1
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Zhu X, Xu J, Zhang Y, Li B, Tian Y, Wu Y, Liu Z, Ma C, Tan S, Wang B. Revealing Intramolecular Isotope Effects with Chemical-Bond Precision. J Am Chem Soc 2023. [PMID: 37338304 DOI: 10.1021/jacs.3c02728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Isotope substitution of a molecule not only changes its vibrational frequencies but also changes its vibrational distributions in real-space. Quantitatively measuring the isotope effects inside a polyatomic molecule requires both energy and spatial resolutions at the single-bond level, which has been a long-lasting challenge in macroscopic techniques. By achieving ångström resolution in tip-enhanced Raman spectroscopy (TERS), we record the corresponding local vibrational modes of pentacene and its fully deuterated form, enabling us to identify and measure the isotope effect of each vibrational mode. The measured frequency ratio νH/νD varies from 1.02 to 1.33 in different vibrational modes, indicating different isotopic contributions of H/D atoms, which can be distinguished from TERS maps in real-space and well described by the potential energy distribution simulations. Our study demonstrates that TERS can serve as a non-destructive and highly sensitive methodology for isotope detection and recognition with chemical-bond precision.
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Affiliation(s)
- Xiang Zhu
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jiayu Xu
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Zhang
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Bin Li
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Yishu Tian
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yingying Wu
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhiwei Liu
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chuanxu Ma
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Shijing Tan
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
| | - Bing Wang
- Hefei National Research Center for Physical Sciences at the Microscale and Synergetic Innovation Center of Quantum Information & Quantum Physics, New Cornerstone Science Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei, Anhui 230088, China
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2
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Burchill L, Males A, Kaur A, Davies GJ, Williams SJ. Structure, Function and Mechanism of N‐Glycan Processing Enzymes:
endo
‐α‐1,2‐Mannanase and
endo
‐α‐1,2‐Mannosidase. Isr J Chem 2022. [DOI: 10.1002/ijch.202200067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Alexandra Males
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
| | - Gideon J. Davies
- Department of Chemistry University of York York YO10 5DD United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne Parkville Victoria Australia 3010
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3
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Ben-Tal Y, Boaler PJ, Dale HJA, Dooley RE, Fohn NA, Gao Y, García-Domínguez A, Grant KM, Hall AMR, Hayes HLD, Kucharski MM, Wei R, Lloyd-Jones GC. Mechanistic analysis by NMR spectroscopy: A users guide. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 129:28-106. [PMID: 35292133 DOI: 10.1016/j.pnmrs.2022.01.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (1/2H, 10/11B, 13C, 15N, 19F, 29Si, 31P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, 1H/19F DOSY NMR, and in situ illumination NMR.
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Affiliation(s)
- Yael Ben-Tal
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Patrick J Boaler
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Harvey J A Dale
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ruth E Dooley
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom; Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Nicole A Fohn
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Yuan Gao
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrés García-Domínguez
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Katie M Grant
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Andrew M R Hall
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Hannah L D Hayes
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Maciej M Kucharski
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Ran Wei
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom
| | - Guy C Lloyd-Jones
- School of Chemistry, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, United Kingdom.
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4
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Dale HJA, Leach AG, Lloyd-Jones GC. Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point? J Am Chem Soc 2021; 143:21079-21099. [PMID: 34870970 DOI: 10.1021/jacs.1c07351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.
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Affiliation(s)
- Harvey J A Dale
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrew G Leach
- School of Health Sciences, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Guy C Lloyd-Jones
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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5
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Athavale SV, Gao S, Liu Z, Mallojjala SC, Hirschi JS, Arnold FH. Biocatalytic, Intermolecular C-H Bond Functionalization for the Synthesis of Enantioenriched Amides. Angew Chem Int Ed Engl 2021; 60:24864-24869. [PMID: 34534409 DOI: 10.1002/anie.202110873] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/16/2021] [Indexed: 11/07/2022]
Abstract
Directed evolution of heme proteins has opened access to new-to-nature enzymatic activity that can be harnessed to tackle synthetic challenges. Among these, reactions resulting from active site iron-nitrenoid intermediates present a powerful strategy to forge C-N bonds with high site- and stereoselectivity. Here we report a biocatalytic, intermolecular benzylic C-H amidation reaction operating at mild and scalable conditions. With hydroxamate esters as nitrene precursors, feedstock aromatic compounds can be converted to chiral amides with excellent enantioselectivity (up to >99 % ee) and high yields (up to 87 %). Kinetic and computational analysis of the enzymatic reaction reveals rate-determining nitrenoid formation followed by stepwise hydrogen atom transfer-mediated C-H functionalization.
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Affiliation(s)
- Soumitra V Athavale
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California, 91125, USA
| | - Shilong Gao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California, 91125, USA
| | - Zhen Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California, 91125, USA
| | | | - Jennifer S Hirschi
- Department of Chemistry, Binghamton University, Binghamton, New York, 13902, USA
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California, 91125, USA
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6
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Athavale SV, Gao S, Liu Z, Mallojjala SC, Hirschi JS, Arnold FH. Biocatalytic, Intermolecular C−H Bond Functionalization for the Synthesis of Enantioenriched Amides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Soumitra V. Athavale
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard, MC 210-41 Pasadena California 91125 USA
| | - Shilong Gao
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard, MC 210-41 Pasadena California 91125 USA
| | - Zhen Liu
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard, MC 210-41 Pasadena California 91125 USA
| | | | | | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering California Institute of Technology 1200 East California Boulevard, MC 210-41 Pasadena California 91125 USA
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7
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Ren W, Farren-Dai M, Sannikova N, Świderek K, Wang Y, Akintola O, Britton R, Moliner V, Bennet AJ. Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design. Chem Sci 2020; 11:10488-10495. [PMID: 34094307 PMCID: PMC8162432 DOI: 10.1039/d0sc04401f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, SN2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds. Positive charge stabilized on remote C5-allylic center with catalysis occurring via a loose SN2 transition state.![]()
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Affiliation(s)
- Weiwu Ren
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Marco Farren-Dai
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Natalia Sannikova
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Yang Wang
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Oluwafemi Akintola
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Robert Britton
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I 12560 Castellón Spain
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S6 Canada +1-778-782-8814
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8
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Sobala L, Speciale G, Zhu S, Raich L, Sannikova N, Thompson AJ, Hakki Z, Lu D, Shamsi Kazem Abadi S, Lewis AR, Rojas-Cervellera V, Bernardo-Seisdedos G, Zhang Y, Millet O, Jiménez-Barbero J, Bennet AJ, Sollogoub M, Rovira C, Davies GJ, Williams SJ. An Epoxide Intermediate in Glycosidase Catalysis. ACS CENTRAL SCIENCE 2020; 6:760-770. [PMID: 32490192 PMCID: PMC7256955 DOI: 10.1021/acscentsci.0c00111] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Indexed: 05/18/2023]
Abstract
Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope (E 3) conformation. Kinetic isotope effects (k cat/K M) for anomeric-2H and anomeric-13C support an oxocarbenium ion-like transition state, and that for C2-18O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.
