1
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Lönnberg H. Structural modifications as tools in mechanistic studies of the cleavage of RNA phosphodiester linkages. CHEM REC 2022; 22:e202200141. [PMID: 35832010 DOI: 10.1002/tcr.202200141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/28/2022] [Indexed: 11/06/2022]
Abstract
The cleavage of RNA phosphodiester bonds by RNase A and hammerhead ribozyme at neutral pH fundamentally differs from the spontaneous reactions of these bonds under the same conditions. While the predominant spontaneous reaction is isomerization of the 3',5'-phosphodiester linkages to their 2',5'-counterparts, this reaction has never been reported to compete with the enzymatic cleavage reaction, not even as a minor side reaction. Comparative kinetic measurements with structurally modified di-nucleoside monophosphates and oligomeric phosphodiesters have played an important role in clarification of mechanistic details of the buffer-independent and buffer-catalyzed reactions. More recently, heavy atom isotope effects and theoretical calculations have refined the picture. The primary aim of all these studies has been to form a solid basis for mechanistic analyses of the action of more complicated catalytic machineries. In other words, to contribute to conception of a plausible unified picture of RNA cleavage by biocatalysts, such as RNAse A, hammerhead ribozyme and DNAzymes. In addition, structurally modified trinucleoside monophosphates as transition state models for Group I and II introns have clarified some features of the action of large ribozymes.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 University of, Turku
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2
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Czescik J, Mancin F, Strömberg R, Scrimin P. The Mechanism of Cleavage of RNA Phosphodiesters by a Gold Nanoparticle Nanozyme. Chemistry 2021; 27:8143-8148. [PMID: 33780067 PMCID: PMC8251847 DOI: 10.1002/chem.202100299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 01/08/2023]
Abstract
The cleavage of uridine 3'-phosphodiesters bearing alcohols with pKa ranging from 7.14 to 14.5 catalyzed by AuNPs functionalized with 1,4,7-triazacyclononane-Zn(II) complexes has been studied to unravel the source of catalysis by these nanosystems (nanozymes). The results have been compared with those obtained with two Zn(II) dinuclear catalysts for which the mechanism is fairly understood. Binding to the Zn(II) ions by the substrate and the uracil of uridine was observed. The latter leads to inhibition of the process and formation of less productive binding complexes than in the absence of the nucleobase. The nanozyme operates with these substrates mostly via a nucleophilic mechanism with little stabilization of the pentacoordinated phosphorane and moderate assistance in leaving group departure. This is attributed to a decrease of binding strength of the substrate to the catalytic site in reaching the transition state due to an unfavorable binding mode with the uracil. The nanozyme favors substrates with better leaving groups than the less acidic ones.
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Affiliation(s)
- Joanna Czescik
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
- Current address: School of Life and Health SciencesAston UniversityB4 7ETBirminghamUK
| | - Fabrizio Mancin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
| | | | - Paolo Scrimin
- Department of Chemical SciencesUniversity of PadovaVia Marzolo, 135131PadovaItaly
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3
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Erxleben A. Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned? Front Chem 2019; 7:82. [PMID: 30847339 PMCID: PMC6393734 DOI: 10.3389/fchem.2019.00082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.
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Affiliation(s)
- Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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4
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Phosphoryl-Transfer Reaction in RNA under Alkaline Conditions. Chemistry 2018; 24:13565-13572. [PMID: 29943454 DOI: 10.1002/chem.201802332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/20/2018] [Indexed: 11/09/2022]
Abstract
The phosphoryl-transfer reaction in RNA under alkaline conditions by exploring the influence of several solvents theoretically was studied. The calculations were carried out by using the M06-2X functional and the solvents were taken as a continuum by using the solvent model density (SMD) method. The main findings show that the O2'-P-O5' angle in the reactants, the free activation energies, and the reaction mechanism are clearly dependent on the dielectric constant of the environment, thus showing that the electrostatic term is the determining factor for this chemical system with two negative charges. Our study seems to indicate that water, the solvent with the greatest dielectric constant, would be the solvent that increases the reaction rate the most. As this outcome was not the case in enzymatic catalysis, one has to conclude that, in the case of proteins as well as for ribozymes, the enzymatic catalysis is not mainly due to the solvent reaction field, but to local electrical fields as a result of enzyme preorganization.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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5
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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6
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents? J Phys Chem A 2017; 121:8525-8534. [PMID: 29039953 DOI: 10.1021/acs.jpca.7b09156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.
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Affiliation(s)
- Carles Acosta-Silva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Joan Bertran
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Antoni Oliva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
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7
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Harris ME, York DM, Piccirilli JA, Anderson VE. Kinetic Isotope Effect Analysis of RNA 2′- O -Transphosphorylation. Methods Enzymol 2017; 596:433-457. [DOI: 10.1016/bs.mie.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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8
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Duarte F, Barrozo A, Åqvist J, Williams NH, Kamerlin SCL. The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis. J Am Chem Soc 2016; 138:10664-73. [PMID: 27471914 PMCID: PMC4999962 DOI: 10.1021/jacs.6b06277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite the numerous
experimental and theoretical studies on phosphate
monoester hydrolysis, significant questions remain concerning the
mechanistic details of these biologically critical reactions. In the
present work we construct a linear free energy relationship for phosphate
monoester hydrolysis to explore the effect of modulating leaving group
pKa on the competition between solvent-
and substrate-assisted pathways for the hydrolysis of these compounds.
