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Szántó JK, Dietschreit JCB, Shein M, Schütz AK, Ochsenfeld C. Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment. J Chem Theory Comput 2024; 20:2433-2444. [PMID: 38497488 DOI: 10.1021/acs.jctc.3c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.
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Affiliation(s)
- Judit Katalin Szántó
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mikhail Shein
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Anne K Schütz
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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2
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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.
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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
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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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Zhang H, Yang L, Ding W, Ma Y. Theoretical Studies on the Catalytic Cycle of Histidine Acid Phosphatases Revealing an Acid Proof Mechanism. J Phys Chem B 2018; 122:7530-7538. [DOI: 10.1021/acs.jpcb.8b04808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, P. R. China
| | - Ling Yang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Wanjian Ding
- College of Chemistry, Beijing Normal University, Beijing 100086, P. R. China
| | - Yingying Ma
- Institute of Mining Technology, Inner Mongolia University of Technology. Hohhot 010051, P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation. Hohhot 010051, P. R. China
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5
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Mota CS, Gonçalves AMD, de Sanctis D. Deinococcus radiodurans DR2231 is a two-metal-ion mechanism hydrolase with exclusive activity on dUTP. FEBS J 2016; 283:4274-4290. [PMID: 27739259 DOI: 10.1111/febs.13923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/27/2016] [Accepted: 10/11/2016] [Indexed: 02/04/2023]
Abstract
DR2231 from Deinococcus radiodurans was previously functionally and structurally characterized as an all-α NTP pyrophosphohydrolase with specific dUTPase activity. dUTPases have a central role in the regulation of dUTP intracellular levels and dTTP nucleotide metabolism. DR2231 presents a conserved dimetal catalytic site, similar to all-α dimeric dUTPases, but contrary to these enzymes, it is unable to process dUDP. In this article, we present functional and structural evidence of single-point mutations that affect directly or indirectly the enzyme catalysis and provide a complete description of the all-α NTP pyrophosphohydrolase mechanism. Activity assays, isothermal titration calorimetry and the crystal structures of these mutants obtained in complex with dUMP or a dUTP analogue aid in probing the reaction mechanism. Our results demonstrate that the two metals are necessary for enzyme processing and also important to modulate the substrate binding affinity. Single-point mutations located in a structurally mobile lid-like loop show that the interactions with the nucleoside monophosphate are essential for induction of the closed conformation and ultimately for substrate processing. β- and γ-phosphates are held in place through coordination with the second metal, which is responsible for the substrate 'gauche' orientation in the catalytic position. The lack of sufficient contacts to orient the dUDP β-phosphate for hydrolysis explains DR2231 preference towards dUTP. Sequence and structural similarities with MazG proteins suggest that a similar mechanism might be conserved within the protein family. DATABASE Structural data are available in the PDB under the accession numbers 5HVA, 5HWU, 5HX1, 5HYL, 5I0J, 5HZZ, 5I0M.
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Affiliation(s)
| | - Ana Maria D Gonçalves
- Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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6
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Bredeston LM, González Flecha FL. The promiscuous phosphomonoestearase activity of Archaeoglobus fulgidus CopA, a thermophilic Cu+ transport ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1471-8. [PMID: 27086711 DOI: 10.1016/j.bbamem.2016.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/01/2016] [Accepted: 04/13/2016] [Indexed: 11/19/2022]
Abstract
Membrane transport P-type ATPases display two characteristic enzymatic activities: a principal ATPase activity provides the driving force for ion transport across biological membranes, whereas a promiscuous secondary activity catalyzes the hydrolysis of phosphate monoesters. This last activity is usually denoted as the phosphatase activity of P-ATPases. In the present study, we characterize the phosphatase activity of the Cu(+)-transport ATPase from Archaeglobus fulgidus (Af-CopA) and compare it with the principal ATPase activity. Our results show that the phosphatase turnover number was 20 times higher than that corresponding to the ATPase activity, but it is compensated by a high value of Km, producing a less efficient catalysis for pNPP. This secondary activity is enhanced by Mg(2+) (essential activator) and phospholipids (non-essential activator), and inhibited by salts and Cu(+). Transition state analysis of the catalyzed and noncatalyzed hydrolysis of pNPP indicates that Af-CopA enhances the reaction rates by a factor of 10(5) (ΔΔG(‡)=38 kJ/mol) mainly by reducing the enthalpy of activation (ΔΔH(‡)=30 kJ/mol), whereas the entropy of activation is less negative on the enzyme than in solution. For the ATPase activity, the decrease in the enthalpic component of the barrier is higher (ΔΔH(‡)=39 kJ/mol) and the entropic component is small on both the enzyme and in solution. These results suggest that different mechanisms are involved in the transference of the phosphoryl group of p-nitrophenyl phosphate and ATP.
