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Schnettler JD, Klein OJ, Kaminski TS, Colin PY, Hollfelder F. Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase. J Am Chem Soc 2023; 145:1083-1096. [PMID: 36583539 PMCID: PMC9853848 DOI: 10.1021/jacs.2c10673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a kcat/KM of ≈7 × 105 M-1 s-1) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.
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Affiliation(s)
- J David Schnettler
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Oskar James Klein
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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2
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Silva VB, Campos RB, Pavez P, Medeiros M, Orth ES. Nucleophilic Neutralization of Organophosphates: Lack of Selectivity or Plenty of Versatility? CHEM REC 2021; 21:2638-2665. [PMID: 34117695 DOI: 10.1002/tcr.202100123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/17/2021] [Indexed: 12/13/2022]
Abstract
Neutralization of organophosphates is an issue of public health and safety, involving agrochemicals and chemical warfare. A promising approach is the nucleophilic neutralization, scope of this review, which focuses on the molecular nucleophiles: hydroxide, imidazole derivatives, alpha nucleophiles, amines and other nucleophiles. A reactivity mapping is given correlating the pathways and reaction efficiency with structural dependence of the nucleophile (basicity) and the organophosphate (electrophilic centers, P=O/P=S shift, leaving and non-leaving group). Reactions extremely unfavorable (>20 years) can be reduced to seconds with various nucleophiles, some which are catalytic. Although there is no universal nucleophile, a lack of selectivity in some cases accounts for plenty of versatility in other reactions. The ideal neutralization requires a solid mechanistic understanding, together with balancing factors such as milder conditions, fast process, selectivity and less toxic products.
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Affiliation(s)
- Valmir B Silva
- Department of Chemistry, Universidade Federal do Paraná, CP 19081, CEP 81531-990, Curitiba, PR, Brazil
| | - Renan B Campos
- Academic Department of Chemistry and Biology, Universidade Tecnológica Federal do Paraná, ZIP 81280-340, Curitiba, PR, Brazil
| | - Paulina Pavez
- Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Casilla 306, 6094411, Santiago, Chile
| | - Michelle Medeiros
- Department of Chemistry, Universidade Federal de Santa Catarina, CEP 88040-900, Florianópolis, SC, Brazil
| | - Elisa S Orth
- Department of Chemistry, Universidade Federal do Paraná, CP 19081, CEP 81531-990, Curitiba, PR, Brazil
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3
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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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4
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Majumdar S, Zhang H, Soleimani M, van Benthem RATM, Heuts JPA, Sijbesma RP. Phosphate Triester Dynamic Covalent Networks. ACS Macro Lett 2020; 9:1753-1758. [PMID: 35653678 DOI: 10.1021/acsmacrolett.0c00636] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic covalent networks are a class of polymeric materials that combine the merits of classical thermosets and thermoplastics, in terms of mechanical properties and reprocessability, in one material. Various dynamic covalent chemistries have thus been implemented in polymeric materials with recent interests shifting toward chemistries that would allow rearrangements in network topology without the aid of external catalysts. Here we introduce transesterification in phosphate triesters as a new dynamic covalent chemistry in polymeric networks. A simple one-step synthetic strategy has been utilized to synthesize polytetrahydrofuran networks with phosphate triester cross-links. The materials showed finite viscous flow at elevated temperatures via transesterification at the cross-links without externally added catalyst. This approach provides an easy method for cross-linking OH-end-functionalized polyethers and has the potential for general use with other OH-functionalized polymers.
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Affiliation(s)
- Soumabrata Majumdar
- Department of Chemical Engineering & Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Huiyi Zhang
- Department of Chemical Engineering & Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Mohammad Soleimani
- Department of Chemical Engineering & Chemistry, Laboratory of Physical Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Rolf A. T. M. van Benthem
- Department of Chemical Engineering & Chemistry, Laboratory of Physical Chemistry and Center for Multiscale Electron Microscopy, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- DSM Materials Science Center, 6167 RD Geleen, The Netherlands
| | - Johan P. A. Heuts
- Department of Chemical Engineering & Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Rint P. Sijbesma
- Department of Chemical Engineering & Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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5
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Unusual resistance of cobalt bis dicarbollide phosphate and phosphorothioate bridged esters towards alkaline hydrolysis: The “metallacarborane effect”. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Christian S, Pradhan P, Jans U. Investigation of the Nucleophilic Attack of Dichlorvos by Reduced Sulfur Species Using 1H NMR. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:424-431. [PMID: 29224357 DOI: 10.1021/acs.jafc.7b04749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mechanism of the reaction of dichlorvos through hydrolysis reactions and through the reaction with polysulfide (Sn2-) and thiophenolate (PhS-) was investigated by proton nuclear magnetic resonance (1H NMR). The study confirmed product identities of an organophosphorus insecticide reacting with reduced sulfur species using 1H NMR in oxygen sensitive solutions. The experiments of dichlorvos with polysulfide led to the detection of a previously undetected product. The thiophenolate experiments were further advanced to investigate second-order rate kinetics using an internal standard. The experiments provide new evidence for a nucleophilic attack by the reduced sulfur species at the methoxy carbon of dichlorvos. In addition, the observation of in situ reaction dynamics illustrates the applicability of 1H NMR spectroscopy toward kinetic investigations in environmental science.