Through detailed comparative electronic-structure studies of methyl
phosphate and a series of substituted aryl phosphate monoesters, we
demonstrate that the preferred mechanism is dependent on the nature
of the leaving group. For good leaving groups, a strong preference
is observed for a more dissociative solvent-assisted pathway. However,
the energy difference between the two pathways gradually reduces as
the leaving group pKa increases and creates
mechanistic ambiguity for reactions involving relatively poor alkoxy
leaving groups. Our calculations show that the transition-state structures
vary smoothly across the range of pKas
studied and that the pathways remain discrete mechanistic alternatives.
Therefore, while not impossible, a biological catalyst would have
to surmount a significantly higher activation barrier to facilitate
a substrate-assisted pathway than for the solvent-assisted pathway
when phosphate is bonded to good leaving groups. For poor leaving
groups, this intrinsic preference disappears.
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Affiliation(s)
- Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Nicholas H Williams
- Department of Chemistry, Sheffield University , Sheffield S3 7HF, United Kingdom
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
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9
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Lain L, Lönnberg H, Lönnberg TA. Buffer catalyzed cleavage of uridylyl-3',5'-uridine in aqueous DMSO: comparison to its activated analog, 2-hydroxypropyl 4-nitrophenyl phosphate. Org Biomol Chem 2015; 13:3484-92. [PMID: 25669674 DOI: 10.1039/c4ob02682a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Buffer catalysis of the cleavage and isomerization of uridylyl-3',5'-uridine (UpU) has been studied over a wide pH range in 80% aq. DMSO. The diminished hydroxide ion concentration in this solvent system made catalysis by amine buffers (morpholine, 4-hydroxypiperidine and piperidine) visible even at relatively low buffer concentrations (10-200 mmol L(-1)). The observed catalysis was, however, much weaker than what has been previously reported for the activated RNA model 2-hydroxypropyl 4-nitrophenyl phosphate (HPNP) in the same solvent system. In the case of morpholine, contribution of both the acidic and the basic buffer constituent was significant, whereas with 4-hydroxypiperidine and piperidine participation of the acidic constituent could not be established unambiguously. The results underline the importance of using realistic model compounds, along with activated ones, in the study of the general acid/base catalysis of RNA cleavage.
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Affiliation(s)
- L Lain
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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10
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Huang M, York DM. Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations. Phys Chem Chem Phys 2015; 16:15846-55. [PMID: 24961771 DOI: 10.1039/c4cp01050g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to transition state structure and bonding. Overall, results obtained from the polarizable continuum solvation model with UAKS radii produce the best linear correlations and closest overall agreement with experimental results. Reactions with a poor leaving group are predicted to proceed via a stepwise mechanism with a late transition state that is rate controlling. As leaving group becomes more acidic and labile, the barriers of both early and late transition states decrease. LFERs for each transition state are computed, with the late transition state barrier showing greater sensitivity to leaving group pKa. For sufficiently enhanced leaving groups, the reaction mechanism transits to a concerted mechanism characterized by a single early transition state. Further linear relationships were derived for bond lengths and bond orders as a function of leaving group pKa and rate constant values that can be used for prediction. This work provides important benchmark linear free energy data that allows a molecular-level characterization of the structure and bonding of the transition states for this important class of phosphoryl transfer reactions. The relations reported herein can be used to aid in the interpretation of data obtained from experimental studies of non-catalytic and catalytic mechanisms.
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Affiliation(s)
- Ming Huang
- Scientific Computation, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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11
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Harris ME, Piccirilli JA, York DM. Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1801-8. [PMID: 25936517 DOI: 10.1016/j.bbapap.2015.04.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/21/2023]
Abstract
The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, United States.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, United States; Department of Chemistry, University of Chicago, Chicago, IL 60637, United States
| | - Darrin M York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States
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12
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Chen H, Giese TJ, Huang M, Wong KY, Harris ME, York DM. Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions. Chemistry 2014; 20:14336-43. [PMID: 25223953 DOI: 10.1002/chem.201403862] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Indexed: 11/10/2022]
Abstract
Phosphoryl transfer reactions are ubiquitous in biology and the understanding of the mechanisms whereby these reactions are catalyzed by protein and RNA enzymes is central to reveal design principles for new therapeutics. Two of the most powerful experimental probes of chemical mechanism involve the analysis of linear free energy relations (LFERs) and the measurement of kinetic isotope effects (KIEs). These experimental data report directly on differences in bonding between the ground state and the rate-controlling transition state, which is the most critical point along the reaction free energy pathway. However, interpretation of LFER and KIE data in terms of transition-state structure and bonding optimally requires the use of theoretical models. In this work, we apply density-functional calculations to determine KIEs for a series of phosphoryl transfer reactions of direct relevance to the 2'-O-transphosphorylation that leads to cleavage of the phosphodiester backbone of RNA. We first examine a well-studied series of phosphate and phosphorothioate mono-, di- and triesters that are useful as mechanistic probes and for which KIEs have been measured. Close agreement is demonstrated between the calculated and measured KIEs, establishing the reliability of our quantum model calculations. Next, we examine a series of RNA transesterification model reactions with a wide range of leaving groups in order to provide a direct connection between observed Brønsted coefficients and KIEs with the structure and bonding in the transition state. These relations can be used for prediction or to aid in the interpretation of experimental data for similar non-enzymatic and enzymatic reactions. Finally, we apply these relations to RNA phosphoryl transfer catalyzed by ribonuclease A, and demonstrate the reaction coordinate-KIE correlation is reasonably preserved. A prediction of the secondary deuterium KIE in this reaction is also provided. These results demonstrate the utility of building up knowledge of mechanism through the systematic study of model systems to provide insight into more complex biological systems such as phosphoryl transfer enzymes and ribozymes.