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Affiliation(s)
- Luis M Bredeston
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - F Luis González Flecha
- Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.
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7
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Esteves LF, Rey NA, Dos Santos HF, Costa LAS. Theoretical Proposal for the Whole Phosphate Diester Hydrolysis Mechanism Promoted by a Catalytic Promiscuous Dinuclear Copper(II) Complex. Inorg Chem 2016; 55:2806-18. [DOI: 10.1021/acs.inorgchem.5b02604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas F. Esteves
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Nicolás A. Rey
- Laboratório
de Síntese Orgânica e Quı́mica de Coordenação
Aplicada a Sistemas Biológicos (LABSO-BIO), Departamento de
Quı́mica, Centro Técnico Científico (CTC), PUC-Rio, 22453-900 Rio de Janeiro, Rio
de Janeiro, Brazil
| | - Hélio F. Dos Santos
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
| | - Luiz Antônio S. Costa
- NEQC (Núcleo de Estudos em Quı́mica
Computacional), Departamento de Quı́mica, Instituto de
Ciências Exatas (ICE), Universidade Federal de Juiz de Fora, Campus Universitário
Martelos, 36036-900 Juiz de Fora, Minas Gerais, Brazil
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8
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Carvalho ATP, Szeler K, Vavitsas K, Åqvist J, Kamerlin SCL. Modeling the mechanisms of biological GTP hydrolysis. Arch Biochem Biophys 2015; 582:80-90. [PMID: 25731854 DOI: 10.1016/j.abb.2015.02.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/19/2015] [Accepted: 02/21/2015] [Indexed: 01/11/2023]
Abstract
Enzymes that hydrolyze GTP are currently in the spotlight, due to their molecular switch mechanism that controls many cellular processes. One of the best-known classes of these enzymes are small GTPases such as members of the Ras superfamily, which catalyze the hydrolysis of the γ-phosphate bond in GTP. In addition, the availability of an increasing number of crystal structures of translational GTPases such as EF-Tu and EF-G have made it possible to probe the molecular details of GTP hydrolysis on the ribosome. However, despite a wealth of biochemical, structural and computational data, the way in which GTP hydrolysis is activated and regulated is still a controversial topic and well-designed simulations can play an important role in resolving and rationalizing the experimental data. In this review, we discuss the contributions of computational biology to our understanding of GTP hydrolysis on the ribosome and in small GTPases.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Klaudia Szeler
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre (CPSC), Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-751 24 Uppsala, Sweden
| | - 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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Zhang X, Zhu Y, Gao H, Zhao C. Solvolysis Mechanisms of RNA Phosphodiester Analogues Promoted by Mononuclear Zinc(II) Complexes: Mechanisic Determination upon Solvent Medium and Ligand Effects. Inorg Chem 2014; 53:11903-12. [DOI: 10.1021/ic501084a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xuepeng Zhang
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Yajie Zhu
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
| | - Hui Gao
- Key
Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute
of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, P. R. China
| | - Cunyuan Zhao
- MOE
Key Laboratory of Bioinorganic and Synthetic Chemistry, School of
Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, P. R. China
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10
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Zhang X, Zheng X, Phillips DL, Zhao C. Mechanistic investigation of the cleavage of phosphodiester catalyzed by a symmetrical oxyimine-based macrocyclic dinuclear zinc complex: a DFT study. Dalton Trans 2014; 43:16289-99. [DOI: 10.1039/c4dt01491j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Zhang X, Xu X, Xu H, Zhang X, Phillips DL, Zhao C. Mechanistic Investigation into the Cleavage of a Phosphomonoester Mediated by a Symmetrical Oxyimine-Based Macrocyclic Zinc(II) Complex. Chemphyschem 2014; 15:1887-98. [DOI: 10.1002/cphc.201301216] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/24/2014] [Indexed: 11/08/2022]
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12
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Zhang X, Zhu Y, Zheng X, Phillips DL, Zhao C. Mechanismic Investigation on the Cleavage of Phosphate Monoester Catalyzed by Unsymmetrical Macrocyclic Dinuclear Complexes: The Selection of Metal Centers and the Intrinsic Flexibility of the Ligand. Inorg Chem 2014; 53:3354-61. [DOI: 10.1021/ic402717x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xuepeng Zhang
- 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, People’s Republic of China
| | - Yajie Zhu
- 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, People’s Republic of China
| | - Xiaowei Zheng
- 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, People’s Republic of China
| | - David Lee Phillips
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, People’s Republic of 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, People’s Republic of China
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13
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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.