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Affiliation(s)
- Saumil Christian
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Padmanava Pradhan
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Urs Jans
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
- Chemistry Program, The Graduate Center of the City University , New York, New York 10016, United States
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7
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Sumita A, Otani Y, Ohwada T. Chemoselective generation of acyl phosphates, acylium ion equivalents, from carboxylic acids and an organophosphate ester in the presence of a Brønsted acid. Chem Commun (Camb) 2017; 53:1482-1485. [DOI: 10.1039/c6cc09618b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of an organophosphate ester with carboxylic acids proceeded smoothly and chemoselectively in the presence of a Brønsted acid, affording acyl phosphate intermediates, leading to formation of various functional aromatic ketones.
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Affiliation(s)
- Akinari Sumita
- Graduate School of Pharmaceutical Sciences
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences
- The University of Tokyo
- Tokyo 113-0033
- Japan
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8
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Diez-Castellnou M, Martinez A, Mancin F. Phosphate Ester Hydrolysis: The Path From Mechanistic Investigation to the Realization of Artificial Enzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Zafrani Y, Amir D, Yehezkel L, Madmon M, Saphier S, Karton-Lifshin N, Gershonov E. Chemoselective N-Difluoromethylation of Functionalized Tertiary Amines. J Org Chem 2016; 81:9180-9187. [DOI: 10.1021/acs.joc.6b01728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yossi Zafrani
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Dafna Amir
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Lea Yehezkel
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Moran Madmon
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Sigal Saphier
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Naama Karton-Lifshin
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Eytan Gershonov
- The Department
of Organic
Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
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10
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Pabis A, Duarte F, Kamerlin SCL. Promiscuity in the Enzymatic Catalysis of Phosphate and Sulfate Transfer. Biochemistry 2016; 55:3061-81. [PMID: 27187273 PMCID: PMC4899807 DOI: 10.1021/acs.biochem.6b00297] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
enzymes that facilitate phosphate and sulfate hydrolysis are
among the most proficient natural catalysts known to date. Interestingly,
a large number of these enzymes are promiscuous catalysts that exhibit
both phosphatase and sulfatase activities in the same active site
and, on top of that, have also been demonstrated to efficiently catalyze
the hydrolysis of other additional substrates with varying degrees
of efficiency. Understanding the factors that underlie such multifunctionality
is crucial both for understanding functional evolution in enzyme superfamilies
and for the development of artificial enzymes. In this Current Topic,
we have primarily focused on the structural and mechanistic basis
for catalytic promiscuity among enzymes that facilitate both phosphoryl
and sulfuryl transfer in the same active site, while comparing this
to how catalytic promiscuity manifests in other promiscuous phosphatases.
We have also drawn on the large number of experimental and computational
studies of selected model systems in the literature to explore the
different features driving the catalytic promiscuity of such enzymes.
Finally, on the basis of this comparative analysis, we probe the plausible
origins and determinants of catalytic promiscuity in enzymes that
catalyze phosphoryl and sulfuryl transfer.
