1
|
Weissman B, Ekesan Ş, Lin HC, Gardezi S, Li NS, Giese TJ, McCarthy E, Harris ME, York DM, Piccirilli JA. Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis. J Am Chem Soc 2023; 145:2830-2839. [PMID: 36706353 PMCID: PMC10112047 DOI: 10.1021/jacs.2c10079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Ribonucleases and small nucleolytic ribozymes are both able to catalyze RNA strand cleavage through 2'-O-transphosphorylation, provoking the question of whether protein and RNA enzymes facilitate mechanisms that pass through the same or distinct transition states. Here, we report the primary and secondary 18O kinetic isotope effects for hepatitis delta virus ribozyme catalysis that reveal a dissociative, metaphosphate-like transition state in stark contrast to the late, associative transition states observed for reactions catalyzed by specific base, Zn2+ ions, or ribonuclease A. This new information provides evidence for a discrete ribozyme active site design that modulates the RNA cleavage pathway to pass through an altered transition state.
Collapse
Affiliation(s)
- Benjamin Weissman
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Hsuan-Chun Lin
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shahbaz Gardezi
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Nan-Sheng Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Joseph A Piccirilli
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
2
|
Onyido I, Obumselu OF, Egwuatu CI, Okoye NH. Solvent and solvation effects on reactivities and mechanisms of phospho group transfers from phosphate and phosphinate esters to nucleophiles. Front Chem 2023; 11:1176746. [PMID: 37179775 PMCID: PMC10172589 DOI: 10.3389/fchem.2023.1176746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/03/2023] [Indexed: 05/15/2023] Open
Abstract
Organophosphorus esters fulfil many industrial, agricultural, and household roles. Nature has deployed phosphates and their related anhydrides as energy carriers and reservoirs, as constituents of genetic materials in the form of DNA and RNA, and as intermediates in key biochemical conversions. The transfer of the phosphoryl (PO3) group is thus a ubiquitous biological process that is involved in a variety of transformations at the cellular level such as bioenergy and signals transductions. Significant attention has been paid in the last seven decades to understanding the mechanisms of uncatalyzed (solution) chemistry of the phospho group transfer because of the notion that enzymes convert the dissociative transition state structures in the uncatalyzed reactions into associative ones in the biological processes. In this regard, it has also been proposed that the rate enhancements enacted by enzymes result from the desolvation of the ground state in the hydrophobic active site environments, although theoretical calculations seem to disagree with this position. As a result, some attention has been paid to the study of the effects of solvent change, from water to less polar solvents, in uncatalyzed phospho transfer reactions. Such changes have consequences on the stabilities of the ground and the transition states of reactions which affect reactivities and, sometimes, the mechanisms of reactions. This review seeks to collate and evaluate what is known about solvent effects in this domain, especially their effects on rates of reactions of different classes of organophosphorus esters. The outcome of this exercise shows that a systematized study of solvent effects needs to be undertaken to fully understand the physical organic chemistry of the transfer of phosphates and related molecules from aqueous to substantially hydrophobic environments, since significant knowledge gaps exist.
Collapse
|
3
|
Chen H, Snurr RQ. Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters. ACS APPLIED MATERIALS & INTERFACES 2020; 12:14631-14640. [PMID: 31909586 DOI: 10.1021/acsami.9b19484] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al2O2(OH)2@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.
Collapse
Affiliation(s)
- Haoyuan Chen
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Randall Q Snurr
- Department of Chemical & Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| |
Collapse
|
4
|
Rahman AB, Imafuku H, Miyazawa Y, Kafle A, Sakai H, Saga Y, Aoki S. Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Phosphatases Formed from a Monoalkylated Dizinc(II) Complex, Cyclic Diimide Units, and Copper(II) in Two-Phase Solvent System. Inorg Chem 2019; 58:5603-5616. [PMID: 30969761 DOI: 10.1021/acs.inorgchem.8b03586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Design and synthesis of enzyme mimic with programmed molecular interaction among several building blocks including metal complexes and metal chelators is of intellectual and practical significance. The preparation of artificial enzymes that mimic the natural enzymes such as hydrolases, phosphatases, etc. remains a great challenge in the field of supramolecular chemistry. Herein we report on the design and synthesis of asymmetric (nonsymmetric) supermolecules by the 2:2:2 self-assembly of an amphiphilic zinc(II)-cyclen complex containing a 2,2'-bipyridyl linker and one long alkyl chain (Zn2L3), barbital analogues, and Cu2+ as model compounds of an enzyme alkaline phosphatase that catalyzes the hydrolysis of phosphate monoesters such as mono(4-nitrophenyl)phosphate at neutral pH in two-phase solvent system (H2O/CHCl3) in pH 7.4 and 37 °C. Hydrolytic activity of these complexes was found to be catalytic, and their catalytic turnover numbers are 3-4. The mechanistic studies based on the UV/vis and emission spectra of the H2O and CHCl3 phases of the reaction mixtures suggest that the hydrophilicity/hydrophobicity balance of the supramolecular catalysts is an important factor for catalytic activity.