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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. ; ;
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14
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Abstract
Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been identified by in vitro selection for various catalytic activities. Expanding the limits of DNA catalysis is an important fundamental objective and may facilitate practical utility of catalysts that can be obtained from entirely unbiased (random) sequence populations. In this study, we show that DNA can catalyze Zn(2+)-dependent phosphomonoester hydrolysis of tyrosine and serine side chains (i.e., exhibit phosphatase activity). The best deoxyribozyme decreases the half-life for phosphoserine hydrolysis from as high as >10(10) y to <1 h. The phosphatase activity also occurs with nonpeptidic substrates but with reduced efficiency, indicating a preference for phosphopeptides. The newly identified deoxyribozymes can function with multiple turnover using free peptide substrates, have activity in the presence of human cell lysate or BSA, and catalyze dephosphorylation of a larger protein substrate, suggesting broader application of DNA catalysts as artificial phosphatases.
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Abstract
Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, 'Why Nature Chose Phosphate' (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that nature really chose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.
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16
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Rahimian M, Gejji SP. Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3'-O, 5'-S) thymidine phosphodiester derivatives. J Mol Model 2012; 19:1027-37. [PMID: 23111685 DOI: 10.1007/s00894-012-1630-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
Abstract
Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3'-O, 5'-S) thymidine phosphodiester (Tp-ST) (1), 3'-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH(2)CF(3)) (2), 3'-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3'-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO(2))) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A(N)D(N)) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol(-1)) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.
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17
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Luo J, van Loo B, Kamerlin SCL. Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: a comparison to analogous phosphatases. Proteins 2012; 80:1211-26. [PMID: 22275090 DOI: 10.1002/prot.24020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 12/25/2022]
Abstract
Pseudomonas aeruginosa arylsulfatase (PAS) is a bacterial sulfatase capable of hydrolyzing a range of sulfate esters. Recently, it has been demonstrated to also show very high proficiency for phosphate ester hydrolysis. Such proficient catalytic promiscuity is significant, as promiscuity has been suggested to play an important role in enzyme evolution. Additionally, a comparative study of the hydrolyses of the p-nitrophenyl phosphate and sulfate monoesters in aqueous solution has demonstrated that despite superficial similarities, the two reactions proceed through markedly different transition states with very different solvation effects, indicating that the requirements for the efficient catalysis of the two reactions by an enzyme will also be very different (and yet they are both catalyzed by the same active site). This work explores the promiscuous phosphomonoesterase activity of PAS. Specifically, we have investigated the identity of the most likely base for the initial activation of the unusual formylglycine hydrate nucleophile (which is common to many sulfatases), and demonstrate that a concerted substrate-as-base mechanism is fully consistent with the experimentally observed data. This is very similar to other related systems, and suggests that, as far as the phosphomonoesterase activity of PAS is concerned, the sulfatase behaves like a "classical" phosphatase, despite the fact that such a mechanism is unlikely to be available to the native substrate (based on pK(a) considerations and studies of model systems). Understanding such catalytic versatility can be used to design novel artificial enzymes that are far more proficient than the current generation of designer enzymes.