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Affiliation(s)
- Anna Pabis
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Shina C L Kamerlin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University , BMC Box 596, S-751 24 Uppsala, Sweden
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11
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Manfredi AM, Demos W, Wanderlind EH, Silva BV, Pinto AC, Souza BS, Nome F. Rapid cleavage of phosphate triesters by the oxime 2-(hydroxyimino)-N
-phenyl-acetamide. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3549] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alex M. Manfredi
- INCT-Catalysis, Departamento de Química; Universidade Federal de Santa Catarina; Florianópolis SC 88040-900 Brazil
| | - Willian Demos
- INCT-Catalysis, Departamento de Química; Universidade Federal de Santa Catarina; Florianópolis SC 88040-900 Brazil
| | - Eduardo H. Wanderlind
- INCT-Catalysis, Departamento de Química; Universidade Federal de Santa Catarina; Florianópolis SC 88040-900 Brazil
| | - Bárbara V. Silva
- Instituto de Química-CT, Bloco A; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ 21941-970 Brazil
| | - Angelo C. Pinto
- Instituto de Química-CT, Bloco A; Universidade Federal do Rio de Janeiro; Rio de Janeiro RJ 21941-970 Brazil
| | - Bruno S. Souza
- INCT-Catalysis, Departamento de Química; Universidade Federal de Santa Catarina; Florianópolis SC 88040-900 Brazil
| | - Faruk Nome
- INCT-Catalysis, Departamento de Química; Universidade Federal de Santa Catarina; Florianópolis SC 88040-900 Brazil
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12
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Bromberg L, Creasy WR, McGarvey DJ, Wilusz E, Hatton TA. Nucleophilic Polymers and Gels in Hydrolytic Degradation of Chemical Warfare Agents. ACS APPLIED MATERIALS & INTERFACES 2015; 7:22001-22011. [PMID: 26359671 DOI: 10.1021/acsami.5b06905] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Water- and solvent-soluble polymeric materials based on polyalkylamines modified with nucleophilic groups are introduced as catalysts of chemical warfare agent (CWA) hydrolysis. A comparative study conducted at constant pH and based on the criteria of the synthetic route simplicity, aqueous solubility, and rate of hydrolysis of CWA mimic, diisopropylfluorophosphate (DFP), indicated that 4-aminopyridine-substituted polyallylamine (PAAm-APy) and polyvinylamine substituted with 4-aminopyridine (PVAm-APy) were advantageous over 4-pyridinealdoxime-modified PVAm and PAAm, poly(butadiene-co-pyrrolidinopyridine), and PAAm modified with bipyridine and its complex with Cu(II). The synthesis of PVAm-APy and PAAm-APy involved generation of a betaine derivative of acrylamide and its covalent attachment onto the polyalkylamine chain followed by basic hydrolysis. Hydrogel particles of PAAm-APy and PVAm-APy cross-linked by epichlorohydrin exhibited pH-dependent swelling and ionization patterns that affected the rate constants of DFP nucleophilic hydrolysis. Deprotonation of the aminopyridine and amine groups increased the rates of the nucleophilic hydrolysis. The second-order rate of nucleophilic hydrolysis was 5.5- to 10-fold higher with the nucleophile-modified gels compared to those obtained by cross-linking of unmodified PAAm, throughout the pH range. Testing of VX and soman (GD) was conducted in 2.5-3.7 wt % PVAm-APy suspensions or gels swollen in water or DMSO/water mixtures. The half-lives of GD in aqueous PVAm-APy were 12 and 770 min at pH 8.5 and 5, respectively. Addition of VX into 3.5-3.7 wt % suspensions of PVAm-APy in DMSO-d6 and D2O at initial VX concentration of 0.2 vol % resulted in 100% VX degradation in less than 20 min. The unmodified PVAm and PAAm were 2 orders of magnitude less active than PVAm-APy and PAAm-APy, with VX half-lives in the range of 24 h. Furthermore, the PVAm-APy and PAAm-APy gels facilitated the dehydrochlorination reaction of sulfur mustard (HD) and its analogue 2-chloroethyl ethylsulfide (CEES). The ability of the reported aminopyridine-modified polyalkylamine materials to degrade the most persistent of CWAs, coupled with aqueous solubility, and the presence of numerous amino groups that provide convenient "handles" for covalent attachment on polymeric and inorganic supports yields promise for applications such as protective fabric and textile treatment and components of decontaminating materials.
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Affiliation(s)
- Lev Bromberg
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - William R Creasy
- Leidos Corp. , P.O. Box 68, Gunpowder, Maryland 21010, United States
| | - David J McGarvey
- Analytical Toxicology Branch, R&T Directorate, U.S. Army Edgewood Chemical and Biological Center , Aberdeen Proving Ground, Maryland 21010, United States
| | - Eugene Wilusz
- Materials Science and Engineering Branch, U.S. Army Natick Soldier Research, Development & Engineering Center , Natick, Massachusetts 01760, United States
| | - T Alan Hatton
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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13
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Fridkin G, Columbus I, Saphier S, Yehezkel L, Goldvaser M, Marciano D, Ashkenazi N, Zafrani Y. Component mobility by a minute quantity of the appropriate solvent as a principal motif in the acceleration of solid-supported reactions. J Org Chem 2015; 80:5176-88. [PMID: 25901764 DOI: 10.1021/acs.joc.5b00492] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects solvents have on fluoride-promoted heterogeneous hydrolysis and alcoholysis of various organo-phosphorus (OP) compounds on the surface of KF/Al2O3 are described. Solid-state magic angle spinning NMR analyses and SEM microscopy have shown that not only is the identity of the solvent important in these reactions but also its quantity. That is, minimal solvent amounts are favored and much more effective in such solid-supported reactions (and maybe generally) than those featuring solvent-free or excess solvent (>50 wt %) conditions. The addition of a minute quantity of the correct solvent (3-10 wt %, molar equivalent scale) avoids reagents leaching from the matrix, permits mobility (mass transport) of the reaction components and ensures their very high local concentration in close proximity to the solid-support large porous surface area. Accordingly, significant acceleration of reactions rates by orders of magnitude is obtained. Fascinatingly, even challenging phosphoesters with poor leaving groups, which were found to be very stable in the presence of solvent-free KF/Al2O3 or wetted with excess water, were efficiently hydrolyzed with a minute amount of this solvent.