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Affiliation(s)
- Lukasz
F. Sobala
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sha Zhu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Lluís Raich
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Natalia Sannikova
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Thompson
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Zalihe Hakki
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dan Lu
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Saeideh Shamsi Kazem Abadi
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew R. Lewis
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Víctor Rojas-Cervellera
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Ganeko Bernardo-Seisdedos
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Yongmin Zhang
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
| | - Oscar Millet
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- Ikerbasque,
Basque Foundation for Science, Marıá Dıáz de Haro 3, 48013 Bilbao, Spain
- Molecular
Recognition and Host−Pathogen Interactions, CIC bioGUNE, Basque Research Technology Alliance (BRTA), Bizkaia Technology Park, Building
800, 48160 Derio, Spain
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- Department
of Biochemistry and Molecular Biology, Simon
Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
- E-mail:
| | - Matthieu Sollogoub
- Sorbonne
Université, CNRS, Institut Parisien de Chimie Moléculaire,
UMR 8232, 4 place Jussieu, 75005 Paris, France
- E-mail:
| | - Carme Rovira
- Departament
de Química Inorgànica
i Orgànica (Secció de Química Orgànica) &
Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys
23, 08010 Barcelona, Spain
- E-mail:
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
- E-mail:
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
- E-mail:
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9
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Vocadlo DJ. A Shut-and-Open Case: An Epoxide Intermediate Spotted in the Reaction Coordinate of a Family of Glycoside Hydrolases. ACS CENTRAL SCIENCE 2020; 6:619-621. [PMID: 32490180 PMCID: PMC7256941 DOI: 10.1021/acscentsci.0c00482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- David J. Vocadlo
- Department of
Chemistry and Department of Molecular
Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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10
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Zimmermann J, Halloran LJS, Hunkeler D. Tracking chlorinated contaminants in the subsurface using compound-specific chlorine isotope analysis: A review of principles, current challenges and applications. CHEMOSPHERE 2020; 244:125476. [PMID: 31830644 DOI: 10.1016/j.chemosphere.2019.125476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Many chlorinated hydrocarbons have gained notoriety as persistent organic pollutants in the environment. Engineered and natural remediation efforts require a monitoring tool to track the progress of degradation processes. Compound-specific isotope analysis (CSIA) is a robust method to evaluate the origin and fate of contaminants in the environment and does not rely on concentration measurements. While carbon CSIA has established itself in the routine assessment of contaminated sites, studies incorporating chlorine isotopes have only recently become more common. Although some aspects of chlorine isotope analysis are more challenging than carbon isotope analysis, having additional isotopic data yields valuable information for contaminated site management. This review provides an overview of chlorine isotope fractionation of chlorinated contaminants in the subsurface by different processes and presents analytical techniques and unresolved challenges in chlorine isotope analysis. A summary of successful field applications illustrates the potential of using chlorine isotope data. Finally, approaches in modelling chlorine isotope fractionation due to degradation, diffusion, and sorption processes are discussed.
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Affiliation(s)
- Jeremy Zimmermann
- Centre for Hydrogeology and Geothermics, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland.
| | - Landon J S Halloran
- Centre for Hydrogeology and Geothermics, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
| | - Daniel Hunkeler
- Centre for Hydrogeology and Geothermics, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
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11
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Colombo C, Bennet AJ. The physical organic chemistry of glycopyranosyl transfer reactions in solution and enzyme-catalyzed. Curr Opin Chem Biol 2019; 53:145-157. [PMID: 31689605 DOI: 10.1016/j.cbpa.2019.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Our understanding of the mechanisms of glycopyranosyl transfer that occur in solution, both for the chemical synthesis of complex structures and that for the cleavage of glycosidic bonds has allowed us to design biologically active molecules. Recent efforts on the reactivity of glycopyranosides, which are critical entities in all biological systems, coupled with the advent of modern spectroscopic instrumentation have allowed physical organic chemists to broaden our knowledge of glycosyl transfer reaction transition states, both in solution and for enzyme-catalyzed processes, and of critical high energy intermediates. This review details recent physical organic, kinetic and structural studies that have led to elucidation of several different mechanism for the transfer of glycopyranosyl moieties from various substrates to acceptors, such as water or a sugar hydroxyl group.
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12
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Howe GW, van der Donk WA. 18O Kinetic Isotope Effects Reveal an Associative Transition State for Phosphite Dehydrogenase Catalyzed Phosphoryl Transfer. J Am Chem Soc 2018; 140:17820-17824. [PMID: 30525552 DOI: 10.1021/jacs.8b06301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphite dehydrogenase (PTDH) catalyzes an unusual phosphoryl transfer reaction in which water displaces a hydride leaving group. Despite extensive effort, it remains unclear whether PTDH catalysis proceeds via an associative or dissociative mechanism. Here, primary 2H and secondary 18O kinetic isotope effects (KIEs) were determined and used together with computation to characterize the transition state (TS) catalyzed by a thermostable PTDH (17X-PTDH). The large, normal 18O KIEs suggest an associative mechanism. Various transition state structures were computed within a model of the enzyme active site and 2H and 18O KIEs were predicted to evaluate the accuracy of each TS. This analysis suggests that 17X-PTDH catalyzes an associative process with little leaving group displacement and extensive nucleophilic participation. This tight TS is likely a consequence of the extremely poor leaving group requiring significant P-O bond formation to expel the hydride. This finding contrasts with the dissociative TSs in most phosphoryl transfer reactions from phosphate mono- and diesters.