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Affiliation(s)
- Jinghui Luo
- Department of Cell and Molecular Biology (ICM), Uppsala University, Uppsala Biomedical Center (BMC), Uppsala, Sweden
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18
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Theoretical investigation of the enzymatic phosphoryl transfer of β-phosphoglucomutase: revisiting both steps of the catalytic cycle. J Mol Model 2012; 18:3169-79. [PMID: 22238068 DOI: 10.1007/s00894-011-1344-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
Abstract
Enzyme catalyzed phosphate transfer is a part of almost all metabolic processes. Such reactions are of central importance for the energy balance in all organisms and play important roles in cellular control at all levels. Mutases transfer a phosphoryl group while nucleases cleave the phosphodiester linkages between two nucleotides. The subject of our present study is the Lactococcus lactis β-phosphoglucomutase (β-PGM), which effectively catalyzes the interconversion of β-D-glucose-1-phosphate (β-G1P) to β-D-glucose-6-phosphate (β-G6P) and vice versa via stabile intermediate β-D-glucose-1,6-(bis)phosphate (β-G1,6diP) in the presence of Mg(2+). In this paper we revisited the reaction mechanism of the phosphoryl transfer starting from the bisphosphate β-G1,6diP in both directions (toward β-G1P and β-G6P) combining docking techniques and QM/MM theoretical method at the DFT/PBE0 level of theory. In addition we performed NEB (nudged elastic band) and free energy calculations to optimize the path and to identify the transition states and the energies involved in the catalytic cycle. Our calculations reveal that both steps proceed via dissociative pentacoordinated phosphorane, which is not a stabile intermediate but rather a transition state. In addition to the Mg(2+) ion, Ser114 and Lys145 also play important roles in stabilizing the large negative charge on the phosphate through strong coordination with the phosphate oxygens and guiding the phosphate group throughout the catalytic process. The calculated energy barrier of the reaction for the β-G1P to β-G1,6diP step is only slightly higher than for the β-G1,6diP to β-G6P step (16.10 kcal mol(-1) versus 15.10 kcal mol(-1)) and is in excellent agreement with experimental findings (14.65 kcal mol(-1)).
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Kamerlin SCL. Theoretical Comparison of p-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer. J Org Chem 2011; 76:9228-38. [DOI: 10.1021/jo201104v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Re S, Sugita Y. [Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method]. YAKUGAKU ZASSHI 2011; 131:1171-82. [PMID: 21804320 DOI: 10.1248/yakushi.131.1171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes, in particular the nature of transition state (TS), remains a subject of active debate. Structural evidence supports an associative TS, whereas physical organic studies point to a dissociative character. In this article, we briefly introduce our recent effort using the hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to resolve the controversy. We perform QM/MM simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP), which belongs to one of the largest phosphotransferase families characterized to data. Both phosphorylation and dephosphorylation reactions are investigated based on the two-dimensional energy surfaces along phosphoryl and proton transfer coordinates. The resultant structures of the active site at TS in both reactions have compact geometries but a less electron density of the phosphoryl group. This suggests that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database searches on phosphotransferases suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, Saitama, Japan
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21
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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.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
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Re S, Imai T, Jung J, Ten-No S, Sugita Y. Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation. J Comput Chem 2010; 32:260-70. [DOI: 10.1002/jcc.21615] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Elsässer B, Fels G. Atomistic details of the associative phosphodiester cleavage in human ribonuclease H. Phys Chem Chem Phys 2010; 12:11081-8. [PMID: 20672157 DOI: 10.1039/c001097a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During translation of the genetic information of DNA into proteins, mRNA is synthesized by RNA polymerase and after the transcription process degraded by RNase H. The endoribonuclease RNase H is a member of the nucleotidyl-transferase (NT) superfamily and is known to hydrolyze the phosphodiester bonds of RNA which is hybridized to DNA. Retroviral RNase H is part of the viral reverse transcriptase enzyme that is indispensable for the proliferation of retroviruses, such as HIV. Inhibitors of this enzyme could therefore provide new drugs against diseases like AIDS. In our study we investigated the molecular mechanism of RNA cleavage by human RNase H using a comprehensive high level DFT/B3LYP QM/MM theoretical method for the calculation of the stationary points and nudged elastic band (NEB) and free energy calculations to identify the transition state structures, the rate limiting step and the reaction barrier. Our calculations reveal that the catalytic mechanism proceeds in two steps and that the nature of the nucleophile is a water molecule. In the first step, the water attack on the scissile phosphorous is followed by a proton transfer from the water to the O2P oxygen and a trigonal bipyramidal pentacoordinated phosphorane is formed. Subsequently, in the second step the proton is shuttled to the O3' oxygen to generate the product state. During the reaction mechanism two Mg(2+) ions support the formation of a stable associated in-line S(N)2-type phosphorane intermediate. Our calculated energy barrier of 19.3 kcal mol(-1) is in excellent agreement with experimental findings (20.5 kcal mol(-1)). These results may contribute to the clarification and understanding of the RNase H reaction mechanism and of further enzymes from the RNase family.