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Affiliation(s)
- Gil Fridkin
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Ishay Columbus
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Sigal Saphier
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Lea Yehezkel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Michael Goldvaser
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Daniele Marciano
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Nissan Ashkenazi
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
| | - Yossi Zafrani
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness-Ziona 74100, Israel
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14
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Cochran JC. Kinesin Motor Enzymology: Chemistry, Structure, and Physics of Nanoscale Molecular Machines. Biophys Rev 2015; 7:269-299. [PMID: 28510227 DOI: 10.1007/s12551-014-0150-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/16/2014] [Indexed: 11/25/2022] Open
Abstract
Molecular motors are enzymes that convert chemical potential energy into controlled kinetic energy for mechanical work inside cells. Understanding the biophysics of these motors is essential for appreciating life as well as apprehending diseases that arise from motor malfunction. This review focuses on kinesin motor enzymology with special emphasis on the literature that reports the chemistry, structure and physics of several different kinesin superfamily members.
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Affiliation(s)
- J C Cochran
- Department of Molecular & Cellular Biochemistry, Indiana University, Simon Hall Room 405C, 212 S. Hawthorne Dr., Bloomington, IN, 47405, USA.
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15
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Density functional calculations on alcoholysis and thiolysis of phosphate triesters: Stepwise or concerted? COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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17
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Medeiros M, Wanderlind EH, Mora JR, Moreira R, Kirby AJ, Nome F. Major mechanistic differences between the reactions of hydroxylamine with phosphate di- and tri-esters. Org Biomol Chem 2013; 11:6272-84. [DOI: 10.1039/c3ob40988k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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New light on phosphate transfer from triesters. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:454-63. [DOI: 10.1016/j.bbapap.2012.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 04/12/2012] [Accepted: 04/24/2012] [Indexed: 11/18/2022]
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Marciano D, Columbus I, Elias S, Goldvaser M, Shoshanim O, Ashkenazi N, Zafrani Y. Role of the P–F Bond in Fluoride-Promoted Aqueous VX Hydrolysis: An Experimental and Theoretical Study. J Org Chem 2012; 77:10042-9. [DOI: 10.1021/jo301549z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniele Marciano
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Ishay Columbus
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Shlomi Elias
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Michael Goldvaser
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Ofir Shoshanim
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Nissan Ashkenazi
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
| | - Yossi Zafrani
- Department
of Organic Chemistry and ‡Department of Environmental Physics, Israel Institute for Biological Research, Ness-Ziona,
74100, Israel
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20
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Mora JR, Kirby AJ, Nome F. Theoretical Study of the Importance of the Spectator Groups on the Hydrolysis of Phosphate Triesters. J Org Chem 2012; 77:7061-70. [DOI: 10.1021/jo301380v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José R. Mora
- Department of Chemistry, National
Institute of Catalysis, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Anthony J. Kirby
- University Chemical Laboratory, University of Cambridge, Cambridge
CB2 1EW, U.K
| | - Faruk Nome
- Department of Chemistry, National
Institute of Catalysis, Federal University of Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil
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21
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A. R. Raycroft M, Liu CT, Brown RS. Comparison of Cu(II)-Promoted Leaving Group Stabilization of the Cleavage of a Homologous Set of Phosphate Mono-, Di-, and Triesters in Water, Methanol, and Ethanol. Inorg Chem 2012; 51:3846-54. [DOI: 10.1021/ic300059e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Mark A. R. Raycroft
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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22
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Babtie AC, Lima MF, Kirby AJ, Hollfelder F. Kinetic and computational evidence for an intermediate in the hydrolysis of sulfonate esters. Org Biomol Chem 2012; 10:8095-101. [DOI: 10.1039/c2ob25699a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Lönnberg T, Kero KM. Impact of steric constraints on the product distribution of phosphate-branched oligonucleotide models of the large ribozymes. Org Biomol Chem 2011; 10:569-74. [PMID: 22113401 DOI: 10.1039/c1ob06399e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To assess the extent to which steric constraints may influence the product distribution of the reactions of the large ribozymes, phosphate-branched oligonucleotides of varying length and sequence have been synthesized and their alkaline hydrolysis studied over a wide temperature range. At low temperatures, the branching trinucleoside-3',3',5'-monophosphate moiety is hydrolyzed almost exclusively by P-O3' fission. At higher temperatures, P-O5' fission competes, accounting at most for 22% of the overall reaction. The results suggest that steric constraints imposed by the secondary structure of the reaction site may significantly contribute to the observed regioselectivity of the transesterification reactions catalyzed by the large ribozymes.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland.
