2006.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 02/21/2006] [Accepted: 02/25/2006] [Indexed: 10/24/2022]
Abstract
This work outlines a new on-line database of quantum calculations for RNA catalysis (QCRNA) available via the worldwide web at http://theory.chem.umn.edu/QCRNA. The database contains high-level density functional calculations for a large range of molecules, complexes and chemical mechanisms important to phosphoryl transfer reactions and RNA catalysis. Calculations are performed using a strict, consistent protocol such that a wealth of cross-comparisons can be made to elucidate meaningful trends in biological phosphate reactivity. Currently, around 2000 molecules have been collected in varying charge states in the gas phase and in solution. Solvation was treated with both the PCM and COSMO continuum solvation models. The data can be used to study important trends in reactivity of biological phosphates, or used as benchmark data for the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations.
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Affiliation(s)
- Timothy J Giese
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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Zhang L, Xie D, Xu D, Guo H. Reactivity of Metaphosphate and Thiometaphosphate in Water: A DFT Study. J Phys Chem A 2005; 109:11295-303. [PMID: 16331914 DOI: 10.1021/jp054430t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metaphosphate is known to be highly reactive to water, whereas thiometaphosphate is relatively stable in aqueous solution. The difference in their reactivity has important mechanistic implications in interpreting the "thio effect" in phosphoryl transfer reactions. In this work, density functional theory is used to investigate the reactivity of both metaphosphate and its thio-substitute in their complexes with one, two, and three waters, and in aqueous solution. Barrier heights for converting metaphosphate to orthophosphate have been determined by geometry optimization. The results confirm that metaphosphate is consistently more reactive than thiometaphosphate and the activation free energy for both species decreases with the number of water molecules. The relative stability of thiometaphosphate is attributed to its less positively charged phosphorus atom.
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Affiliation(s)
- Lidong Zhang
- Department of Chemistry and Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, China
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