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Affiliation(s)
- Graeme W Howe
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States.,Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States.,Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , 1206 West Gregory Drive , Urbana , Illinois 61801 , United States
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13
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Evans GB, Schramm VL, Tyler PC. The transition to magic bullets - transition state analogue drug design. MEDCHEMCOMM 2018; 9:1983-1993. [PMID: 30627387 PMCID: PMC6295874 DOI: 10.1039/c8md00372f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/24/2018] [Indexed: 12/17/2022]
Abstract
In the absence of industry partnerships, most academic groups lack the infrastructure to rationally design and build drugs via methods used in industry. Instead, academia needs to work smarter using mechanism-based design. Working smarter can mean the development of new drug discovery paradigms and then demonstrating their utility and reproducibility to industry. The collaboration between Vern Schramm's group at the Albert Einstein College of Medicine, USA and Peter Tyler at the Ferrier Research Institute at The Victoria University of Wellington, NZ has refined a drug discovery process called transition state analogue design. This process has been applied to several biomedically relevant nucleoside processing enzymes. In 2017, Mundesine®, conceived using transition state analogue design, received market approval for the treatment of peripheral T-cell lymphoma in Japan. This short review looks at a brief history of transition state analogue design, the fundamentals behind the development of this process, and the success of enzyme inhibitors produced using this drug design methodology.
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Affiliation(s)
- Gary B Evans
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
- The Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Auckland , New Zealand
| | - Vern L Schramm
- Department of Biochemistry , Albert Einstein College of Medicine , Bronx , NY 10461 , USA
| | - Peter C Tyler
- The Ferrier Research Institute , Victoria University of Wellington , 69 Gracefield Rd , Lower Hutt , 5010 , New Zealand . ; Tel: +64 4 463 0048
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14
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Sannikova N, Gerak CAN, Shidmoossavee FS, King DT, Shamsi Kazem Abadi S, Lewis AR, Bennet AJ. Both Chemical and Non-Chemical Steps Limit the Catalytic Efficiency of Family 4 Glycoside Hydrolases. Biochemistry 2018; 57:3378-3386. [PMID: 29630821 DOI: 10.1021/acs.biochem.8b00117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The glycoside hydrolase family 4 (GH4) α-galactosidase from Citrobacter freundii (MelA) catalyzes the hydrolysis of fluoro-substituted phenyl α-d-galactopyranosides by utilizing two cofactors, NAD+ and a metal cation, under reducing conditions. In order to refine the mechanistic understanding of this GH4 enzyme, leaving group effects were measured with various metal cations. The derived βlg value on V/ K for strontium activation is indistinguishable from zero (0.05 ± 0.12). Deuterium kinetic isotope effects (KIEs) were measured for the activated substrates 2-fluorophenyl and 4-fluorophenyl α-d-galactopyranosides in the presence of Sr2+, Y3+, and Mn2+, where the isotopic substitution was on the carbohydrate at C-2 and/or C-3. To determine the contributing factors to the virtual transition state (TS) on which the KIEs report, kinetic isotope effects on isotope effects were measured on these KIEs using doubly deuterated substrates. The measured D V/ K KIEs for MelA-catalyzed hydrolysis of 2-fluorophenyl α-d-galactopyranoside are closer to unity than the measured effects on 4-fluorophenyl α-d-galactopyranoside, irrespective of the site of isotopic substitution and of the metal cation activator. These observations are consistent with hydride transfer at C-3 to the on-board NAD+, deprotonation at C-2, and a non-chemical step contributing to the virtual TS for V/ K.
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15
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Colombo C, Podlipnik Č, Lo Presti L, Niikura M, Bennet AJ, Bernardi A. Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase. PLoS One 2018; 13:e0193623. [PMID: 29489903 PMCID: PMC5831633 DOI: 10.1371/journal.pone.0193623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/14/2018] [Indexed: 11/19/2022] Open
Abstract
The rise of drug-resistant influenza A virus strains motivates the development of new antiviral drugs, with different structural motifs and substitution. Recently, we explored the use of a bicyclic (bicyclo[3.1.0]hexane) analogue of sialic acid that was designed to mimic the conformation adopted during enzymatic cleavage within the neuraminidase (NA; sialidase) active site. Given that our first series of compounds were at least four orders of magnitude less active than available drugs, we hypothesized that the new carbon skeleton did not elicit the same interactions as the cyclohexene frameworks used previously. Herein, we tried to address this critical point with the aid of molecular modeling and we proposed new structures with different functionalization, such as the introduction of free ammonium and guanidinium groups and ether side chains other than the 3-pentyl side chain, the characteristic side chain in Oseltamivir. A highly simplified synthetic route was developed, starting from the cyclopropanation of cyclopentenone and followed by an aziridination and further functionalization of the five-member ring. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. The results show that none of the new structural variants synthesized, including those containing guanidinium groups rather than free ammonium ions, displayed activity against influenza A neuraminidases at concentrations less than 2 mM. We conclude that the choice and positioning of functional groups on the bicyclo[3.1.0]hexyl system still need to be properly tuned for producing complementary interactions within the catalytic site.
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Affiliation(s)
- Cinzia Colombo
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
| | - Črtomir Podlipnik
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Leonardo Lo Presti
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
| | - Masahiro Niikura
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Anna Bernardi
- Università degli Studi di Milano, Dipartimento di Chimica, Milano, Italy
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16
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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17
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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18
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Kwan EE, Park Y, Besser HA, Anderson TL, Jacobsen EN. Sensitive and Accurate 13C Kinetic Isotope Effect Measurements Enabled by Polarization Transfer. J Am Chem Soc 2017; 139:43-46. [PMID: 28005341 PMCID: PMC5674980 DOI: 10.1021/jacs.6b10621] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polarization transfer is demonstrated as a sensitive technique for the measurement of isotopic fractionation of protonated carbons at natural abundance. This method allows kinetic isotope effects (KIEs) to be determined with substantially less material or shorter acquisition time compared with traditional experiments. Computations quantitatively reproduce the KIEs in a Diels-Alder reaction and a catalytic glycosylation. The glycosylation is shown to occur by an effectively concerted mechanism.