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Affiliation(s)
- Brigitta Elsässer
- Department of Organic Chemistry, University of Paderborn, Warburgerstr. 100, D-33098, Paderborn, Germany.
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Imagawa H, Oda M, Takemoto T, Yamauchi R, Yoshikawa T, Yamamoto H, Nishizawa M, Takahashi H, Hashimoto M, Yabiku K, Nagahama M, Sakurai J. Synthesis and evaluation of novel phosphate ester analogs as neutral sphingomyelinase inhibitors. Bioorg Med Chem Lett 2010; 20:3868-71. [PMID: 20627555 DOI: 10.1016/j.bmcl.2010.05.042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 05/08/2010] [Accepted: 05/12/2010] [Indexed: 11/28/2022]
Abstract
A novel sphingomyelin inhibitor RY221B-a, which contains a bipyridyl moiety as a metal coordination site was designed based upon the mechanism of phosphate ester hydrolysis. RY221B-a was synthesized from N-Boc-sphingosine in three steps via selective etherification using stannyl acetal. Synthesized RY221B-a exhibited relatively-strong inhibitory activity against Bc-SMase (IC(50)=1.2microM).
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25
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Rucker R, Oelschlaeger P, Warshel A. A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases. Proteins 2010; 78:671-80. [PMID: 19842163 DOI: 10.1002/prot.22596] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
DNA polymerase beta (pol beta) is a small eukaryotic enzyme with the ability to repair short single-stranded DNA gaps that has found use as a model system for larger replicative DNA polymerases. For all DNA polymerases, the factors determining their catalytic power and fidelity are the interactions between the bases of the base pair, amino acids near the active site, and the two magnesium ions. In this report, we study effects of all three aspects on human pol beta transition state (TS) binding free energies by reproducing a consistent set of experimentally determined data for different structures. Our calculations comprise the combination of four different base pairs (incoming pyrimidine nucleotides incorporated opposite both matched and mismatched purines) with four different pol beta structures (wild type and three mutants). We generate three fragments of the incoming deoxynucleoside 5'-triphosphate-TS and run separate calculations for the neutral base part and the highly charged triphosphate part, using different dielectric constants in order to account for the specific dielectric response. This new approach improves our ability to predict the effect of matched and mismatched base pairing and of mutations in DNA polymerases on fidelity and may be a useful tool in studying the potential of DNA polymerase mutations in the development of cancer. It also supports our point of view with regards to the origin of the structural control of fidelity, allowing for a quantified description of the fidelity of DNA polymerases.
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Affiliation(s)
- Robert Rucker
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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Dupureur CM. One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies. Metallomics 2010; 2:609-20. [PMID: 21072352 DOI: 10.1039/c0mt00013b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Cynthia M Dupureur
- Department of Chemistry & Biochemistry and The Center for Nanoscience, University of Missouri-St. Louis, One University Blvd., St. Louis, MO 63121, USA.
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27
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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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Alkherraz A, Kamerlin SCL, Feng G, Sheikh QI, Warshel A, Williams NH. Phosphate ester analogues as probes for understanding enzyme catalysed phosphoryl transfer. Faraday Discuss 2010. [DOI: 10.1039/b908398g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ferreira DEC, Florentino BPD, Rocha WR, Nome F. Quantum Mechanical/Effective Fragment Potential (QM/EFP) Study of Phosphate Monoester Aminolysis in Aqueous Solution. J Phys Chem B 2009; 113:14831-6. [DOI: 10.1021/jp907014r] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Dalva E. C. Ferreira
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Bruno P. D. Florentino
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Willian R. Rocha
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Faruk Nome
- LQC-MM: Laboratório de Química Computacional e Modelagem Molecular, Departamento de Química, ICEx, Universidade Federal de Minas Gerais, Campus Universitário, Pampulha, Belo Horizonte, MG 31270-901, Brazil, and LACFI: Laboratório de Catálise e Fenômenos Interfaciais Departamento de Química, Universidade Federal de Santa Catarina, Campus Trindade, Florianópolis, Santa Catarina 88040-900, Brazil
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Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. J Comput Chem 2009; 30:1634-41. [PMID: 19462398 PMCID: PMC3098573 DOI: 10.1002/jcc.21312] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations.
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Affiliation(s)
- Edina Rosta
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
| | - H. Lee Woodcock
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892-9314, U.S.A
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892-9314, U.S.A
| | - Gerhard Hummer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
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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.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave., Los Angeles, CA 90089, USA.