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Affiliation(s)
- Haoyuan Chen
- Center for Integrative Proteomics Research, BioMaPS, Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854 (USA)
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13
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Kellerman DL, York DM, Piccirilli JA, Harris ME. Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Curr Opin Chem Biol 2014; 21:96-102. [PMID: 25023967 DOI: 10.1016/j.cbpa.2014.06.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Although there have been great strides in defining the mechanisms of RNA strand cleavage by 2'-O-transphosphorylation, long-standing questions remain. How do different catalytic modes such as acid/base and metal ion catalysis influence transition state charge distribution? Does the large rate enhancement characteristic of biological catalysis result in different transition states relative to solution reactions? Answering these questions is important for understanding biological catalysis in general, and revealing principles for designing small molecule inhibitors. Recent application of linear free energy relationships and kinetic isotope effects together with multi-scale computational simulations are providing tentative answers to these questions for this fundamentally important class of phosphoryl transfer reactions.
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Affiliation(s)
- Daniel L Kellerman
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, Piscataway, NJ, United States
| | - Joseph A Piccirilli
- Department of Biochemistry & Molecular Biology, and Chemistry, University of Chicago, Chicago, IL, United States
| | - Michael E Harris
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, United States.
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14
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Duarte F, Geng T, Marloie G, Al Hussain AO, Williams NH, Kamerlin SCL. The alkaline hydrolysis of sulfonate esters: challenges in interpreting experimental and theoretical data. J Org Chem 2014; 79:2816-28. [PMID: 24279349 PMCID: PMC3982930 DOI: 10.1021/jo402420t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Indexed: 01/12/2023]
Abstract
Sulfonate ester hydrolysis has been the subject of recent debate, with experimental evidence interpreted in terms of both stepwise and concerted mechanisms. In particular, a recent study of the alkaline hydrolysis of a series of benzene arylsulfonates (Babtie et al., Org. Biomol. Chem. 10, 2012, 8095) presented a nonlinear Brønsted plot, which was explained in terms of a change from a stepwise mechanism involving a pentavalent intermediate for poorer leaving groups to a fully concerted mechanism for good leaving groups and supported by a theoretical study. In the present work, we have performed a detailed computational study of the hydrolysis of these compounds and find no computational evidence for a thermodynamically stable intermediate for any of these compounds. Additionally, we have extended the experimental data to include pyridine-3-yl benzene sulfonate and its N-oxide and N-methylpyridinium derivatives. Inclusion of these compounds converts the Brønsted plot to a moderately scattered but linear correlation and gives a very good Hammett correlation. These data suggest a concerted pathway for this reaction that proceeds via an early transition state with little bond cleavage to the leaving group, highlighting the care that needs to be taken with the interpretation of experimental and especially theoretical data.
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Affiliation(s)
- Fernanda Duarte
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Ting Geng
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Gaël Marloie
- Department
of Cell and Molecular Biology, Uppsala University, Uppsala 751 05, Sweden
| | - Adel O. Al Hussain
- Department
of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Nicholas H. Williams
- Department
of Chemistry, The University of Sheffield, Sheffield S3 7HF, United Kingdom
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15
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Elsässer B, Fels G, Weare JH. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. J Am Chem Soc 2014; 136:927-36. [PMID: 24372083 DOI: 10.1021/ja406122c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
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Affiliation(s)
- Brigitta Elsässer
- Department of Chemistry, University of Paderborn , Warburgerstr. 100, D-33098 Paderborn, Germany
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16
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Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation. Proc Natl Acad Sci U S A 2013; 110:13002-7. [PMID: 23878223 DOI: 10.1073/pnas.1215086110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2'-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the (18)O KIEs on the 2'O nucleophile, 5'O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5'O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5'O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2'-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure.
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Korhonen H, Koivusalo T, Toivola S, Mikkola S. There is no universal mechanism for the cleavage of RNA model compounds in the presence of metal ion catalysts. Org Biomol Chem 2013; 11:8324-39. [DOI: 10.1039/c3ob41554f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Ora M, Martikainen K, Lautkoski K. Hydrolytic reactions of cyclic bis(3′-5′)diadenylic acid (c-di-AMP). J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.3070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mikko Ora
- University of Turku; Department of Chemistry; Turku Finland
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19
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Lönnberg T, Luomala M. Intracomplex general acid/base catalyzed cleavage of RNA phosphodiester bonds: the leaving group effect. Org Biomol Chem 2012; 10:6785-91. [PMID: 22825538 DOI: 10.1039/c2ob25958c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The general acid/base catalyzed cleavage of a number of alkyl esters of uridine-3'- (and -5'-)phosphate has been studied by utilizing a cleaving agent, in which the catalytic moiety (a substituted 1,3,5-triazine) is tethered to an anchoring Zn(II):cyclen moiety. Around pH 7, formation of a strong ternary complex between uracil, Zn(II) and cyclen brings the general acid/base catalyst close to the scissile phosphodiester linkage, resulting in rate acceleration of 1-2 orders of magnitude with the uridine-3'-phosphodiesters. Curiously, no acceleration was observed with their 5'-counterparts. A β(lg) value of -0.7 has been determined for the general acid/base catalyzed cleavage, consistent with a proton transfer to the leaving group in the rate-limiting step.