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Affiliation(s)
- Eugene E. Kwan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yongho Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Harrison A. Besser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Thayer L. Anderson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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19
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Measurement of Kinetic Isotope Effects by Continuously Monitoring Isotopologue Ratios Using NMR Spectroscopy. Methods Enzymol 2017. [DOI: 10.1016/bs.mie.2017.06.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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20
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Linscott JA, Kapilashrami K, Wang Z, Senevirathne C, Bothwell IR, Blum G, Luo M. Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8. Proc Natl Acad Sci U S A 2016; 113:E8369-E8378. [PMID: 27940912 PMCID: PMC5206543 DOI: 10.1073/pnas.1609032114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35-2.40 Å and 2.00-2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors.
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Affiliation(s)
- Joshua A Linscott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
| | - Kanishk Kapilashrami
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhen Wang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ian R Bothwell
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Gil Blum
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
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21
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Tormos JR, Suarez MB, Fitzpatrick PF. 13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects. Arch Biochem Biophys 2016; 612:115-119. [PMID: 27815088 PMCID: PMC5257176 DOI: 10.1016/j.abb.2016.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 12/14/2022]
Abstract
A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N'-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.
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Affiliation(s)
- José R Tormos
- Department of Chemistry and Biochemistry, St. Mary's University, San Antonio, TX 78228, United States
| | - Marina B Suarez
- Department of Geological Sciences, University of Texas-San Antonio, San Antonio, TX 78249, United States
| | - Paul F Fitzpatrick
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, United States.
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22
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23
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Speciale G, Farren-Dai M, Shidmoossavee FS, Williams SJ, Bennet AJ. C2-Oxyanion Neighboring Group Participation: Transition State Structure for the Hydroxide-Promoted Hydrolysis of 4-Nitrophenyl α-d-Mannopyranoside. J Am Chem Soc 2016; 138:14012-14019. [DOI: 10.1021/jacs.6b07935] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gaetano Speciale
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Marco Farren-Dai
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Fahimeh S. Shidmoossavee
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Road, Parkville, Victoria 3010, Australia
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, B.C. V5A 1S6, Canada
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24
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Offenbacher AR, Zhu H, Klinman JP. Synthesis of Site-Specifically 13C Labeled Linoleic Acids. Tetrahedron Lett 2016; 57:4537-4540. [PMID: 28260819 DOI: 10.1016/j.tetlet.2016.08.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Soybean lipoxygenase-1 (SLO-1) catalyzes the C-H abstraction from the reactive carbon (C-11) in linoleic acid as the first and rate-determining step in the formation of alkylhydroperoxides. While previous labeling strategies have focused on deuterium labeling to ascertain the primary and secondary kinetic isotope effects for this reaction, there is an emerging interest and need for selectively enriched 13C isotopologues. In this report, we present synthetic strategies for site-specific 13C labeled linoleic acid substrates. We take advantage of a Corey-Fuchs formyl to terminal 13C-labeled alkyne conversion, using 13CBr4 as the labeling source, to reduce the number of steps from a previous fatty acid 13C synthetic labeling approach. The labeled linoleic acid substrates are useful as nuclear tunneling markers and for extracting active site geometries of the enzyme-substrate complex in lipoxygenase.
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Affiliation(s)
- Adam R Offenbacher
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720; Quantitative Institutes of Biosciences, University of California, Berkeley, Berkeley, California, 94720
| | - Hui Zhu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720; Quantitative Institutes of Biosciences, University of California, Berkeley, Berkeley, California, 94720
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, California, 94720; Quantitative Institutes of Biosciences, University of California, Berkeley, Berkeley, California, 94720; Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, 94720
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25
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Colombo C, Pinto BM, Bernardi A, Bennet AJ. Synthesis and evaluation of influenza A viral neuraminidase candidate inhibitors based on a bicyclo[3.1.0]hexane scaffold. Org Biomol Chem 2016; 14:6539-53. [DOI: 10.1039/c6ob00999a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the synthesis of constrained oseltamivir analogues designed to mimic the proposed boat conformation of the enzymatic transition state.
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Affiliation(s)
- Cinzia Colombo
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - B. Mario Pinto
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
| | - Anna Bernardi
- Università degli Studi di Milano
- Dipartimento di Chimica
- I-20133 Milano
- Italy
| | - Andrew J. Bennet
- Department of Chemistry
- Simon Fraser University
- 8888 University Drive
- British Columbia
- Canada V5A 1S6
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26
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Measuring specificity in multi-substrate/product systems as a tool to investigate selectivity in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:70-6. [PMID: 26321598 DOI: 10.1016/j.bbapap.2015.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 08/07/2015] [Accepted: 08/25/2015] [Indexed: 01/24/2023]
Abstract
Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated systems, as well as accurately describe the interactions through kinetic parameters. This review looks at different methods for studying multiple substrate enzymes, as well as explores options on how to most accurately describe an enzyme's activity within these multi-substrate systems. Identifying and defining this enzymatic activity should help clear the way to using in vitro systems to accurately predicting the behavior of multi-substrate enzymes in vivo. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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27
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Adero PO, Furukawa T, Huang M, Mukherjee D, Retailleau P, Bohé L, Crich D. Cation Clock Reactions for the Determination of Relative Reaction Kinetics in Glycosylation Reactions: Applications to Gluco- and Mannopyranosyl Sulfoxide and Trichloroacetimidate Type Donors. J Am Chem Soc 2015; 137:10336-45. [PMID: 26207807 PMCID: PMC4545385 DOI: 10.1021/jacs.5b06126] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The development of a cation clock method based on the intramolecular Sakurai reaction for probing the concentration dependence of the nucleophile in glycosylation reactions is described. The method is developed for the sulfoxide and trichloroacetimidate glycosylation protocols. The method reveals that O-glycosylation reactions have stronger concentration dependencies than C-glycosylation reactions consistent with a more associative, S(N)2-like character. For the 4,6-O-benzylidene-directed mannosylation reaction a significant difference in concentration dependence is found for the formation of the β- and α-anomers, suggesting a difference in mechanism and a rationale for the optimization of selectivity regardless of the type of donor employed. In the mannose series the cyclization reaction employed as clock results in the formation of cis and trans-fused oxabicyclo[4,4,0]decanes as products with the latter being strongly indicative of the involvement of a conformationally mobile transient glycosyl oxocarbenium ion. With identical protecting group arrays cyclization in the glucopyranose series is more rapid than in the mannopyranose manifold. The potential application of related clock reactions in other carbenium ion-based branches of organic synthesis is considered.