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24
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Kirby AJ, Medeiros M, Oliveira PSM, Orth ES, Brandão TAS, Wanderlind EH, Amer A, Williams NH, Nome F. Activating Water: Important Effects of Non-leaving Groups on the Hydrolysis of Phosphate Triesters. Chemistry 2011; 17:14996-5004. [DOI: 10.1002/chem.201101926] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 11/09/2022]
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25
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Maxwell CI, Liu CT, Neverov AA, Mosey NJ, Brown RS. Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide-promoted cleavages of phosphorothioate and phosphate triesters in water and methanol. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - C. Tony Liu
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Robert Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
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26
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Lassila JK, Zalatan JG, Herschlag D. Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem 2011; 80:669-702. [PMID: 21513457 DOI: 10.1146/annurev-biochem-060409-092741] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phosphoryl-transfer reactions are central to biology. These reactions also have some of the slowest nonenzymatic rates and thus require enormous rate accelerations from biological catalysts. Despite the central importance of phosphoryl transfer and the fascinating catalytic challenges it presents, substantial confusion persists about the properties of these reactions. This confusion exists despite decades of research on the chemical mechanisms underlying these reactions. Here we review phosphoryl-transfer reactions with the goal of providing the reader with the conceptual and experimental background to understand this body of work, to evaluate new results and proposals, and to apply this understanding to enzymes. We describe likely resolutions to some controversies, while emphasizing the limits of our current approaches and understanding. We apply this understanding to enzyme-catalyzed phosphoryl transfer and provide illustrative examples of how this mechanistic background can guide and deepen our understanding of enzymes and their mechanisms of action. Finally, we present important future challenges for this field.
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Affiliation(s)
- Jonathan K Lassila
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
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27
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Weijnen JGJ, Engbersen JFJ. Catalytic hydrolysis of phosphate esters by metallocomplexes of 1,10-phenanthroline derivatives in micellar solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19931120608] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Orth ES, Brandão TAS, Souza BS, Pliego JR, Vaz BG, Eberlin MN, Kirby AJ, Nome F. Intramolecular Catalysis of Phosphodiester Hydrolysis by Two Imidazoles. J Am Chem Soc 2010; 132:8513-23. [DOI: 10.1021/ja1034733] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elisa S. Orth
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Tiago A. S. Brandão
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Bruno S. Souza
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Josefredo R. Pliego
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Boniek G. Vaz
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Marcos N. Eberlin
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Anthony J. Kirby
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
| | - Faruk Nome
- INCT-Catálise, Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina 88040-900, Brazil, Universidade Federal de São João Del-Rei, Sao Joao Del Rei, MG, 36301-160, Brazil, ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas-UNICAMP, Campinas, SP, Brazil 88040-900, and University Chemical Laboratory, Cambridge CB2 1EW, U.K
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29
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Rougier NM, Vico RV, de Rossi RH, Buján EI. Reactivity of the Insecticide Fenitrothion toward O and N Nucleophiles. J Org Chem 2010; 75:3427-36. [DOI: 10.1021/jo100541y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalia M. Rougier
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, X5000HUA, Córdoba, Argentina
| | - Raquel V. Vico
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, X5000HUA, Córdoba, Argentina
| | - Rita H. de Rossi
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, X5000HUA, Córdoba, Argentina
| | - Elba I. Buján
- Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Medina Allende y Haya de la Torre, X5000HUA, Córdoba, Argentina
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30
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Liu CT, Neverov AA, Maxwell CI, Brown RS. Demonstration of Prominent Cu(II)-Promoted Leaving Group Stabilization of the Cleavage of a Homologous Set of Phosphate Mono-, Di-, and Triesters in Methanol. J Am Chem Soc 2010; 132:3561-73. [DOI: 10.1021/ja910111q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | | | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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31
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Tarrat N. Alkaline hydrolysis of phosphate triesters in solution: Stepwise or concerted? A theoretical study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Edwards DR, Liu CT, Garrett GE, Neverov AA, Brown RS. Leaving Group Assistance in the La3+-Catalyzed Cleavage of Dimethyl (o-Methoxycarbonyl)aryl Phosphate Triesters in Methanol. J Am Chem Soc 2009; 131:13738-48. [DOI: 10.1021/ja904659e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- David R. Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Graham E. Garrett
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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33
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Activating Water: Efficient Intramolecular General Base Catalysis of the Hydrolysis of a Phosphate Triester. Chemistry 2009; 15:8475-8479. [DOI: 10.1002/chem.200901096] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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34
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Neverov AA, Liu CT, Bunn SE, Edwards D, White CJ, Melnychuk SA, Brown RS. A Simple DNase Model System Comprising a Dinuclear Zn(II) Complex in Methanol Accelerates the Cleavage of a Series of Methyl Aryl Phosphate Diesters by 1011−1013. J Am Chem Soc 2008; 130:6639-49. [DOI: 10.1021/ja8006963] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - Shannon E. Bunn
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - David Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | | | | | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
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35
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Stivers JT, Nagarajan R. Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens. Chem Rev 2007; 106:3443-67. [PMID: 16895336 PMCID: PMC2729714 DOI: 10.1021/cr050317n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA.