Collapse
|
5
|
Diez-Castellnou M, Martinez A, Mancin F. Phosphate Ester Hydrolysis: The Path From Mechanistic Investigation to the Realization of Artificial Enzymes. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2017. [DOI: 10.1016/bs.apoc.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
6
|
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]
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Zulkefeli M, Hisamatsu Y, Suzuki A, Miyazawa Y, Shiro M, Aoki S. Supramolecular Phosphatases Formed by the Self-Assembly of the Bis(Zn2+-Cyclen) Complex, Copper(II), and Barbital Derivatives in Water. Chem Asian J 2014; 9:2831-41. [DOI: 10.1002/asia.201402513] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/05/2014] [Indexed: 01/19/2023]
|
9
|
Massoud SS, Perkins RS, Louka FR, Xu W, Le Roux A, Dutercq Q, Fischer RC, Mautner FA, Handa M, Hiraoka Y, Kreft GL, Bortolotto T, Terenzi H. Efficient hydrolytic cleavage of plasmid DNA by chloro-cobalt(II) complexes based on sterically hindered pyridyl tripod tetraamine ligands: synthesis, crystal structure and DNA cleavage. Dalton Trans 2014; 43:10086-103. [PMID: 24872210 DOI: 10.1039/c4dt00615a] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Four new cobalt(ii) complexes [Co(6-MeTPA)Cl]ClO4/PF6 (2/2a), [Co(6-Me2TPA)Cl]ClO4/PF6 (3/3a), [Co(BPQA)Cl]ClO4/PF6 (4/4a) and [Co(BQPA)Cl]ClO4/PF6 (5/5a) as well as [Co(TPA)Cl]ClO4 (1) where TPA = tris(2-pyridylmethyl)amine, 6-MeTPA = ((6-methyl-2-pyridyl)methyl)bis(2-pyridylmethyl)amine, 6-Me2TPA = bis(6-methyl-2-pyridyl)methyl)-(2-pyridylmethyl)amine, BPQA = bis(2-pyridylmethyl)-(2-quinolylmethyl)-amine and BQPA = bis(2-quinolylmethyl)-(2-pyridylmethyl)amine were synthesized and structurally characterized. Single crystal X-ray crystallography confirmed the distorted trigonal bipyramidal geometries of complexes 2a-5a. Spectrophotometric titrations and conductivity measurements of the complexes in the CH3CN-H2O mixture showed that the chloro complexes exist in equilibrium with the corresponding hydrolyzed aqua species, [Co(L)(H2O)](2+). The pKa values of the coordinated H2O in aqua complexes vary from 8.4 to 8.7 (37 °C). The interactions of the complexes (1-5) with DNA have been investigated at pH = 7.0 and 9.0 (10 mM Tris-HCl buffer) and 37 °C where very high catalytic cleavage was observed. Under pseudo Michaelis-Menten kinetic conditions, the catalytic rate constants, kcat, decrease in the order 4>2>5>1>3. At pH 7.0 (10 mM Tris-HCl buffer) and 37 °C, the kcat value for complex 4 (6.02 h(-1)), where [Co(BPQA)(H2O)](2+) is the major species, corresponds to 170 million rate enhancement over the non-catalyzed DNA. Electrophoretic experiments conducted in the presence and absence of radical scavengers (DMSO, KI, NaN3) ruled out the oxidative mechanistic pathway of the reaction and suggested that the hydrolytic mechanism is the preferred one. This finding was in agreement with the observed increase in the kcat values at pH 9.0 compared to the corresponding values at pH 7.0 as a result of the increased concentration of the reactive hydroxo species, [Co(L)(OH)](+). The reactivity of the synthesized complexes in catalyzing the DNA cleavage is discussed in relation to the steric effect imposed by the coordinated pyridyl ligand around the central cobalt(ii) center.