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Affiliation(s)
- Philip O. Adero
- Department of Chemistry, Wayne State University, 5101 Cass Avenue Detroit, MI 48202, USA
| | - Takayuki Furukawa
- Department of Chemistry, Wayne State University, 5101 Cass Avenue Detroit, MI 48202, USA
| | - Min Huang
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Debaraj Mukherjee
- Department of Chemistry, Wayne State University, 5101 Cass Avenue Detroit, MI 48202, USA
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Luis Bohé
- Institut de Chimie des Substances Naturelles, CNRS-ICSN UPR2301, Université Paris-Sud, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - David Crich
- Department of Chemistry, Wayne State University, 5101 Cass Avenue Detroit, MI 48202, USA
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28
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Kellerman DL, Simmons KS, Pedraza M, Piccirilli JA, York DM, Harris ME. Determination of hepatitis delta virus ribozyme N(-1) nucleobase and functional group specificity using internal competition kinetics. Anal Biochem 2015; 483:12-20. [PMID: 25937290 DOI: 10.1016/j.ab.2015.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
Biological catalysis involves interactions distant from the site of chemistry that can position the substrate for reaction. Catalysis of RNA 2'-O-transphosphorylation by the hepatitis delta virus (HDV) ribozyme is sensitive to the identity of the N(-1) nucleotide flanking the reactive phosphoryl group. However, the interactions that affect the conformation of this position, and in turn the 2'O nucleophile, are unclear. Here, we describe the application of multiple substrate internal competition kinetic analyses to understand how the N(-1) nucleobase contributes to HDV catalysis and test the utility of this approach for RNA structure-function studies. Internal competition reactions containing all four substrate sequence variants at the N(-1) position in reactions using ribozyme active site mutations at A77 and A78 were used to test a proposed base-pairing interaction. Mutants A78U, A78G, and A79G retain significant catalytic activity but do not alter the specificity for the N(-1) nucleobase. Effects of nucleobase analog substitutions at N(-1) indicate that U is preferred due to the ability to donate an H-bond in the Watson-Crick face and avoid minor groove steric clash. The results provide information essential for evaluating models of the HDV active site and illustrate multiple substrate kinetic analyses as a practical approach for characterizing structure-function relationships in RNA reactions.
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Affiliation(s)
- Daniel L Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Kandice S Simmons
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Mayra Pedraza
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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29
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Watson DC, Wakarchuk WW, Leclerc S, Schur MJ, Schoenhofen IC, Young NM, Gilbert M. Sialyltransferases with enhanced legionaminic acid transferase activity for the preparation of analogs of sialoglycoconjugates. Glycobiology 2015; 25:767-73. [DOI: 10.1093/glycob/cwv017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/10/2015] [Indexed: 11/15/2022] Open
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30
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Kholodar S, Allen CL, Gulick AM, Murkin AS. The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces. J Am Chem Soc 2015; 137:2748-56. [PMID: 25642788 PMCID: PMC4507815 DOI: 10.1021/ja512911f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 01/17/2023]
Abstract
Several mechanistically unrelated enzymes utilize the binding energy of their substrate's nonreacting phosphoryl group to accelerate catalysis. Evidence for the involvement of the phosphodianion in transition state formation has come from reactions of the substrate in pieces, in which reaction of a truncated substrate lacking its phosphorylmethyl group is activated by inorganic phosphite. What has remained unknown until now is how the phosphodianion group influences the reaction energetics at different points along the reaction coordinate. 1-Deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR), which catalyzes the isomerization of DXP to 2-C-methyl-D-erythrose 4-phosphate (MEsP) and subsequent NADPH-dependent reduction, presents a unique opportunity to address this concern. Previously, we have reported the effect of covalently linked phosphate on the energetics of DXP turnover. Through the use of chemically synthesized MEsP and its phosphate-truncated analogue, 2-C-methyl-D-glyceraldehyde, the current study revealed a loss of 6.1 kcal/mol of kinetic barrier stabilization upon truncation, of which 4.4 kcal/mol was regained in the presence of phosphite dianion. The activating effect of phosphite was accompanied by apparent tightening of its interactions within the active site at the intermediate stage of the reaction, suggesting a role of the phosphodianion in disfavoring intermediate release and in modulation of the on-enzyme isomerization equilibrium. The results of kinetic isotope effect and structural studies indicate rate limitation by physical steps when the covalent linkage is severed. These striking differences in the energetics of the natural reaction and the reactions in pieces provide a deeper insight into the contribution of enzyme-phosphodianion interactions to the reaction coordinate.