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Crystal structure and biochemical studies of the trans-acting polyketide enoyl reductase LovC from lovastatin biosynthesis. Proc Natl Acad Sci U S A 2012; 109:11144-9. [PMID: 22733743 DOI: 10.1073/pnas.1113029109] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lovastatin is an important statin prescribed for the treatment and prevention of cardiovascular diseases. Biosynthesis of lovastatin uses an iterative type I polyketide synthase (PKS). LovC is a trans-acting enoyl reductase (ER) that specifically reduces three out of eight possible polyketide intermediates during lovastatin biosynthesis. Such trans-acting ERs have been reported across a variety of other fungal PKS enzymes as a strategy in nature to diversify polyketides. How LovC achieves such specificity is unknown. The 1.9-Å structure of LovC reveals that LovC possesses a medium-chain dehydrogenase/reductase (MDR) fold with a unique monomeric assembly. Two LovC cocrystal structures and enzymological studies help elucidate the molecular basis of LovC specificity, define stereochemistry, and identify active-site residues. Sequence alignment indicates a general applicability to trans-acting ERs of fungal PKSs, as well as their potential application to directing biosynthesis.
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21
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Korhonen H, Williams NH, Mikkola S. βLG
values in mechanistic studies on the transesterification of RNA models and their application in a metal ion complex promoted transesterification. J PHYS ORG CHEM 2012. [DOI: 10.1002/poc.2942] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Heidi Korhonen
- Department of Chemistry; University of Turku; 20014 Turku Finland
| | - Nicholas H. Williams
- Centre for Chemical Biology, Department of Chemistry; University of Sheffield; S3 7HF UK
| | - Satu Mikkola
- Department of Chemistry; University of Turku; 20014 Turku Finland
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22
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Babtie AC, Lima MF, Kirby AJ, Hollfelder F. Kinetic and computational evidence for an intermediate in the hydrolysis of sulfonate esters. Org Biomol Chem 2012; 10:8095-101. [DOI: 10.1039/c2ob25699a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Lönnberg TA, Helkearo M, Jancsó A, Gajda T. Mimics of small ribozymes utilizing a supramolecular scaffold. Dalton Trans 2012; 41:3328-38. [DOI: 10.1039/c2dt10193a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Korhonen H, Mikkola S, Williams NH. The mechanism of cleavage and isomerisation of RNA promoted by an efficient dinuclear Zn2+ complex. Chemistry 2011; 18:659-70. [PMID: 22162262 DOI: 10.1002/chem.201100721] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Indexed: 11/11/2022]
Abstract
The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.
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Affiliation(s)
- Heidi Korhonen
- Department of Chemistry, 20014 University of Turku, Turku, Finland
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25
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Kirby AJ, Medeiros M, Oliveira PSM, Orth ES, Brandão TAS, Wanderlind EH, Amer A, Williams NH, Nome F. Activating Water: Important Effects of Non-leaving Groups on the Hydrolysis of Phosphate Triesters. Chemistry 2011; 17:14996-5004. [DOI: 10.1002/chem.201101926] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 11/09/2022]
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26
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Maxwell CI, Liu CT, Neverov AA, Mosey NJ, Brown RS. Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide-promoted cleavages of phosphorothioate and phosphate triesters in water and methanol. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - C. Tony Liu
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Robert Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
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27
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Ora M, Hanski A. Stepwise Mechanism of Hydroxide Ion Catalyzed Cyclization of Uridine 3′-Thiophosphates. Helv Chim Acta 2011. [DOI: 10.1002/hlca.201100115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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29
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Dellinger DJ, Timár Z, Myerson J, Sierzchala AB, Turner J, Ferreira F, Kupihár Z, Dellinger G, Hill KW, Powell JA, Sampson JR, Caruthers MH. Streamlined Process for the Chemical Synthesis of RNA Using 2′-O-Thionocarbamate-Protected Nucleoside Phosphoramidites in the Solid Phase. J Am Chem Soc 2011; 133:11540-56. [DOI: 10.1021/ja201561z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Douglas J. Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Timár
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Joel Myerson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Agnieszka B. Sierzchala
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - John Turner
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Fernando Ferreira
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Zoltán Kupihár
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Geraldine Dellinger
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Kenneth W. Hill
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - James A. Powell
- Agilent Nucleic Acids Solutions Division, 5555 Airport Boulevard, Suite 100, Boulder, Colorado 80301, United States
| | - Jeffrey R. Sampson
- Agilent Laboratories, Agilent Technologies, Inc., 5301 Stevens Creek Boulevard, Santa Clara, California 95051, United States
| | - Marvin H. Caruthers
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
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30
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Seiffert S, Debelak H, Hadwiger P, Jahn-Hofmann K, Roehl I, Vornlocher HP, Noll B. Characterization of side reactions during the annealing of small interfering RNAs. Anal Biochem 2011; 414:47-57. [PMID: 21376008 DOI: 10.1016/j.ab.2011.02.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 02/25/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
Abstract
Small interfering RNAs (siRNAs) are emerging as a novel therapeutic modality for the specific inhibition of target gene expression. The development of siRNA-based therapeutics requires in-depth knowledge of the manufacturing process as well as adequate analytical methods to characterize this class of molecules. Here the impurity formation during the annealing of siRNA was investigated. Two siRNAs containing common chemical RNA modifications (2'-O-methyl, 2'-deoxy-2'-fluoro, 2'-deoxy-ribose, and phosphorothioate linkages) were used to determine major side reactions-such as 2',3'-isomerization, strand scission, and HF elimination-depending on annealing parameters such as RNA concentration, presence of cations, temperature, and time. Individual impurities were characterized using analytical size exclusion chromatography, denaturing and nondenaturing ion-pair reversed-phase high-performance liquid chromatography, differential scanning calorimetry, and ultraviolet spectrometry. The degradation pathways described in this work can lead to significantly reduced product quality and compromised drug activity. The data reported here provide background to successfully address challenges associated with the manufacture of siRNAs and other nucleic acid therapeutics such as aptamers, spiegelmers, and decoy and antisense oligonucleotides.