Collapse
Affiliation(s)
- Salah S Massoud
- Department of Chemistry, University of Louisiana at Lafayette, P.O. Box 44370 Lafayette, LA 70504, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Basallote MG, Martínez M, Vázquez M. The role of hydroxo-bridged dinuclear species and the influence of “innocent” buffers in the reactivity of cis-[CoIII(cyclen)(H2O)2]3+ and [CoIII(tren)(H2O)2]3+ complexes with biologically relevant ligands at physiological pH. Dalton Trans 2014; 43:11048-58. [DOI: 10.1039/c4dt01003e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
11
|
Wu AZ, Wang T. Synthesis, crystal structures and phosphodiesterase activities of alkoxide-bridged asymmetric dinuclear nickel(II) complexes. TRANSIT METAL CHEM 2013. [DOI: 10.1007/s11243-013-9791-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
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.
Collapse
|
13
|
Duarte F, Amrein BA, Kamerlin SCL. Modeling catalytic promiscuity in the alkaline phosphatase superfamily. Phys Chem Chem Phys 2013; 15:11160-77. [PMID: 23728154 PMCID: PMC3693508 DOI: 10.1039/c3cp51179k] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/02/2013] [Indexed: 12/19/2022]
Abstract
In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution.
Collapse
Affiliation(s)
- Fernanda Duarte
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | - Beat Anton Amrein
- Uppsala University, Science for Life Laboratory (SciLifeLab), Cell and Molecular Biology, Uppsala, Sweden. ; ;
| | | |
Collapse
|
14
|
Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
Collapse
|
15
|
Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.
Collapse
Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, I -35131 Padova, Italy.
| | | | | |
Collapse
|
16
|
Lassila JK, Zalatan JG, Herschlag D. Biological phosphoryl-transfer reactions: understanding mechanism and catalysis. Annu Rev Biochem 2011; 80:669-702. [PMID: 21513457 DOI: 10.1146/annurev-biochem-060409-092741] [Citation(s) in RCA: 293] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phosphoryl-transfer reactions are central to biology. These reactions also have some of the slowest nonenzymatic rates and thus require enormous rate accelerations from biological catalysts. Despite the central importance of phosphoryl transfer and the fascinating catalytic challenges it presents, substantial confusion persists about the properties of these reactions. This confusion exists despite decades of research on the chemical mechanisms underlying these reactions. Here we review phosphoryl-transfer reactions with the goal of providing the reader with the conceptual and experimental background to understand this body of work, to evaluate new results and proposals, and to apply this understanding to enzymes. We describe likely resolutions to some controversies, while emphasizing the limits of our current approaches and understanding. We apply this understanding to enzyme-catalyzed phosphoryl transfer and provide illustrative examples of how this mechanistic background can guide and deepen our understanding of enzymes and their mechanisms of action. Finally, we present important future challenges for this field.
Collapse
Affiliation(s)
- Jonathan K Lassila
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA.