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Affiliation(s)
- Svetlana
A. Kholodar
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
| | - C. Leigh Allen
- Hauptman-Woodward
Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew M. Gulick
- Hauptman-Woodward
Institute and Department of Structural Biology, University at Buffalo, Buffalo, New York 14203-1102, United States
| | - Andrew S. Murkin
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260-3000, United States
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31
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Lin HC, Yandek LE, Gjermeni I, Harris ME. Determination of relative rate constants for in vitro RNA processing reactions by internal competition. Anal Biochem 2014; 467:54-61. [PMID: 25173512 DOI: 10.1016/j.ab.2014.08.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/08/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
Abstract
Studies of RNA recognition and catalysis typically involve measurement of rate constants for reactions of individual RNA sequence variants by fitting changes in substrate or product concentration to exponential or linear functions. A complementary approach is determination of relative rate constants by internal competition, which involves quantifying the time-dependent changes in substrate or product ratios in reactions containing multiple substrates. Here, we review approaches for determining relative rate constants by analysis of both substrate and product ratios and illustrate their application using the in vitro processing of precursor transfer RNA (tRNA) by ribonuclease P as a model system. The presence of inactive substrate populations is a common complicating factor in analysis of reactions involving RNA substrates, and approaches for quantitative correction of observed rate constants for these effects are illustrated. These results, together with recent applications in the literature, indicate that internal competition offers an alternate method for analyzing RNA processing kinetics using standard molecular biology methods that directly quantifies substrate specificity and may be extended to a range of applications.
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Affiliation(s)
- Hsuan-Chun Lin
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lindsay E Yandek
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ino Gjermeni
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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32
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Chan J, Sannikova N, Tang A, Bennet AJ. Transition-State Structure for the Quintessential SN2 Reaction of a Carbohydrate: Reaction of α-Glucopyranosyl Fluoride with Azide Ion in Water. J Am Chem Soc 2014; 136:12225-8. [DOI: 10.1021/ja506092h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jefferson Chan
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalia Sannikova
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Ariel Tang
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J. Bennet
- Chemistry Department, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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33
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Xiang S, Meyer MP. A general approach to mechanism in multiproduct reactions: product-specific intermolecular kinetic isotope effects. J Am Chem Soc 2014; 136:5832-5. [PMID: 24721128 DOI: 10.1021/ja412827c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Here we report a general method for the measurement of (13)C kinetic isotope effects at natural abundance for reactions that yield two or more products concurrently. We use, as an example, a recently reported Co-catalyzed reaction between cyclopentene and 1-phenyl-1-propyne. High-precision intermolecular (13)C isotope effects are reported for both the formal [2+2] cycloaddition (major) and Alder-ene (minor) reaction products. Mechanistic possibilities that are in accord with observed isotope effect measurements are discussed.
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Affiliation(s)
- Shuhuai Xiang
- Department of Chemistry and Biochemistry, University of California , Merced, California 95343, United States
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34
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Shidmoossavee FS, Watson JN, Bennet AJ. Chemical insight into the emergence of influenza virus strains that are resistant to Relenza. J Am Chem Soc 2013; 135:13254-7. [PMID: 24001125 DOI: 10.1021/ja405916q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A reagent panel containing ten 4-substituted 4-nitrophenyl α-D-sialosides and a second panel of the corresponding sialic acid glycals were synthesized and used to probe the inhibition mechanism for two neuraminidases, the N2 enzyme from influenza type A virus and the enzyme from Micromonospora viridifaciens. For the viral enzyme the logarithm of the inhibition constant (Ki) correlated with neither the logarithm of the catalytic efficiency (kcat/Km) nor catalytic proficiency (kcat/Km kun). These linear free energy relationship data support the notion that these inhibitors, which include the therapeutic agent Relenza, are not transition state mimics for the enzyme-catalyzed hydrolysis reaction. Moreover, for the influenza enzyme, a correlation (slope, 0.80 ± 0.08) is observed between the logarithms of the inhibition (Ki) and Michaelis (Km) constants. We conclude that the free energy for Relenza binding to the influenza enzyme mimics the enzyme-substrate interactions at the Michaelis complex. Thus, an influenza mutational response to a 4-substituted sialic acid glycal inhibitor can weaken the interactions between the inhibitor and the viral neuraminidase without a concomitant decrease in free energy of binding for the substrate at the enzyme-catalyzed hydrolysis transition state. The current findings make it clear that new structural motifs and/or substitution patterns need to be developed in the search for a bona fide influenza viral neuraminidase transition state analogue inhibitor.
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Affiliation(s)
- Fahimeh S Shidmoossavee
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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35
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Advances in kinetic isotope effect measurement techniques for enzyme mechanism study. Molecules 2013; 18:9278-92. [PMID: 23917115 PMCID: PMC6270257 DOI: 10.3390/molecules18089278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 07/22/2013] [Accepted: 07/29/2013] [Indexed: 11/17/2022] Open
Abstract
Kinetic isotope effects (KIEs) are a very powerful tool for investigating enzyme mechanisms. Precision of measurement is the most important factor for KIE determinations, especially for small heavy atom KIEs. Internal competition is commonly used to measure small KIEs on V/K. Several methods, including such as liquid scintillation counting, mass spectrometry, nuclear magnetic resonance spectroscopy and polarimetry have been used to determine KIEs. In this paper, which does not aspire to be an exhaustive review, we briefly review different experimental approaches for the measurement of KIEs on enzymatic reaction with an emphasis on newer techniques employing mass spectrometry and nuclear magnetic resonance spectrometry as well as some corresponding examples.
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36
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Huang X, Vocadlo DJ. Reports from the award symposia hosted by the American Chemical Society, Division of Carbohydrate Chemistry at the 245th American Chemical Society National Meeting. ACS Chem Biol 2013; 8:1361-5. [PMID: 24491206 DOI: 10.1021/cb400398f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We would like to congratulate all of the award winners for the well deserved honor. The award symposia provided a snapshot of some of the state-of-the-art research at the interface between chemistry and biology in the glycoscience field. The presentations serve as prime examples of the increasing integration of chemical and biological research in the area of glycoscience and how tools of chemistry can be applied to answer interesting, important, and fundamental biological questions. We look forward to many more years of exciting developments in the chemistry and chemical biology of glycoscience and anticipate improved tools and approaches will drive major advances while also spurring interests in the wider field.