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31
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Gao H, Ke Z, DeYonker NJ, Wang J, Xu H, Mao ZW, Phillips DL, Zhao C. Dinuclear Zn(II) Complex Catalyzed Phosphodiester Cleavage Proceeds via a Concerted Mechanism: A Density Functional Theory Study. J Am Chem Soc 2011; 133:2904-15. [DOI: 10.1021/ja106456u] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Hui Gao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zhuofeng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Nathan J. DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152-3550, United States
| | - Juping Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Huiying Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Cunyuan Zhao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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32
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Lönnberg H. Cleavage of RNA phosphodiester bonds by small molecular entities: a mechanistic insight. Org Biomol Chem 2011; 9:1687-703. [PMID: 21258754 DOI: 10.1039/c0ob00486c] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA molecules participate in many fundamental cellular processes either as a carrier of genetic information or as a catalyst, and hence, RNA has received increasing interest both as a chemotherapeutic agent and as a target of chemotherapy. In addition the dual nature of RNA has led to the RNA-world concept, i.e. an assumption that the evolution at an early stage of life was based on RNA-like oligomers that were responsible for the storage and transfer of information and as catalysts maintained primitive metabolism. Accordingly, the kinetics and mechanisms of the cleavage of RNA phosphodiester bonds have received interest and it is hoped they will shed light on the mechanisms of enzyme action and on the development of artificial enzymes. The major mechanistic findings concerning the cleavage by small molecules and ions and their significance for the development of efficient and biologically applicable artificial catalysts for RNA hydrolysis are surveyed in the present perspective.
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Affiliation(s)
- Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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33
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Harris ME, Dai Q, Gu H, Kellerman DL, Piccirilli JA, Anderson VE. Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: nucleophilic activation by specific base. J Am Chem Soc 2010; 132:11613-21. [PMID: 20669950 DOI: 10.1021/ja103550e] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary (18)O kinetic isotope effects (KIEs) and solvent D(2)O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed (18)O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group ((18)k(LG) = 1.034 +/- 0.004) and phosphorus-nucleophile bond formation ((18)k(NUC) = 0.984 +/- 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pK(a) of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 ((18)k(NUC) = 0.995 +/- 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (ca. 1.02) on deprotonation of the 2'-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary (18)O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis.
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Affiliation(s)
- Michael E Harris
- RNA Center and Departmet of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44118, USA.
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34
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Edwards DR, Tsang WY, Neverov AA, Brown RS. On the question of stepwise vs. concerted cleavage of RNA models promoted by a synthetic dinuclear Zn(ii) complex in methanol: implementation of a noncleavable phosphonate probe. Org Biomol Chem 2010; 8:822-7. [DOI: 10.1039/b918310h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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35
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Greig IR. The analysis of enzymic free energy relationships using kinetic and computational models. Chem Soc Rev 2010; 39:2272-301. [DOI: 10.1039/b902741f] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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36
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Dinuclear Zn(II) catalysts as biomimics of RNA and DNA phosphoryl transfer enzymes: changing the medium from water to alcohol provides enzyme-like rate enhancements. J PHYS ORG CHEM 2009. [DOI: 10.1002/poc.1584] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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37
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Tsang WY, Edwards DR, Melnychuk SA, Liu CT, Liu C, Neverov AA, Williams NH, Brown RS. Dinuclear Zn(II) Complex Promotes Cleavage and Isomerization of 2-Hydroxypropyl Alkyl Phosphates by a Common Cyclic Phosphate Intermediate. J Am Chem Soc 2009; 131:4159-66. [DOI: 10.1021/ja900525t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Wing Yin Tsang
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - David R. Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Stephanie A. Melnychuk
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Chaomin Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Nicholas H. Williams
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6, and Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
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38
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Humphry T, Iyer S, Iranzo O, Morrow JR, Richard JP, Paneth P, Hengge AC. Altered transition state for the reaction of an RNA model catalyzed by a dinuclear zinc(II) catalyst. J Am Chem Soc 2009; 130:17858-66. [PMID: 19053445 DOI: 10.1021/ja8059864] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclization of 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group ((18)k(lg) = 1.0064 +/- 0.0009 and (15)k = 1.0002 +/- 0.0002) and that nucleophilic bond formation occurs in the rate-determining step ((18)k(nuc) = 1.0326 +/- 0.0008). In the catalyzed reaction, larger leaving group isotope effects ((18)k(lg) = 1.0113 +/- 0.0005 and (15)k = 1.0015 +/- 0.0005) and a smaller nucleophile isotope effect ((18)k(nuc) = 1.0116 +/- 0.0010) indicate a later TS with greater leaving group bond fission and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2'-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.