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Kamerlin SCL, McKenna CE, Goodman MF, Goondman MF, Warshel A. A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. Biochemistry 2009; 48:5963-71. [PMID: 19391628 DOI: 10.1021/bi900140c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerases make up a family of enzymes responsible for regulating DNA replication and repair, which in turn maintains the integrity of the genome. However, despite intensive kinetic, crystallographic, and computational studies, elucidation of the detailed enzymatic mechanism still presents a significant challenge. We recently developed an alternative strategy for exploring the fidelity and mechanism of DNA polymerases, by probing leaving group effects on nucleotidyl transfer using a series of dGTP bisphosphonate analogues in which the beta,gamma-bridging oxygen was replaced by a series of substituted methylene groups (X = CYZ, where Y and Z = H, halogen, or another substituent). Pre-steady state kinetic measurements of DNA polymerase-catalyzed incorporation of correctly base paired (R) and mispaired (W) analogues demonstrated a strong linear free energy relationship (LFER) between the polymerase rate constant (k(pol)) and the highest pK(a) of the free bisphosphonic acid corresponding to the leaving group. However, unexpectedly, the data segregated into two distinctly different linear correlations depending on the nature of the substituent. The discrepancy between the two lines was considerably greater when the dGTP analogue formed an incorrect (G.T) rather than a correct (G.C) base pair, although the reason for this phenomenon remains unexplained. Here, we have evaluated the complete free energy surfaces for bisphosphonate hydrolysis in aqueous solution and evaluated the corresponding LFER. Our study, which employs several alternative solvation models, finds a split of the calculated LFER for the mono- and dihalogen compounds into two parallel lines, reflecting their behavior in the polymerase-catalyzed condensation reaction. We suggest that the division into two linear subsets may be a generalized solvation phenomenon involving the overall electrostatic interaction between the substrates and their surroundings and would also be observed in polar solvents in the absence of the enzyme, if the reaction in solvent is in fact identical to that of the enzyme. However, the amplified differences between the LFER lines for the incorporation of matched and mismatched deoxynucleotides probably reflects the differences in the electrostatic interaction between the TS charges in the polymerase active site. An understanding of the mechanism of this reaction in solution could thereby provide a steppingstone for understanding the factors governing the fidelity of DNA polymerases.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA.
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Pinjari RV, Kaptan SS, Gejji SP. Alkali metals (Li, Na, and K) in methyl phosphodiester hydrolysis. Phys Chem Chem Phys 2009; 11:5253-62. [PMID: 19551192 DOI: 10.1039/b812000e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The phosphodiester linkage central to biological systems has been modeled by methyl phosphodiester (MPDE) in various theoretical and experimental studies. Under physiological conditions, hydrolysis of the phosphodiester is negligible, however this process can be catalyzed in the presence of metal ions. To understand the role of alkali metals in MPDE hydrolysis and, in particular, how it influences the reaction pathway and the associated energetics, density functional calculations employing the 6-31+G(d,p) basis set have been carried out. Different pathways that include the reactant, intermediates and the products have been investigated for MPDE hydrolysis catalyzed by one or two lithium ions, characterized as stationary point geometries on the potential energy surface. The pathways A and B incorporate a single lithium ion bonded to different oxygens of the diester functionality. In pathway C, a six-membered ring was noticed wherein the nucleophile bridges two lithium ions interacting with different oxygens of the phosphoryl group. Furthermore, in the pathway (D) incorporating two lithium ions, one of the lithium ions interacts with the hydroxyl group and another with the methoxy oxygen; both metal ions are coordinated by the same phosphoryl oxygen. In addition to this, yet another pathway (E), where the metal ions are bound to different oxygens of the phosphoryl group, has also been dealt with. The calculations have shown that the A and B pathways lead to a single step reaction. A three-step mechanism including the nucleophilic (hydroxyl) attack, rotation of a methyl group and, finally, departure of the methoxy group has been predicted for the D and E profiles. Both D and E pathways are favored equally (with a marginal difference of 0.3 kJ mol(-1) in their activation energies) in the gas phase and a transition state corresponding to nucleophilic attack with an energy barrier of 32.5 kJ mol(-1) was located when lithium was used. A penta-coordinated phosphorous intermediate on the potential energy surface was characterized along these pathways. MPDE hydrolysis yielded a lower energy barrier for lithium than those for the remaining alkali metal ions. This agrees well with the experimentally observed trend for the hydrolysis rates: Li > Na > K. Self consistent reaction field (SCRF) calculations reveal the lower energy barrier between the reactant and the transition state for the nucleophilic attack in nonpolar solvents. The extent of bond formation (or cleavage) in different stationary point structures along the reaction path as estimated from the electron density at the bond critical point in the molecular electron density topography, has proven useful in distinguishing the associative or dissociative reaction pathways.