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Affiliation(s)
- Xuefei Huang
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48864, United States
| | - David J. Vocadlo
- Departments of Chemistry, Molecular Biology, and Biochemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC, V5A 1S6, Canada
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37
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Liuni P, Olkhov-Mitsel E, Orellana A, Wilson DJ. Measuring kinetic isotope effects in enzyme reactions using time-resolved electrospray mass spectrometry. Anal Chem 2013; 85:3758-64. [PMID: 23461634 DOI: 10.1021/ac400191t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic isotope effect (KIE) measurements are a powerful tool for studying enzyme mechanisms; they can provide insights into microscopic catalytic processes and even structural constraints for transition states. However, KIEs have not come into widespread use in enzymology, due in large part to the requirement for prohibitively cumbersome experimental procedures and daunting analytical frameworks. In this work, we introduce time-resolved electrospray ionization mass spectrometry (TRESI-MS) as a straightforward, precise, and inexpensive method for measuring KIEs. Neither radioisotopes nor large amounts of material are needed and kinetic measurements for isotopically "labeled" and "unlabeled" species are acquired simultaneously in a single "competitive" assay. The approach is demonstrated first using a relatively large isotope effect associated with yeast alcohol dehydrogenase (YADH) catalyzed oxidation of ethanol. The measured macroscopic KIE of 2.19 ± 0.05 is consistent with comparable measurements in the literature but cannot be interpreted in a way that provides insights into isotope effects in individual microscopic steps. To demonstrate the ability of TRESI-MS to directly measure intrinsic KIEs and to characterize the precision of the technique, we measure a much smaller (12)C/(13)C KIE associated specifically with presteady state acylation of chymotrypsin during hydrolysis of an ester substrate.
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Affiliation(s)
- Peter Liuni
- Department of Chemistry, York University, Toronto, ON, Canada
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38
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A novel synthetic receptor-based immunoassay for influenza vaccine quantification. PLoS One 2013; 8:e55428. [PMID: 23424631 PMCID: PMC3570553 DOI: 10.1371/journal.pone.0055428] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 12/22/2012] [Indexed: 11/19/2022] Open
Abstract
Vaccination is the most effective prophylactic method for preventing influenza. Quantification of influenza vaccine antigens is critically important before the vaccine is used for human immunization. Currently the vaccine antigen quantification relies on hemagglutinin content quantification, the key antigenic component, by single radial immunodiffusion (SRID) assay. Due to the inherent disadvantages associated with the traditional SRID; i.e. low sensitivity, low throughput and need for annual reagents, several approaches have been proposed and investigated as alternatives. Yet, most alternative methods cannot distinguish native hemagglutinin from denatured form, making them less relevant to antigenic analyses. Here, we developed a quantitative immunoassay based on the sialic acid binding property of influenza vaccine antigens. Specifically, we chemically synthesized human and avian influenza virus receptors analogues, N-acetylneuraminic acid-2,6-lactose and N-acetylneuraminic acid-2,3-lactose derivatives with an azidopropyl aglycon, using α-2,6- and α-2,3-sialyltransferases, respectively. The azido group of the two sialyllactose-derivatives was reduced and conjugated to mouse serum albumin through a squarate linkage. We showed that the synthetic α-2,6- and α-2,3-receptors selectively bound to human and avian-derived hemagglutinins, respectively, forming the basis of a new, and robust assay for hemagglutinin quantification. Hemagglutinin treated at high temperature or low pH was measured differentially to untreated samples suggesting native conformation is dependent for optimal binding. Importantly, this receptor-based immunoassay showed excellent specificity and reproducibility, high precision, less turnaround time and significantly higher sensitivity and throughput compared with SRID in analyzing multiple influenza vaccines.
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39
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Kai H, Hinou H, Naruchi K, Matsushita T, Nishimura SI. Macrocyclic Mechanism-Based Inhibitor for Neuraminidases. Chemistry 2012; 19:1364-72. [DOI: 10.1002/chem.201200859] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 10/24/2012] [Indexed: 01/13/2023]
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40
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Manning KA, Sathyamoorthy B, Eletsky A, Szyperski T, Murkin AS. Highly precise measurement of kinetic isotope effects using 1H-detected 2D [13C,1H]-HSQC NMR spectroscopy. J Am Chem Soc 2012; 134:20589-92. [PMID: 23215000 DOI: 10.1021/ja310353c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new method is presented for measuring kinetic isotope effects (KIEs) by (1)H-detected 2D [(13)C,(1)H]-heteronuclear single quantum coherence (HSQC) NMR spectroscopy. The high accuracy of this approach was exemplified for the reaction catalyzed by glucose-6-phosphate dehydrogenase by comparing the 1-(13)C KIE with the published value obtained using isotope ratio mass spectrometry. High precision was demonstrated for the reaction catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis. 2-, 3-, and 4-(13)C KIEs were found to be 1.0031(4), 1.0303(12), and 1.0148(2), respectively. These KIEs provide evidence for a cleanly rate-limiting retroaldol step during isomerization. The high intrinsic sensitivity and signal dispersion of 2D [(13)C,(1)H]-HSQC offer new avenues to study challenging systems where low substrate concentration and/or signal overlap impedes 1D (13)C NMR data acquisition. Moreover, this approach can take advantage of highest-field spectrometers, which are commonly equipped for (1)H detection with cryogenic probes.
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Affiliation(s)
- Kathryn A Manning
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, USA
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41
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Kinetic isotope effects for studying post-translational modifying enzymes. Curr Opin Chem Biol 2012; 16:472-8. [PMID: 23146439 DOI: 10.1016/j.cbpa.2012.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 11/20/2022]
Abstract
The ongoing development of new experimental approaches for the measurement of isotope effects is improving our understanding of the physical and chemical changes that occur during biological catalysis. Biological catalysis involves numerous steps that include binding, conformational changes, chemical catalysis and product release. The critical points on the free energy surface for biologically catalyzed reactions include all bound intermediates and the intervening transition states. Isotope effects can be used to investigate both intermediate (equilibrium isotope effects) and transition state (kinetic isotope effects) structures along the reaction coordinate. This review details new techniques for measuring isotope effects and provides several examples of their use in solving transition state structures for post-translational modifying enzymes.