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Affiliation(s)
- Tim Humphry
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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39
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Liu CT, Neverov AA, Brown RS. Biomimetic Cleavage of RNA Models Promoted by a Dinuclear Zn(II) Complex in Ethanol. Greater than 30 kcal/mol Stabilization of the Transition State for Cleavage of a Phosphate Diester. J Am Chem Soc 2008; 130:16711-20. [DOI: 10.1021/ja806462x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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40
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Harris ME, Cassano AG. Experimental analyses of the chemical dynamics of ribozyme catalysis. Curr Opin Chem Biol 2008; 12:626-39. [PMID: 18952193 DOI: 10.1016/j.cbpa.2008.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 10/13/2008] [Accepted: 10/13/2008] [Indexed: 11/30/2022]
Abstract
Most ribozymes in Nature catalyze alcoholysis or hydrolysis of RNA phosphodiester bonds. Studies of the corresponding non-enzymatic reactions reveal a complex mechanistic landscape allowing for a variety of transition states and both concerted and stepwise mechanisms. High-resolution structures, incisive biochemical studies and computer simulations are providing glimpses into how ribozyme catalyzed reactions traverse this landscape. However, direct experimental tests of mechanistic detail at the chemical level are not easily achieved. Kinetic isotope effects (KIEs) probe directly the differences in the vibrational 'environment' of the atoms undergoing chemical transformation on going from the ground state to the transition state. Thus, KIEs can in principle provide direct information about transition state bonding and so may be instrumental in evaluating possible transition states for ribozyme catalyzed reactions. Understanding charge distribution in the transition state may help resolve how rate acceleration is accomplished and perhaps the similarities and differences in how RNA and protein active sites operate. Several barriers to successful application of KIE analysis to ribozymes have recently been overcome, and new chemical details are beginning to emerge.
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Affiliation(s)
- Michael E Harris
- RNA Center and Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, USA.
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41
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Iyer S, Hengge AC. The effects of sulfur substitution for the nucleophile and bridging oxygen atoms in reactions of hydroxyalkyl phosphate esters. J Org Chem 2008; 73:4819-29. [PMID: 18533704 PMCID: PMC2575009 DOI: 10.1021/jo8002198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of sulfur substitution on the reactions of hydroxyalkyl phosphate esters are examined. These compounds are models for the intramolecular phosphoryl transfer reaction involved in the cleavage of the internucleotide bond in RNA. The models studied here lack the ribose ring and their conformational flexibility results in greater stability and the availability of different reaction pathways. Sulfur in the nucleophilic position shows no nucleophilic reaction at phosphorus, instead rapidly attacking at the beta carbon atom, forming thiirane with departure of a phosphomonoester. Sulfur substitution at either of the two bridging positions leads to cleavage of the diester via formation of a cyclic intermediate, but with significant rate acceleration when compared to the oxygen analogues. The bridge-substituted models react substantially slower than the analogous ribose compounds with sulfur substitution at comparable positions. Kinetic isotope effects reveal significant differences in the transition state depending on which bridging position sulfur occupies. When sulfur is in the scissile bridging position, a highly associative transition state is indicated, with a largely formed bond to the nucleophile and the scissile P-S bond is little changed. When sulfur occupies the other bridging position, the isotope effects imply a very early transition state in a concerted reaction.
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Affiliation(s)
- Subashree Iyer
- Utah State University, Department of Chemistry and Biochemistry, Logan, Utah 84322-0300, USA
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Neverov AA, Liu CT, Bunn SE, Edwards D, White CJ, Melnychuk SA, Brown RS. A Simple DNase Model System Comprising a Dinuclear Zn(II) Complex in Methanol Accelerates the Cleavage of a Series of Methyl Aryl Phosphate Diesters by 1011−1013. J Am Chem Soc 2008; 130:6639-49. [DOI: 10.1021/ja8006963] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - Shannon E. Bunn
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | - David Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
| | | | | | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada, K7L 3N6
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Bunn SE, Liu CT, Lu ZL, Neverov AA, Brown RS. The Dinuclear Zn(II) Complex Catalyzed Cyclization of a Series of 2-Hydroxypropyl Aryl Phosphate RNA Models: Progressive Change in Mechanism from Rate-Limiting P−O Bond Cleavage to Substrate Binding. J Am Chem Soc 2007; 129:16238-48. [DOI: 10.1021/ja076847d] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Shannon E. Bunn
- Contribution from the Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - C. Tony Liu
- Contribution from the Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Zhong-Lin Lu
- Contribution from the Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Contribution from the Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Contribution from the Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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44
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Razkin J, Nilsson H, Baltzer L. Catalysis of the cleavage of uridine 3'-2,2,2-trichloroethylphosphate by a designed helix-loop-helix motif peptide. J Am Chem Soc 2007; 129:14752-8. [PMID: 17985898 DOI: 10.1021/ja075478i] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle has been designed to catalyze the hydrolysis of phosphodiesters. The active site on the surface of the folded catalyst is composed of two histidine and four arginine residues, with the capacity to provide general acid, general base, and/or nucleophilic catalysis as well as transition state stabilization. Uridine 3'-2,2,2 trichloroethylphosphate (2) is a mimic of RNA with a leaving group pKa of 12.3. Its hydrolysis is energetically less favorable than that of commonly used model substrates with p-nitrophenyl leaving groups and therefore a more realistic model for the design of catalysts capable of cleaving RNA. The second-order rate constant for the hydrolysis of 2 at pH 7.0 by the polypeptide catalyst was 418 x 10(-6) M-1 s-1, and that of the imidazole catalyzed reaction was 1.66 x 10(-6) M-1 s-1. The pH dependence suggested that catalysis is due to the unprotonated form of a residue with a pKa of around 5.3, and the observed kinetic solvent isotope effect of 1.9 showed that there is significant hydrogen bonding in the transition state, consistent with general acid-base catalysis. The rate constant ratio k2(Pep)/k2(Im) of 252 is probably due to a combination of nucleophilic and general acid-base catalysis, as well as transition state stabilization. Substrate binding was weak since no sign of saturation kinetics was observed for substrate concentrations in the range from 5 to 40 mM. The results provide a platform for the further development of catalysts for RNA cleavage with a potential role in the development of drugs.