| | | | | |
Collapse
|
17
|
Zulkefeli M, Suzuki A, Shiro M, Hisamatsu Y, Kimura E, Aoki S. Selective Hydrolysis of Phosphate Monoester by a Supramolecular Phosphatase Formed by the Self-Assembly of a Bis(Zn2+-cyclen) Complex, Cyanuric Acid, and Copper in an Aqueous Solution (Cyclen = 1,4,7,10-Tetraazacyclododecane). Inorg Chem 2011; 50:10113-23. [DOI: 10.1021/ic201072q] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mohd Zulkefeli
- Faculty of Pharmacy, Universiti Teknologi MARA, Puncak Alam, Selangor 42300, Malaysia
| | | | - Motoo Shiro
- X-ray Research Laboratory, Rigaku Corporation, 3-9-12 Matsubaracho, Akishima, Tokyo 196-8666, Japan
| | | | - Eiichi Kimura
- Faculty of Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | | |
Collapse
|
18
|
Liu CT, Neverov AA, Brown RS. Palladacycle-Promoted Solvolytic Cleavage of O,O-Dimethyl O-Aryl Phosphorothioates. Converting a Phosphorane-Like Transition State to an Observable Intermediate. Inorg Chem 2011; 50:7852-62. [DOI: 10.1021/ic201062h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
19
|
Kamerlin SCL, Wilkie J. The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis. Org Biomol Chem 2011; 9:5394-406. [PMID: 21655563 DOI: 10.1039/c0ob01210f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present 2-dimensional potential energy surfaces and optimised transition states (TS) for water attack on a series of substituted phosphate monoester monoanions at the DFT level of theory, comparing a standard 6-31++g(d,p) basis set with a larger triple-zeta (augmented cc-pVTZ) basis set. Small fluorinated model compounds are used to simulate increasing leaving group stability without adding further geometrical complexity to the system. We demonstrate that whilst changing the leaving group causes little qualitative change in the potential energy surfaces (with the exception of the system with the most electron withdrawing leaving group, CF(3)O(-), in which the associative pathway changes from a stepwise A(N) + D(N) pathway to a concerted A(N)D(N) pathway), there is a quantitative change in relative gas-phase and solution barriers for the two competing pathways. In line with previous studies, in the case of OCH(3), the barriers for the associative and dissociative pathways are similar in solution, and the two pathways are equally viable and indistinguishable in solution. However, significantly increasing the stability of the leaving group (decreasing proton affinity, PA) results in the progressive favouring of a stepwise dissociative, D(N) + A(N), mechanism over associative mechanisms.
Collapse
Affiliation(s)
- Shina C L Kamerlin
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
| | | |
Collapse
|
20
|
Ren YW, Lu JX, Cai BW, Shi DB, Jiang HF, Chen J, Zheng D, Liu B. A novel asymmetric di-Ni(ii) system as a highly efficient functional model for phosphodiesterase: synthesis, structures, physicochemical properties and catalytic kinetics. Dalton Trans 2011; 40:1372-81. [DOI: 10.1039/c0dt01194k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
21
|
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.
Collapse
Affiliation(s)
- Michael E Harris
- RNA Center and Departmet of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44118, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Brandão TAS, Hengge AC, Johnson SJ. Insights into the reaction of protein-tyrosine phosphatase 1B: crystal structures for transition state analogs of both catalytic steps. J Biol Chem 2010; 285:15874-83. [PMID: 20236928 PMCID: PMC2871455 DOI: 10.1074/jbc.m109.066951] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 03/03/2010] [Indexed: 11/06/2022] Open
Abstract
Catalysis by protein-tyrosine phosphatase 1B (PTP1B) occurs through a two-step mechanism involving a phosphocysteine intermediate. We have solved crystal structures for the transition state analogs for both steps. Together with previously reported crystal structures of apo-PTP1B, the Michaelis complex of an inactive mutant, the phosphoenzyme intermediate, and the product complex, a full picture of all catalytic steps can now be depicted. The transition state analog for the first catalytic step comprises a ternary complex between the catalytic cysteine of PTP1B, vanadate, and the peptide DADEYL, a fragment of a physiological substrate. The equatorial vanadate oxygen atoms bind to the P-loop, and the apical positions are occupied by the peptide tyrosine oxygen and by the PTP1B cysteine sulfur atom. The vanadate assumes a trigonal bipyramidal geometry in both transition state analog structures, with very similar apical O-O distances, denoting similar transition states for both phosphoryl transfer steps. Detailed interactions between the flanking peptide and the enzyme are discussed.