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42
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Lou M, Gilpin ME, Burger SK, Malik AM, Gawuga V, Popović V, Capretta A, Berti PJ. Transition state analysis of acid-catalyzed hydrolysis of an enol ether, enolpyruvylshikimate 3-phosphate (EPSP). J Am Chem Soc 2012; 134:12947-57. [PMID: 22765168 DOI: 10.1021/ja3043382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton transfer to carbon represents a significant catalytic challenge because of the large intrinsic energetic barrier and the frequently unfavorable thermodynamics. Multiple kinetic isotope effects (KIEs) were measured for acid-catalyzed hydrolysis of the enol ether functionality of enolpyruvylshikimate 3-phosphate (EPSP) as a nonenzymatic analog of the EPSP synthase (AroA) reaction. The large solvent deuterium KIE demonstrated that protonating C3 was the rate-limiting step, and the lack of solvent hydron exchange into EPSP demonstrated that protonation was irreversible. The reaction mechanism was stepwise, with C3, the methylene carbon, being protonated to form a discrete oxacarbenium ion intermediate before water attack at the cationic center, that is, an AH(‡)*AN (or AH(‡) + AN) mechanism. The calculated 3-(14)C and 3,3-(2)H2 KIEs varied as a function of the extent of proton transfer at the transition state, as reflected in the C3-H(+) bond order, nC3-H+. The calculated 3-(14)C KIE was a function primarily of C3 coupling with the movement of the transferring proton, as reflected in the reaction coordinate contribution ((light)ν(‡)/(heavy)ν(‡)), rather than of changes in bonding. Coupling was strongest in early and late transition states, where the reaction coordinate frequency was lower. The other calculated (14)C and (18)O KIEs were more sensitive to interactions with counterions and solvation in the model structures than nC3-H+. The KIEs revealed a moderately late transition state with significant oxacarbenium ion character and with a C3-H(+) bond order ≈0.6.
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Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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43
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Lou M, Burger SK, Gilpin ME, Gawuga V, Capretta A, Berti PJ. Transition State Analysis of Enolpyruvylshikimate 3-Phosphate (EPSP) Synthase (AroA)-Catalyzed EPSP Hydrolysis. J Am Chem Soc 2012; 134:12958-69. [PMID: 22765279 DOI: 10.1021/ja304339h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Steven K. Burger
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Meghann E. Gilpin
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Vivian Gawuga
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Alfredo Capretta
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul J. Berti
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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44
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Huang M, Garrett GE, Birlirakis N, Bohé L, Pratt DA, Crich D. Dissecting the mechanisms of a class of chemical glycosylation using primary ¹³C kinetic isotope effects. Nat Chem 2012; 4:663-7. [PMID: 22824899 PMCID: PMC3404748 DOI: 10.1038/nchem.1404] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 06/07/2012] [Indexed: 01/13/2023]
Abstract
Although arguably the most important reaction in glycoscience, chemical glycosylations are among the least well understood of organic chemical reactions, resulting in an unnecessarily high degree of empiricism and a brake on rational development in this critical area. To address this problem, primary (13)C kinetic isotope effects have now been determined for the formation of β- and α-manno- and glucopyranosides using a natural abundance NMR method. In contrast to the common current assumption, for three of the four cases studied the experimental and computed values are indicative of associative displacement of the intermediate covalent glycosyl trifluoromethanesulfonates. For the formation of the α-mannopyranosides, the experimentally determined KIE differs significantly from that computed for an associative displacement, which is strongly suggestive of a dissociative mechanism that approaches the intermediacy of a glycosyl oxocarbenium ion. The application of analogous experiments to other glycosylation systems should shed further light on their mechanisms and thus assist in the design of better reactions conditions with improved stereoselectivity.
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Affiliation(s)
- Min Huang
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, Avenue de Terrasse, 91198 Gif-sur-Yvette, France
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45
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Chan J, Lewis AR, Indurugalla D, Schur M, Wakarchuk W, Bennet AJ. Transition State Analysis of Vibrio cholerae Sialidase-Catalyzed Hydrolyses of Natural Substrate Analogues. J Am Chem Soc 2012; 134:3748-57. [DOI: 10.1021/ja208564y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jefferson Chan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Andrew R. Lewis
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Deepani Indurugalla
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
| | - Melissa Schur
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario,
Canada
| | - Warren Wakarchuk
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario,
Canada
| | - Andrew J. Bennet
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby,
British Columbia, V5A 1S6, Canada
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46
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Meyer MP. New Applications of Isotope Effects in the Determination of Organic Reaction Mechanisms. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2012. [DOI: 10.1016/b978-0-12-398484-5.00002-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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47
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Chan J, Tang A, Bennet AJ. A Stepwise Solvent-Promoted SNi Reaction of α-d-Glucopyranosyl Fluoride: Mechanistic Implications for Retaining Glycosyltransferases. J Am Chem Soc 2011; 134:1212-20. [DOI: 10.1021/ja209339j] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jefferson Chan
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
| | - Ariel Tang
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
| | - Andrew J. Bennet
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6,
Canada
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48
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Schramm VL. Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 2011; 80:703-32. [PMID: 21675920 DOI: 10.1146/annurev-biochem-061809-100742] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein's dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states.
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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49
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Pabis A, Kamiński R, Ciepielowski G, Jankowski S, Paneth P. Measurements of Heavy-Atom Isotope Effects Using 1H NMR Spectroscopy. J Org Chem 2011; 76:8033-5. [DOI: 10.1021/jo201226g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Pabis
- Institute of Applied Radiation Chemistry and ‡Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Rafał Kamiński
- Institute of Applied Radiation Chemistry and ‡Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Grzegorz Ciepielowski
- Institute of Applied Radiation Chemistry and ‡Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Stefan Jankowski
- Institute of Applied Radiation Chemistry and ‡Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Piotr Paneth
- Institute of Applied Radiation Chemistry and ‡Institute of Organic Chemistry, Faculty of Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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Lee SS, Hong SY, Errey JC, Izumi A, Davies GJ, Davis BG. Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase. Nat Chem Biol 2011; 7:631-8. [DOI: 10.1038/nchembio.628] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/10/2011] [Indexed: 01/14/2023]
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