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36
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Hoque MEU, Dey NK, Kim CK, Lee BS, Lee HW. Kinetics and mechanism of the aminolysis of aryl ethyl chloro and chlorothio phosphates with anilines. Org Biomol Chem 2007; 5:3944-50. [DOI: 10.1039/b713167d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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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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38
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Whiteside T, Hilal S, Carreira L. Estimation of Phosphate Ester Hydrolysis Rate Constants. I. Alkaline Hydrolysis. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/qsar.200530148] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Horvat CM, Wolfenden RV. A persistent pesticide residue and the unusual catalytic proficiency of a dehalogenating enzyme. Proc Natl Acad Sci U S A 2005; 102:16199-202. [PMID: 16260733 PMCID: PMC1283461 DOI: 10.1073/pnas.0508176102] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The soil of potato fields in The Netherlands harbors bacteria with the ability to metabolize 3-chloroacrylic acid, generated by the degradation of a pesticide (1,3-dichloropropene) that entered the environment in 1946. From examination of rate constants at elevated temperatures, we infer that the half-time at 25 degrees C for spontaneous hydrolytic dechlorination of trans-3-chloroacrylic acid is 10,000 years, several orders of magnitude longer than half-times for spontaneous decomposition of other environmental pollutants such as 1,2-dichloroethane (72 years), paraoxon (13 months), atrazine (5 months), and aziridine (52 h). With thermodynamic parameters for activation similar to those for the spontaneous hydration of fumarate at pH 6.8, this slow reaction proceeds at a constant rate through the pH range between 2 and 12. However, at the active site of the enzyme 3-chloroacrylate dehalogenase (CaaD), isolated from a pseudomonad growing in these soils, hydrolytic dechlorination proceeds with a half-time of 0.18 s. Neither k(cat) nor k(cat)/K(m) is reduced by increasing solvent viscosity with trehalose, implying that the rate of enzymatic dechlorination is controlled by chemical events in catalysis rather than by diffusion-limited substrate binding or product release. CaaD achieves an approximately 10(12)-fold rate enhancement, matching or surpassing the rate enhancements produced by many enzymes that act on more conventional biological substrates. One of those enzymes is 4-oxalocrotonate tautomerase, with which CaaD seems to share a common evolutionary origin.
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Affiliation(s)
- Christopher M Horvat
- Department of Biochemistry and Biophysics and Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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40
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Lewis RE, Neverov AA, Stan Brown R. Mechanistic studies of La3+ and Zn2+-catalyzed methanolysis of O-ethyl O-aryl methylphosphonate esters. An effective solvolytic method for the catalytic destruction of phosphonate CW simulants. Org Biomol Chem 2005; 3:4082-8. [PMID: 16267587 DOI: 10.1039/b511550g] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The kinetics of methanolysis of six O-ethyl O-aryl methylphosphonates (6a-f) promoted by methoxide, La3+ and 1,5,9-triazacyclododecane complex of Zn2+(-OCH3) (5:Zn2+(-OCH3)) were studied as simulants for chemical warfare (CW) agents, and analyzed through the use of Brønsted plots. The beta(lg) values are, respectively, -0.76, -1.26 and -1.06, pointing to significant weakening of the P-OAr bond in the transition state. For the metal-catalyzed reactions the data are consistent with a concerted process where the P-OAr bond rupture has progressed to the extent of 84% in the La3+ reaction and ca. 70% in the Zn2+ catalyzed reaction. The catalysis afforded by the metal ions is remarkable, being about 10(6)-fold and 10(8)-fold for poor and good leaving groups, respectively, relative to the background reactions at pH 9.1. Solvent deuterium kinetic isotope studies for two of the substrates promoted by 5:Zn2+(-OCH3) give kH/kD = 1.0 +/- 0.1, consistent with a nucleophilic mechanism. A unified mechanism for the metal-catalyzed reactions is presented which involves pre-equilibrium coordination of the substrate to the metal ion followed by intramolecular delivery of a coordinated methoxide.