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Affiliation(s)
- Jesus Razkin
- Department of Applied Chemistry, Public University of Navarra, 31006 Pamplona, Navarra, Spain.
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45
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Ora M, Ojanperä J, Lönnberg H. Hydrolytic Reactions of Thymidine 5′-O-Phenyl-N-Alkylphosphoramidates, Models of Nucleoside 5′-Monophosphate Prodrugs. Chemistry 2007; 13:8591-9. [PMID: 17654626 DOI: 10.1002/chem.200700623] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To obtain detailed data on the kinetics of hydrolytic reactions of triester-like nucleoside 5'-O-aryl-N-alkylphosphoramidates, potential prodrugs of antiviral nucleoside monophosphates, the hydrolysis of diastereomeric (Rp/Sp) thymidine 5'-{O-phenyl-N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (3), a phosphoramidate derived from the methyl ester of L-alanine, has been followed by reversed-phase HPLC over the range from Ho=0 to pH 8 at 90 degrees C. According to the time-dependent product distributions, the hydrolysis of 3 proceeds at pH<4 by two parallel routes, namely by nucleophilic displacement of the alaninyl ester moiety by a water molecule and by hydrolysis of the carboxylic ester linkage that allows intramolecular attack of the carboxy group on the phosphorus atom, thereby resulting in the departure of either thymidine or phenol without marked accumulation of any intermediates. Both routes represent about half of the overall disappearance of 3. The departure of phenol eventually leads to the formation of thymidine 5'-phosphate. At pH>5, the predominant reaction is hydrolysis of the carboxylic ester linkage followed by intramolecular displacement of a phenoxide ion by the carboxylate ion and hydrolysis of the resulting cyclic mixed anhydride into an acyclic diester-like thymidine 5'-phosphoramidate. The latter product accumulated quantitatively without any indication of further decomposition. Hydroxide-ion-catalyzed P--OPh bond cleavage of the starting material 3 occurred as a side reaction. Comparative measurements with thymidine 5'-{N-[(1S)-2-oxo-2-methoxy-1-methylethyl]phosphoramidate} (4) revealed that, under acidic conditions, this diester-like compound is hydrolyzed by P--N bond cleavage three orders of magnitude more rapidly than the triester-like 3. At pH>5, the stability order is reversed, with 3 being hydrolyzed six times as rapidly as 4. Mechanisms of the partial reactions are discussed.
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Affiliation(s)
- Mikko Ora
- Department of Chemistry, University of Turku, 20014 Turku, Finland.
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46
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Mathews RA, Rossiter CS, Morrow JR, Richard JP. A minimalist approach to understanding the efficiency of mononuclear Zn(II) complexes as catalysts of cleavage of an RNA analog. Dalton Trans 2007:3804-11. [PMID: 17712447 DOI: 10.1039/b707409c] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mononuclear complexes between Zn(2+) and the following four macrocycles were prepared: 1,4,7,10-tetraazacyclododecane (1), 1-oxa-4,7,10-triazacyclododecane (2), 1,5,9-triazacyclododecane (3) and 1-hydroxyethyl-1,4,7-triazacyclononane (4). The pH rate profiles of values of the observed second-order rate constant log (k(Zn))(app) for Zn(X)(OH(2))-catalyzed cleavage (X = 1, 2, 3 and 4) of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) show downward breaks centered at the pK(a) for ionization of the respective zinc bound water. At low pH, where the rate acceleration for the catalyzed reaction is largest, the stabilizing interaction between the catalyst and the bound transition state is 5.7, 7.4, 7.4 and 5.9 kcal mol(-1) for the reactions catalyzed by Zn(1)(OH(2)), Zn(2)(OH(2)), Zn(3)(OH(2)) and Zn(4)(OH(2)), respectively. The interactions between the metal cation and the macrocycle cause either a modest increase or reduction in transition state stabilization compared with 6.6 kcal mol(-1) stabilization for catalysis by Zn(OH(2))(6). The best Zn(II)-macrocycle catalysts are those for which the interactions between the metal ion and macrocycle are the weakest. Inhibition studies show that each of the four catalysts form complexes with phosphate and oxalate dianions with a much higher affinity than diethyl phosphate monoanion, consistent with stronger interaction of the catalysts with the transition state dianion compared with the substrate monoanion HpPNP. The pH-dependence of methyl phosphate inhibition of Zn(2) catalyzed cleavage of HpPNP shows that only the Zn(2)(OH(2)) species binds the inhibitor. This result is consistent with a mechanism that has Zn(2)(OH(2)) as the active catalytic species.