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Affiliation(s)
- Rahul V Pinjari
- Department of Chemistry, University of Pune, Ganeshkhind, Pune 411007, India
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Michielssens S, Tien Trung N, Froeyen M, Herdewijn P, Tho Nguyen M, Ceulemans A. Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study. Phys Chem Chem Phys 2009; 11:7274-85. [PMID: 19672539 DOI: 10.1039/b906020k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyadenosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate.
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Affiliation(s)
- Servaas Michielssens
- Katholieke Universiteit Leuven, Department of Chemistry and LMCC-Mathematical Modeling and Computational Science Center, Leuven, Belgium.
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Kamerlin SCL, Haranczyk M, Warshel A. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. J Phys Chem B 2009; 113:1253-72. [PMID: 19055405 PMCID: PMC2679392 DOI: 10.1021/jp8071712] [Citation(s) in RCA: 241] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
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Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Maciej Haranczyk
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 50F-1650, Berkeley, CA 94720-8139, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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Kamerlin SCL, Florián J, Warshel A. Associative versus dissociative mechanisms of phosphate monoester hydrolysis: on the interpretation of activation entropies. Chemphyschem 2009; 9:1767-73. [PMID: 18666265 DOI: 10.1002/cphc.200800356] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phosphate monoester and anhydride hydrolysis is ubiquitous in biology, being involved in, amongst other things, signal transduction, energy production, and the regulation of protein function. Therefore, this reaction has understandably been the focus of intensive research. Nevertheless, the precise mechanism by which phosphate monoester hydrolysis proceeds remains controversial. Traditionally, it has been assumed and frequently implied that a near-zero activation entropy is indicative of a dissociative pathway. Herein, we examine free-energy surfaces for the hydrolysis of the methyl phosphate dianion and the methyl pyrophosphate trianion in aqueous solution. In both cases, the reaction can proceed through either compact or expansive concerted (A(N)D(N)) transition states, with fairly similar barriers. We have evaluated the activation entropies for each transition state and demonstrate that both associative and dissociative transition states have near-zero entropies of activation that are in good agreement with experimental values. Therefore, we believe that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include (but are not limited to) steric factors determining the configurational volumes available to reactants during the reaction, solvation and desolvation effects that may be associated with charge redistribution upon approaching the transition state and entropy changes associated with intramolecular degrees of freedom as the transition state is approached.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Ave, Los Angeles, CA 90089, USA.
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Sharma S, Juffer AH. Hydrolysis of phosphohistidine in water and in prostatic acid phosphatase. Chem Commun (Camb) 2009:6385-7. [DOI: 10.1039/b910451h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Souza BS, Brandão TAS, Orth ES, Roma AC, Longo RL, Bunton CA, Nome F. Hydrolysis of 8-Quinolyl Phosphate Monoester: Kinetic and Theoretical Studies of the Effect of Lanthanide Ions. J Org Chem 2008; 74:1042-53. [DOI: 10.1021/jo801870v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno S. Souza
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Tiago A. S. Brandão
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Elisa S. Orth
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Ana C. Roma
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Ricardo L. Longo
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Clifford A. Bunton
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
| | - Faruk Nome
- Departamento de Química, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, 88040-900, Brazil, Departamento de Química Fundamental, Universidade Federal de Recife, Pernambuco, 50740-540, Brazil, and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, 93106-9510
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Kamerlin SCL, Williams NH, Warshel A. Dineopentyl phosphate hydrolysis: evidence for stepwise water attack. J Org Chem 2008; 73:6960-9. [PMID: 18729515 DOI: 10.1021/jo801207q] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphate ester hydrolysis is ubiquitous in biology, playing a central role in energy production, signaling, biosynthesis, and the regulation of protein function among other things. Although the mechanism of action of the enzymes regulating this reaction has been the focus of intensive research in the past few decades, the correct description of this apparently simple reaction remains controversial. A clear understanding of the mechanism that takes place in solution is crucial to be able to evaluate whether proposals for the enzyme-catalyzed mechanisms are reasonable. For the pH-independent hydrolysis of phosphate diesters, several kinetically equivalent mechanisms are plausible, including hydroxide attack on the neutral phosphate. However, it is very difficult to measure the rate of this reaction directly by experimental methods, so it has been evaluated by examining the rate of hydrolysis of neutral phosphate triesters, where a methyl group has replaced a proton. This may not be an accurate model of the neutral phosphate diester and does not provide information about a reaction pathway that is concerted with nucleophilic attack to generate a similar phosphorane. We have carefully mapped out free energy surfaces for both hydroxide and water attack on the dineopentyl phosphate anion and for water attack on the neutral diester. In doing so, we have accurately reproduced existing experimental data and demonstrate that water attack proceeds through an associative mechanism with proton transfer to the phosphate to generate a phosphorane intermediate. Our data show that the substrate-as-base mechanism is viable for phosphate ester hydrolysis, which may have important implications for the studies of phosphate ester hydrolysis by enzymes.