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Affiliation(s)
- Roxanne E Lewis
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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41
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Hengge AC. Mechanistic studies on enzyme-catalyzed phosphoryl transfer. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2005. [DOI: 10.1016/s0065-3160(05)40002-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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42
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Liu T, Neverov AA, Tsang JSW, Brown RS. Mechanistic studies of La3+- and Zn2+-catalyzed methanolysis of aryl phosphate and phosphorothioate triesters. Development of artificial phosphotriesterase systems. Org Biomol Chem 2005; 3:1525-33. [PMID: 15827652 DOI: 10.1039/b502569a] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The methanolyses of a series of O,O-diethyl O-aryl phosphates (2,5) and O,O-diethyl S-aryl phosphorothioates (6) promoted by methoxide and two metal ion systems, (La3+)2(-OCH3)2 and 4:Zn2+:-OCH3 (4 = 1,5,9-triazacyclododecane) has been studied in methanol at 25 degrees C. Brønsted plots of the logk2 values vs. pKa for the phenol leaving groups give beta(lg) values of -0.70, -1.43 and -1.12 for the methanolysis of the phosphates and -0.63, -0.87 and -0.74 for the methanolysis of the phosphorothioates promoted by the methoxide, La3+ and Zn2+ systems respectively. The kinetic data for the metal-catalyzed reactions are analyzed in terms of a common mechanism where there is extensive cleavage of the P-XAr bond in the rate-limiting transition state. The relevance of these findings to the mechanism of action of the phosphotriesterase enzyme is discussed.
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Affiliation(s)
- Tony Liu
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
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43
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Cassano AG, Anderson VE, Harris ME. Understanding the transition states of phosphodiester bond cleavage: insights from heavy atom isotope effects. Biopolymers 2004; 73:110-29. [PMID: 14691944 DOI: 10.1002/bip.10517] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleotides of DNA and RNA are joined by phosphodiester linkages whose synthesis and hydrolysis are catalyzed by numerous essential enzymes. Two prominent mechanisms have been proposed for RNA and protein enzyme catalyzed cleavage of phosphodiester bonds in RNA: (a) intramolecular nucleophilic attack by the 2'-hydroxyl group adjacent to the reactive phosphate; and (b) intermolecular nucleophilic attack by hydroxide, or other oxyanion. The general features of these two mechanisms have been established by physical organic chemical analyses; however, a more detailed understanding of the transition states of these reactions is emerging from recent kinetic isotope effect (KIE) studies. The recent data show interesting differences between the chemical mechanisms and transition state structures of the inter- and intramolecular reactions, as well as provide information on the impact of metal ion, acid, and base catalysis on these mechanisms. Importantly, recent nonenzymatic model studies show that interactions with divalent metal ions, an important feature of many phosphodiesterase active sites, can influence both the mechanism and transition state structure of nonenzymatic phosphodiester cleavage. Such detailed investigations are important because they mimic catalytic strategies employed by both RNA and protein phosphodiesterases, and so set the stage for explorations of enzyme-catalyzed transition states. Application of KIE analyses for this class of enzymes is just beginning, and several important technical challenges remain to be overcome. Nonetheless, such studies hold great promise since they will provide novel insights into the role of metal ions and other active site interactions.
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Affiliation(s)
- Adam G Cassano
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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Zhang ZY. Mechanistic studies on protein tyrosine phosphatases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 73:171-220. [PMID: 12882518 DOI: 10.1016/s0079-6603(03)01006-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The human genome encodes approximately 100 phosphatases that belong to the protein tyrosine phosphatase (PTP) superfamily. The hallmark for this superfamily is the active site sequence C(X)5R, also known as the PTP signature motif. The PTPs are key regulatory components in signal transduction pathways and the importance of PTPs in the control of cellular signaling is well established. Based on structure and substrate specificity, the PTP superfamily is divided into four distinct subfamilies: (1) pTyr-specific PTPs, (2) dual specificity phosphatases, (3) Cdc25 phosphatases, and (4) LMW PTPs. The PTPs have similar core structures made of a central parallel beta-sheet with flanking a-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif. Site-directed mutagenesis of conserved amino acids in the Yersinia PTP and several other phosphatases in the PTP superfamily combined with detailed kinetic and mechanistic analyses have revealed a common chemical mechanism for phosphate hydrolysis despite the differences in substrate specificity. This article reviews our current knowledge of the common features important for PTP catalysis, the nature of the enzymatic transition state, and the roles of essential residues in transition stabilization. Future mechanistic studies of PTPs will focus on the use of physiological substrates to determine the molecular basis of substrate recognition and regulation, which is essential for understanding the specific functional role of PTPs in cellular signaling.
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Affiliation(s)
- Zhong-Yin Zhang
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Jackson MD, Denu JM. Molecular reactions of protein phosphatases--insights from structure and chemistry. Chem Rev 2001; 101:2313-40. [PMID: 11749375 DOI: 10.1021/cr000247e] [Citation(s) in RCA: 168] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M D Jackson
- Department of Biochemistry and Molecular Biology, Oregon Health Sciences University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97201, USA
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Ablooglu AJ, Till JH, Kim K, Parang K, Cole PA, Hubbard SR, Kohanski RA. Probing the catalytic mechanism of the insulin receptor kinase with a tetrafluorotyrosine-containing peptide substrate. J Biol Chem 2000; 275:30394-8. [PMID: 10869355 DOI: 10.1074/jbc.m003524200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction of a synthetic tetrafluorotyrosyl peptide substrate with the activated tyrosine kinase domain of the insulin receptor was studied by steady-state kinetics and x-ray crystallography. The pH-rate profiles indicate that the neutral phenol, rather than the chemically more reactive phenoxide ion, is required for enzyme-catalyzed phosphorylation. The pK(a) of the tetrafluorotyrosyl hydroxyl is elevated 2 pH units on the enzyme compared with solution, whereas the phenoxide anion species behaves as a weak competitive inhibitor of the tyrosine kinase. A structure of the binary enzyme-substrate complex shows the tetrafluorotyrosyl OH group at hydrogen bonding distances from the side chains of Asp(1132) and Arg(1136), consistent with elevation of the pK(a). These findings strongly support a reaction mechanism favoring a dissociative transition state.