Collapse
Affiliation(s)
- Tiago A. S. Brandão
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Alvan C. Hengge
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Sean J. Johnson
- From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300
| |
Collapse
|
23
|
Liu CT, Neverov AA, Maxwell CI, Brown RS. Demonstration of Prominent Cu(II)-Promoted Leaving Group Stabilization of the Cleavage of a Homologous Set of Phosphate Mono-, Di-, and Triesters in Methanol. J Am Chem Soc 2010; 132:3561-73. [DOI: 10.1021/ja910111q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | | | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| |
Collapse
|
24
|
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]
|
25
|
Dong H. A computational study towards understanding the mechanism of phosphodiester cleavage by two mononuclear Zn(ii) complexes. Phys Chem Chem Phys 2010; 12:10434-43. [DOI: 10.1039/c004064a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
26
|
Yamamichi H. Verification of the Mechanism of Phosphoryl Transfer Reactions and Development of Artificial Enzymes for the Reactions. J SYN ORG CHEM JPN 2010. [DOI: 10.5059/yukigoseikyokaishi.68.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
27
|
Feng G, Tanifum EA, Adams H, Hengge AC, Williams NH. Mechanism and transition state structure of aryl methylphosphonate esters doubly coordinated to a dinuclear cobalt(III) center. J Am Chem Soc 2009; 131:12771-9. [PMID: 19673521 DOI: 10.1021/ja904134n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Reactivities of five phosphonate esters each coordinated to a dinuclear Co(III) complex were investigated ([Co(2)(tacn)(2)(OH)(2){O(2)P(Me)OAr}](3+); tacn = 1,4,7-triazacyclononane; substituent = m-F, p-NO(2) (1a); p-NO(2) (1b); m-NO(2) (1c); p-Cl (1d); unsubstituted (1e)). Hydrolysis of the phosphonate esters in 1a to 1e is specific base catalyzed and takes place by intramolecular oxide attack on the bridging phosphonate. These data define a Brønsted beta(lg) of -1.12, considerably more negative than that of the hydrolysis of the uncomplexed phosphonates (-0.69). For 1b, the kinetic isotope effects in the leaving group are (18)k(lg) = 1.0228 and (15)k = 1.0014, at the nonbridging phosphoryl oxygens (18)k(nonbridge) = 0.9954, and at the nucleophilic oxygen(18)k(nuc) = 1.0105. The KIEs and the beta(lg) data point to a transition state for the alkaline hydrolysis of 1b that is similar to that of a phosphate monoester complex with the same leaving group, rather than the isoelectronic diester complex. The data from these model systems parallel the observation that in protein phosphatase-1, which has an active site that resembles the structures of these complexes, the catalyzed hydrolysis of aryl methylphosphonates and aryl phosphates are much more similar to one another than the uncomplexed hydrolysis reactions of the two substrates.
Collapse
Affiliation(s)
- Guoqiang Feng
- University of Sheffield, Centre for Chemical Biology, Department of Chemistry, Sheffield, UK S3 7HF
| | | | | | | | | |
Collapse
|
28
|
Mautner FA, Taylor ER, Rozas DM, Massoud SS. Synthesis and structural characterization of dicopper(II) and dipalladium(II) complexes of 1,1,2,2-tetrakis(carboxamido-2-methylpyridyl)ethane. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
29
|
Edwards DR, Liu CT, Garrett GE, Neverov AA, Brown RS. Leaving Group Assistance in the La3+-Catalyzed Cleavage of Dimethyl (o-Methoxycarbonyl)aryl Phosphate Triesters in Methanol. J Am Chem Soc 2009; 131:13738-48. [DOI: 10.1021/ja904659e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- David R. Edwards
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - C. Tony Liu
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Graham E. Garrett
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| |
Collapse
|
30
|
Mautner FA, Grebowicz J, Deifik PJ, Perkins RS, Massoud SS. Structural characterization of copper(II) complexes based on a new 10-membered binucleating 1,6-diazecine ligand. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.05.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
31
|
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]
|
32
|
Frederiksen JK, Piccirilli JA. Identification of catalytic metal ion ligands in ribozymes. Methods 2009; 49:148-66. [PMID: 19651216 DOI: 10.1016/j.ymeth.2009.07.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/20/2009] [Accepted: 07/29/2009] [Indexed: 01/05/2023] Open
Abstract
Site-bound metal ions participate in the catalytic mechanisms of many ribozymes. Understanding these mechanisms therefore requires knowledge of the specific ligands on both substrate and ribozyme that coordinate these catalytic metal ions. A number of different structural and biochemical strategies have been developed and refined for identifying metal ion binding sites within ribozymes, and for assessing the catalytic contributions of the metal ions bound at those sites. We review these approaches and provide examples of their application, focusing in particular on metal ion rescue experiments and their roles in the construction of the transition state models for the Tetrahymena group I and RNase P ribozymes.