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Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, SGM 418, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA.
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The associative nature of adenylyl transfer catalyzed by T4 DNA ligase. Proc Natl Acad Sci U S A 2008; 105:8563-8. [PMID: 18562298 DOI: 10.1073/pnas.0709140105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA ligase seals nicks in dsDNA using chemical energy of the phosphoanhydride bond in ATP or NAD(+) and assistance of a divalent metal cofactor Mg(2+). Molecular details of ligase catalysis are essential for understanding the mechanism of metal-promoted phosphoryl transfer reactions in the living cell responsible for a wide range of processes, e.g., DNA replication and transcription, signaling and differentiation, energy coupling and metabolism. Here we report a single-turnover (31)P solid-state NMR study of adenylyl transfer catalyzed by DNA ligase from bacteriophage T4. Formation of a high-energy covalent ligase-nucleotide complex is triggered in situ by the photo release of caged Mg(2+), and sequentially formed intermediates are monitored by NMR. Analyses of reaction kinetics and chemical-shift changes indicate that the pentacoordinated phosphorane intermediate builds up to 35% of the total reacting species after 4-5 h of reaction. This is direct experimental evidence of the associative nature of adenylyl transfer catalyzed by DNA ligase. NMR spectroscopy in rotating solids is introduced as an analytical tool for recording molecular movies of reaction processes. Presented work pioneers a promising direction in structural studies of biochemical transformations.
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Rosta E, Kamerlin SCL, Warshel A. On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution. Biochemistry 2008; 47:3725-35. [PMID: 18307312 DOI: 10.1021/bi702106m] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrolysis of phosphate esters is crucially important to biological systems, being involved in, among other things, signaling, energy transduction, biosynthesis, and the regulation of protein function. Despite this, there are many questions that remain unanswered in this important field, particularly with regard to the preferred mechanism of hydrolysis of phosphate esters, which can proceed through any of multiple pathways that are either associative or dissociative in nature. Previous comparisons of calculated and observed linear free energy relationships (LFERs) for phosphate monoester dianions with different leaving groups showed that the TS character gradually changes from associative to dissociative with the increasing acidity of the leaving group, while reproducing the experimental LFER. Here, we have generated ab initio potential energy surfaces for the hydrolysis of phosphate diesters in solution, with a variety of leaving groups. Once again, the reaction changes from a compact concerted pathway to one that is more expansive in character when the acidity of the leaving group increases. When such systems are examined in solution, it is essential to take into consideration the contribution of solute to the overall activation entropy, which remains a major computational challenge. The popular method of calculating the entropy using a quasi-harmonic approximation appears to markedly overestimate the configurational entropy for systems with multiple occupied energy wells. We introduce an improved restraint release approach for evaluating configurational entropies and apply this approach to our systems. We demonstrate that when this factor is taken into account, it is possible to reproduce the experimental LFER for this system with reasonable accuracy.
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Affiliation(s)
- Edina Rosta
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA
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Ferreira DEC, De Almeida WB, Neves A, Rocha WR. Theoretical investigation of the reaction mechanism for the phosphate diester hydrolysis using an asymmetric dinuclear metal complex as a biomimetic model of the purple acid phosphatase enzyme. Phys Chem Chem Phys 2008; 10:7039-46. [DOI: 10.1039/b809189g] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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