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Affiliation(s)
- A J Ablooglu
- Mount Sinai School of Medicine, Department of Biochemistry and Molecular Biology, New York, New York 10029, USA
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Raushel FM, Holden HM. Phosphotriesterase: an enzyme in search of its natural substrate. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2000; 74:51-93. [PMID: 10800593 DOI: 10.1002/9780470123201.ch2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The bacterial PTE is able to catalyze the hydrolysis of a wide range of organophosphate nerve agents. The active site has been shown to consist of a unique binuclear metal center that has evolved to deliver hydroxide to the site of bond cleavage. The reaction rate for the hydrolysis of activated substrates such as paraoxon is limited by product release or an associated protein conformational change.
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Affiliation(s)
- F M Raushel
- Department of Chemistry, Texas A&M University, College Station 77843, USA
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Spivak DA, Hoffman TZ, Moore AH, Taylor MJ, Janda KD. A comparison of flexible and constrained haptens in eliciting antibody catalysts for paraoxon hydrolysis. Bioorg Med Chem 1999; 7:1145-50. [PMID: 10428386 DOI: 10.1016/s0968-0896(99)00026-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new amine-oxide hapten was employed as an antigen, producing seven monoclonal antibodies (mAbs) from a panel of 20 that catalyzed paraoxon hydrolysis. The current hapten design differs from that previously described in that the molecule is inherently more flexible than its constrained predecessor. One of the seven antibody catalysts, mAb 1H9, showed the highest activity and was selected for detailed study. At pH = 8.77, the catalytic hydrolysis of paraoxon by mAb 1H9 followed Michaelis Menten kinetics affording a k(cat) = 3.73 x 10(-4) min(-1) and a Km = 1.12 mM with a rate acceleration k(cat)/k(uncat) = 56. The hapten was found to be a competitive inhibitor of antibody-catalyzed paraoxon hydrolysis with a Ki = 0.54 mM. A comparison of both the number and proficiency of antibody catalysts obtained when utilizing a flexible versus constrained hapten indicates that, for paraoxon hydrolysis, constrained haptens elicit superior catalysts, suggesting that further development should begin with the use of constrained haptens in producing more proficient antibody catalysts for paraoxon hydrolysis.
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Affiliation(s)
- D A Spivak
- The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA
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Cole PA, Sondhi D, Kim K. Chemical approaches to the study of protein tyrosine kinases and their implications for mechanism and inhibitor design. Pharmacol Ther 1999; 82:219-29. [PMID: 10454199 DOI: 10.1016/s0163-7258(98)00046-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Protein tyrosine kinases are critical enzymes for signal transduction. Using C-terminal Src kinase (Csk) as a model system, we discuss progress in three main areas. First, we describe our efforts to measure the transition state of the reaction using peptide substrates containing fluorotyrosine analogs. It is shown that the Brønsted nucleophile coefficient for the reaction is near zero (similar to the nonenzymatic reaction) and the required nucleophile is the neutral phenol (rather than the more chemically reactive phenoxide anion). By studying the kinase reaction in the reverse direction, a Brønsted leaving group coefficient of -0.3 was measured, indicative of protonation of the departing phenol in the transition state. Taken together, these results strongly support a dissociative transition state mechanism for the kinase. These findings set constraints on the design of transition state analog inhibitors. Second, we describe efforts toward defining the specificity of Csk for peptide and protein substrates. The main findings are that local amino acids surrounding a phosphorylated tyrosine can influence recognition, but that long-range interactions probably are more important in a physiologic protein substrate. These findings underscore the complexities in how protein kinases select protein substrates. Third, we describe a new method in protein engineering that has been applied to the study of protein kinases. The method, expressed protein ligation, allows a general approach for ligating synthetic peptides to recombinant proteins. Using expressed protein ligation, obtaining site-specifically phosphorylated proteins and proteins with the incorporation of biophysical probes becomes relatively straightforward. We have used this method to generate a tail phosphorylated, conformationally altered Csk that showed an unexpected increase in kinase activity.
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Affiliation(s)
- P A Cole
- Laboratory of Bioorganic Chemistry, The Rockefeller University, New York, NY 10021, USA
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