Collapse
Affiliation(s)
- John K Frederiksen
- The Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | | |
Collapse
|
33
|
Kamerlin SCL, Haranczyk M, Warshel A. Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models. Chemphyschem 2009; 10:1125-34. [PMID: 19301306 DOI: 10.1002/cphc.200800753] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phosphate hydrolysis is ubiquitous in biology. However, despite intensive research on this class of reactions, the precise nature of the reaction mechanism remains controversial. Herein, we have examined the hydrolysis of three homologous phosphate diesters. The solvation free energy was simulated by means of either an implicit solvation model (COSMO), hybrid quantum mechanical/molecular mechanical free energy perturbation (QM/MM-FEP) or a mixed solvation model in which N water molecules were explicitly included in the ab initio description of the reacting system (where N=1-3), with the remainder of the solvent being implicitly modelled as a continuum. Here, both COSMO and QM/MM-FEP reproduce DeltaG(obs) within an error of about 1 kcal mol(-1). However, we demonstrate that in order to obtain any kind of reliable results from a mixed model, it is essential to carefully select the explicit water molecules from short QM/MM runs that act as a model for the true infinite system. Additionally, the mixed models tend to be increasingly unstable and miss larger entropic contributions as more explicit water molecules are placed into the system. Thus, our analysis indicates that this approach provides an unreliable way for modelling phosphate hydrolysis in solution.
Collapse
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles, CA 90089, USA.
| | | | | |
Collapse
|
34
|
Xu W, Louka FR, Doulain PE, Landry CA, Mautner FA, Massoud SS. Hydrolytic cleavage of DNA promoted by cobalt(III)–tetraamine complexes: Synthesis and characterization of carbonatobis[2-(2-pyridylethyl)]-(2-pyridylmethyl)aminecobalt(III) perchlorate. Polyhedron 2009. [DOI: 10.1016/j.poly.2009.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
35
|
Edwards DR, Neverov AA, Brown RS. Dissociative solvolytic cleavage of methyl (ortho-carboxymethyl)aryl phosphate diesters mediated by Yb3+ in methanol gives a 10(12)-fold rate acceleration attributable to leaving group assistance. J Am Chem Soc 2009; 131:368-77. [PMID: 19055404 DOI: 10.1021/ja807984f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David R Edwards
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada, K7L 3N6
| | | | | |
Collapse
|
36
|
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
| |
Collapse
|
37
|
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.
Collapse
Affiliation(s)
- Michael E Harris
- RNA Center and Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44118, USA.
| | | |
Collapse
|
38
|
Singh UP, Babbar P, Tyagi P, Weyhermüller T. A mononuclear cobalt(II) hydroxo complex: synthesis, molecular structure, and reactivity studies. TRANSIT METAL CHEM 2008. [DOI: 10.1007/s11243-008-9143-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
39
|
Ma Y, Lu G. A Calcium(II)-Based l-Arginine for ATP Binding and Hydrolysis. J Inorg Organomet Polym Mater 2008. [DOI: 10.1007/s10904-008-9225-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
40
|
Murugavel R, Choudhury A, Walawalkar MG, Pothiraja R, Rao CNR. Metal Complexes of Organophosphate Esters and Open-Framework Metal Phosphates: Synthesis, Structure, Transformations, and Applications. Chem Rev 2008; 108:3549-655. [DOI: 10.1021/cr000119q] [Citation(s) in RCA: 278] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. Murugavel
- Department of Chemistry, IIT-Bombay, Powai, Mumbai-400076, India, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Center of Advanced Scientific Research, Jakkur P.O., Bangalore-560 064, India
| | - Amitava Choudhury
- Department of Chemistry, IIT-Bombay, Powai, Mumbai-400076, India, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Center of Advanced Scientific Research, Jakkur P.O., Bangalore-560 064, India
| | - M. G. Walawalkar
- Department of Chemistry, IIT-Bombay, Powai, Mumbai-400076, India, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Center of Advanced Scientific Research, Jakkur P.O., Bangalore-560 064, India
| | - R. Pothiraja