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Affiliation(s)
- Ryan A Mathews
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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Fan Y, Gao YQ. A DFT Study on the Mechanism of Phosphodiester Cleavage Mediated by Monozinc Complexes. J Am Chem Soc 2007; 129:905-13. [PMID: 17243827 DOI: 10.1021/ja0660251] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (DFT), Tao-Perdew-Staroverov-Scuseria (TPSS), is employed to study the reaction mechanism for the zinc-mediated phosphodiester cleavage reaction. The calculations indicate a general base catalysis mechanism. The flexibility of Zn(II) ion's coordination number (5 and 6) as well as the formation of hydrogen bonds between the coordinating water and the ester are responsible for the trapping (namely, coordinating to the Zn complexes) of the phosphodiester. The hydrogen bonds, between the water, the ester, and the nitrogen-ligand, tris(6-amino-2-pyridylmethyl)amine, not only stabilize the key five-coordinated phosphorus intermediates with a trigonal pyramidal PO5 unit but also lower the energy barriers for the proton transfer within the complexes by gaining stronger solvation energies.
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Affiliation(s)
- Yubo Fan
- Department of Chemistry, Texas A & M University, College Station, Texas 77843-3255, USA
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48
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Wang Q, Lönnberg H. Simultaneous Interaction with Base and Phosphate Moieties Modulates the Phosphodiester Cleavage of Dinucleoside 3‘,5‘-Monophosphates by Dinuclear Zn2+Complexes of Di(azacrown) Ligands. J Am Chem Soc 2006; 128:10716-28. [PMID: 16910666 DOI: 10.1021/ja058806s] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Five dinucleating ligands (1-5) and one trinucleating ligand (6) incorporating 1,5,9-triazacyclododecan-3-yloxy groups attached to an aromatic scaffold have been synthesized. The ability of the Zn(2+) complexes of these ligands to promote the transesterification of dinucleoside 3',5'-monophosphates to a 2',3'-cyclic phosphate derived from the 3'-linked nucleoside by release of the 5'-linked nucleoside has been studied over a narrow pH range, from pH 5.8 to 7.2, at 90 degrees C. The dinuclear complexes show marked base moiety selectivity. Among the four dinucleotide 3',5'-phosphates studied, viz. adenylyl-3',5'-adenosine (ApA), adenylyl-3',5'-uridine (ApU), uridylyl-3',5'-adenosine (UpA), and uridylyl-3',5'-uridine (UpU), the dimers containing one uracil base (ApU and UpA) are cleaved up to 2 orders of magnitude more readily than those containing either two uracil bases (UpU) or two adenine bases (ApA). The trinuclear complex (6), however, cleaves UpU as readily as ApU and UpA, while the cleavage of ApA remains slow. UV spectrophotometric and (1)H NMR spectroscopic studies with one of the dinucleating ligands (3) verify binding to the bases of UpU and ApU at less than millimolar concentrations, while no interaction with the base moieties of ApA is observed. With ApU and UpA, one of the Zn(2+)-azacrown moieties in all likelihood anchors the cleaving agent to the uracil base of the substrate, while the other azacrown moiety serves as a catalyst for the phosphodiester transesterification. With UpU, two azacrown moieties are engaged in the base moiety binding. The catalytic activity is, hence, lost, but it can be restored by addition of a third azacrown group on the cleaving agent.
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Affiliation(s)
- Qi Wang
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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49
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Affiliation(s)
- W Wallace Cleland
- Institute for Enzyme Research and Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.
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50
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Lopez X, Dejaegere A, Leclerc F, York DM, Karplus M. Nucleophilic Attack on Phosphate Diesters: A Density Functional Study of In−Line Reactivity in Dianionic, Monoanionic, and Neutral Systems. J Phys Chem B 2006; 110:11525-39. [PMID: 16771429 DOI: 10.1021/jp0603942] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the hydrolysis reaction of phosphodiesters with a series of attacking nucleophiles in the gas phase and in solution is presented. The nucleophiles HOH, HO-, CH3OH, and CH3O- were studied in reactions with ethylene phosphate, 2'3'-ribose cyclic phosphate and in their neutral (protonated) and monoanionic forms. Stationary-point geometries for the reactions were determined at the density functional B3LYP/6-31++G(d,p) level followed by energy refinement at the B3LYP/6-311++G(3df,2p) level. Solvation effects were estimated by using a dielectric approximation with the polarizable continuum model (PCM) at the gas-phase optimized geometries. This series of reactions characterizes factors that influence the intrinsic reactivity of the model phosphate compounds, including the effect of nucleophile, protonation state, cyclic structure, and solvent. The present study of the in-line mechanism for phosphodiester hydrolysis, a reaction of considerable biological importance, has implications for enzymatic mechanisms. The analysis generally supports the associative mechanism for phosphate ester hydrolysis. The results highlight the importance for the reaction barrier of charge neutralization resulting from the protonation of the nonbridging phosphoryl oxygens and the role of internal hydrogen transfer in the gas-phase mechanism. It also shows that solvent stabilization has a profound influence on the relative barrier heights for the dianionic, monoanionic, and neutral reactions. The calculations provide a comprehensive data set for the in-line hydrolysis mechanisms that can be used for the development of improved semiempirical quantum models for phosphate hydrolysis reactions.
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Affiliation(s)
- Xabier Lopez
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Euskadi, Spain.
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