- Department of Chemistry, IIT-Bombay, Powai, Mumbai-400076, India, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Center of Advanced Scientific Research, Jakkur P.O., Bangalore-560 064, India
| | - C. N. R. Rao
- Department of Chemistry, IIT-Bombay, Powai, Mumbai-400076, India, and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Center of Advanced Scientific Research, Jakkur P.O., Bangalore-560 064, India
| |
Collapse
|
41
|
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
| |
Collapse
|
42
|
|
43
|
Taran O, Medrano F, Yatsimirsky AK. Rapid hydrolysis of model phosphate diesters by alkaline-earth cations in aqueous DMSO: speciation and kinetics. Dalton Trans 2008:6609-18. [DOI: 10.1039/b807030j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
44
|
Anilinolysis of Diphenyl Thiophosphinic Chloride and Theoretical Studies on Various R 1R 2P(O or S)Cl. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.11.2003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
45
|
|
46
|
Pepi F, Barone V, Cimino P, Ricci A. Gas-Phase Chemistry of Diphosphate Anions as a Tool To Investigate the Intrinsic Requirements of Phosphate Ester Enzymatic Reactions: The [M1M2HP2O7]− Ions. Chemistry 2007; 13:2096-108. [PMID: 17143922 DOI: 10.1002/chem.200601093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Experimental studies on gaseous inorganic phosphate ions are practically nonexistent, yet they can prove helpful for a better understanding of the mechanisms of phosphate ester enzymatic processes. The present contribution extends our previous investigations on the gas-phase ion chemistry of diphosphate species to the [M(1)M(2)HP(2)O(7)](-) ions where M(1) and M(2) are the same or different and correspond to the Li, Na, K, Cs, and Rb cations. The diphosphate ions are formed by electrospray ionization of 10(-4) M solutions of Na(5)P(3)O(10) in CH(3)CN/H(2)O (1/1) and MOH bases or M salts as a source of M(+) cations. The joint application of mass spectrometric techniques and quantum-mechanical calculations makes it possible to characterize the gaseous [M(1)M(2)HP(2)O(7)](-) ions as a mixed ionic population formed by two isomeric species: linear diphosphate anion coordinated to two M(+) cations (group I) and [PO(3)M(1)M(2)HPO(4)](-) clusters (group II). The relative gas-phase stabilities and activation barriers for the isomerization I-->II, which depend on the nature of the M(+) cations, highlight the electronic susceptibility of P-O-P bond breaking in the active site of enzymes. The previously unexplored gas-phase reactivity of [M(1)M(2)HP(2)O(7)](-) ions towards alcohols of different acidity was investigated by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The reaction proceeds by addition of the alcohol molecule followed by elimination of a water molecule.
Collapse
Affiliation(s)
- Federico Pepi
- Dipartamento di Studi di Chimica e Tecnologia delle Sostanze Biologicamente Attive, Università degli Studi di Roma La Sapienza, Piazzale A. Moro 5, 00185 Rome, Italy
| | | | | | | |
Collapse
|
47
|
Abstract
Many phosphatases make use of metal ions to aid catalysis of phosphate ester hydrolysis. Here, we investigate the impact of metal ions on the potential energy surface (PES), and hence the preferred reaction mechanism, for a simple model for hydrolysis of phosphate ester monoanions. We show that, while both associative (A(N) + D(N)) and dissociative (D(N) + A(N)) mechanisms are represented on the potential energy surfaces both in the presence and absence of metal ions, the D(N) + A(N) process is favoured when there are no metal ions present and the A(N) + D(N) process is favoured in the presence of two metal ions. A concerted (A(N)D(N)) process is also available in the presence of two metal ions, but proceeds via a high-energy transition state. In the presence of only a single metal ion the A(N)D(N) process is the most favoured, but still proceeds via a high-energy transition state. Thus, we conclude that metallo-enzyme phosphatases are likely to utilise an associative process, while those that function without metal ions may well follow a dissociative process.
Collapse
Affiliation(s)
- Shina C L Kamerlin
- University of Vienna, Institute of Biomolecular Structural Chemistry, Vienna, Austria.
| | | |
Collapse
|
48
|
Rawlings J, Cleland WW, Hengge AC. Metal-Catalyzed Phosphodiester Cleavage: Secondary 18O Isotope Effects as an Indicator of Mechanism. J Am Chem Soc 2006; 128:17120-5. [PMID: 17177465 DOI: 10.1021/ja065931a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Information about the transition states of metal-catalyzed hydrolysis reactions of model phosphate compounds has been obtained through determination of isotope effects (IEs) on the hydrolysis reactions. Metal complexation has been found to significantly alter the transition state of the reaction from the alkaline hydrolysis reaction, and the transition state is quite dependent on the particular metal ion used. For the diester, ethyl p-nitrophenyl phosphate, the nonbridge 18O effect for the hydrolysis reactions catalyzed by Co(III) 1,5,9-triazacyclononane and Eu(III) were 1.0006 and 1.0016, respectively, indicative of a slightly associative transition state and little net change in bonding to the nonbridge oxygen. The reaction catalyzed by Zn(II) 1,4,7,10-tetraazacyclododecane had an 18O nonbridge IE of 1.0108, showing the reaction differs significantly from the reaction of the noncomplexed diester and resembles the reactions of triesters. Reaction with Co(III) 1,4,7,10-tetraazacyclododecane showed an inverse effect of 0.9948 reflecting the effects of bonding of the diester to the Co(III). Lanthanide-catalyzed hydrolysis has been observed to have unusually large 15N effects. To further investigate this effect, the 15N effect on the reaction catalyzed by Ce(IV) bis-Tris propane solutions at pH 8 was determined to be 1.0012. The 15N effects were also measured for the reaction of the monoester p-nitrophenyl phosphate by Ce(IV) bis-Tris propane (1.0014) and Eu(III) bis-Tris propane (1.0012). These smaller effects at pH 8 indicate that a smaller negative charge develops on the nitrogen during the hydrolysis reaction.
Collapse
Affiliation(s)
- Jill Rawlings
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53726, USA
| | | | | |
Collapse
|
49
|
Gómez K, González G, Martínez M, Mendoza C, Sienra B. Absence of phosphate hydrolysis in the nucleotide substitution reaction on cis-[Co(H2O)2(cyclen)]3+ at physiological pH: Importance of hydrogen-bonding and conjugate base-catalysis. Polyhedron 2006. [DOI: 10.1016/j.poly.2006.06.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
50
|
Aullón G, Bernhardt PV, Bozoglian F, Font-Bardía M, Macpherson BP, Martínez M, Rodríguez C, Solans X. Isomeric Distribution and Catalyzed Isomerization of Cobalt(III) Complexes with Pentadentate Macrocyclic Ligands. Importance of Hydrogen Bonding. Inorg Chem 2006; 45:8551-62. [PMID: 17029366 DOI: 10.1021/ic060720s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the isomeric distribution and rearrangement of complexes of the type [CoXLn]2+,3+ (where X = Cl-, OH-, H2O, and Ln represents a pentadentate 13-, 14-, and 15-membered tetra-aza or diaza-dithia (N4 or N2S2) macrocycle bearing a pendant primary amine). The preparative procedures for chloro complexes produced almost exclusively kinetically preferred cis isomers (where the pendant primary amine is cis to the chloro ligand) that can be separated by careful cation-exchange chromatography. For L13 and L14 the so-called cis-V isomer is isolated as the kinetic product, and for L15 the cis-VI form (an N-based diastereomer) is the preferred, while for the L14(S) complex both cis-V and trans-I forms are obtained. All these complexes rearrange to form stable trans isomers in which the pendent primary amine is trans to the monodentate aqua or hydroxo ligand, depending on pH and the workup procedure. In total 11 different complexes have been studied. From these, two different trans isomers of [CoClL14(S)]2+ have been characterized crystallographically for the first time in addition to a new structure of cis-V-[CoClL14(S)]2+; all were isolated as their chloride perchlorate salts. Two additional isomers have been identified and characterized by NMR as reaction intermediates. The remaining seven forms correspond to the complexes already known, produced in preparative procedures. The kinetic, thermal, and baric activation parameters for all the isomerization reactions have been determined and involve large activation enthalpies and positive volumes of activation. Activation entropies indicate a very important degree of hydrogen bonding in the reactivity of the complexes, confirmed by density functional theory studies on the stability of the different isomeric forms. The isomerization processes are not simple and even some unstable intermediates have been detected and characterized as part of the above-mentioned 11 forms of the complexes. A common reaction mechanism for the isomerization reactions has been proposed for all the complexes derived from the observed kinetic and solution behavior.
Collapse
Affiliation(s)
- Gabriel Aullón
- Departament de Química Inorgànica, Universitat de Barcelona, Martí i Franquès 1-11, E-08028 Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|