1
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Nardi AN, Olivieri A, D'Abramo M, Amadei A. A Theoretical-Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature. Chemphyschem 2024; 25:e202300952. [PMID: 38372713 DOI: 10.1002/cphc.202300952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/19/2024] [Accepted: 02/19/2024] [Indexed: 02/20/2024]
Abstract
The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study the cleavage of this bond by means of a theoretical-computational method in a model system, the dineopentyl phosphate. By such an approach, we reconstructed the kinetics and related thermodynamics of this chemical reaction along an isochore. In particular, we evaluated the kinetic constants of all the reaction steps within a wide range of temperatures, mostly corresponding to conditions where no experimental measures are available due to the extremely slow kinetics. Our results, in good agreement with the experimental data, show the robustness of our theoretical-computational methodology which can be easily extended to more complex systems.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Andrea Amadei
- Department of Technological and Chemical Sciences, Tor Vergata University of Rome, Italy
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2
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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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3
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Modelling Complex Bimolecular Reactions in a Condensed Phase: The Case of Phosphodiester Hydrolysis. Molecules 2023; 28:molecules28052152. [PMID: 36903398 PMCID: PMC10004441 DOI: 10.3390/molecules28052152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
(1) Background: the theoretical modelling of reactions occurring in liquid phase is a research line of primary importance both in theoretical-computational chemistry and in the context of organic and biological chemistry. Here we present the modelling of the kinetics of the hydroxide-promoted hydrolysis of phosphoric diesters. (2) Method: the theoretical-computational procedure involves a hybrid quantum/classical approach based on the perturbed matrix method (PMM) in conjunction with molecular mechanics. (3) Results: the presented study reproduces the experimental data both in the rate constants and in the mechanistic aspects (C-O bond vs. O-P bond reactivity). The study suggests that the basic hydrolysis of phosphodiesters occurs through a concerted ANDN mechanism, with no formation of penta-coordinated species as reaction intermediates. (4) Conclusions: the presented approach, despite the approximations, is potentially applicable to a large number of bimolecular transformations in solution and therefore leads the way to a fast and general method to predict the rate constants and reactivities/selectivities in complex environments.
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4
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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5
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ATP Analogues for Structural Investigations: Case Studies of a DnaB Helicase and an ABC Transporter. Molecules 2020; 25:molecules25225268. [PMID: 33198135 PMCID: PMC7698047 DOI: 10.3390/molecules25225268] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleoside triphosphates (NTPs) are used as chemical energy source in a variety of cell systems. Structural snapshots along the NTP hydrolysis reaction coordinate are typically obtained by adding stable, nonhydrolyzable adenosine triphosphate (ATP) -analogues to the proteins, with the goal to arrest a state that mimics as closely as possible a physiologically relevant state, e.g., the pre-hydrolytic, transition and post-hydrolytic states. We here present the lessons learned on two distinct ATPases on the best use and unexpected pitfalls observed for different analogues. The proteins investigated are the bacterial DnaB helicase from Helicobacter pylori and the multidrug ATP binding cassette (ABC) transporter BmrA from Bacillus subtilis, both belonging to the same division of P-loop fold NTPases. We review the magnetic-resonance strategies which can be of use to probe the binding of the ATP-mimics, and present carbon-13, phosphorus-31, and vanadium-51 solid-state nuclear magnetic resonance (NMR) spectra of the proteins or the bound molecules to unravel conformational and dynamic changes upon binding of the ATP-mimics. Electron paramagnetic resonance (EPR), and in particular W-band electron-electron double resonance (ELDOR)-detected NMR, is of complementary use to assess binding of vanadate. We discuss which analogues best mimic the different hydrolysis states for the DnaB helicase and the ABC transporter BmrA. These might be relevant also to structural and functional studies of other NTPases.
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6
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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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7
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Segreto GE, Alba J, Salvio R, D’Abramo M. DNA cleavage by endonuclease I-DmoI: a QM/MM study and comparison with experimental data provide indications on the environmental effects. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2585-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Manna RN, Dutta M, Jana B. Mechanistic study of the ATP hydrolysis reaction in dynein motor protein. Phys Chem Chem Phys 2019; 22:1534-1542. [PMID: 31872818 DOI: 10.1039/c9cp02194a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dynein, a large and complex motor protein, harnesses energy from adenosine triphosphate (ATP) hydrolysis to regulate essential cellular activities. The ATP hydrolysis mechanism for the dynein motor is still shrouded in mystery. Herein, molecular dynamics simulations of a dynein motor disclosed that two water molecules are present close to the γ-phosphate of ATP and Glu1742 at the AAA1 site of dynein. We have proposed three possible mechanisms for the ATP hydrolysis. We divulge by using a quantum mechanics/molecular mechanics (QM/MM) study that two water molecules and Glu1742 are crucial for facilitating the ATP hydrolysis reaction in dynein. Moreover, the ATP hydrolysis step is initiated by the activation of lytic water (W1) by Glu1742 through relay proton transfers with the help of auxiliary water (W2) yielding HPO42- and ADP, as a product. In the next step, a proton is shifted back from Glu1742 to generate inorganic phosphate (H2PO4-) via another relay proton transfer event. The overall activation barrier for the Glu1742 assisted ATP hydrolysis is found to be the most favourable pathway compared to other plausible pathways. We also unearthed that ATP hydrolysis in dynein follows a so-called associative-like pathway in its rate-limiting step. Our study ascertained the important indirect roles of the two amino acids (such as Arg2109, Asn1792) and Mg2+ ion in the ATP hydrolysis of dynein. Additionally, multiple sequence alignment of the different organisms of dynein motors has conveyed the evolutionary importance of the Glu1742, Asn1742, and Arg2109 residues, respectively. As similar mechanisms are also prevalent in other motors, and GTPase and ATPase enzymes, the present finding spells out the definitive requirement of a proton relay process through an extended water-chain as one of the key components in an enzymatic ATP hydrolysis reaction.
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Affiliation(s)
- Rabindra Nath Manna
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
| | - Mandira Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata-700032, India.
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9
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Nath S. Consolidation of Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling in oxidative phosphorylation and photophosphorylation. Biophys Chem 2019; 257:106279. [PMID: 31757522 DOI: 10.1016/j.bpc.2019.106279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 01/09/2023]
Abstract
In a recent publication, Manoj raises criticisms against consensus views on the ATP synthase. The radical statements and assertions are shown to contradict a vast body of available knowledge that includes i) pioneering single-molecule biochemical and biophysical studies from the respected experimental groups of Kinosita, Yoshida, Noji, Börsch, Dunn, Gräber, Frasch, and Dimroth etc., ii) state-of-the-art X-ray and EM/cryo-EM structural information garnered over the decades by the expert groups of Leslie-Walker, Kühlbrandt, Mueller, Meier, Rubinstein, Sazanov, Duncan, and Pedersen on ATP synthase, iii) the pioneering energy-based computer simulations of Warshel, and iv) the novel theoretical and experimental works of Nath. Valid objections against Mitchell's chemiosmotic theory and Boyer's binding change mechanism put forth by Manoj have been addressed satisfactorily by Nath's torsional mechanism of ATP synthesis and two-ion theory of energy coupling and published 10 to 20 years ago, but these papers are not cited by him. This communication shows conclusively and in great detail that none of his objections apply to Nath's mechanism/theory. Nath's theory is further consolidated based on its previous predictive record, its consistency with biochemical evidence, its unified nature, its application to other related energy transductions and to disease, and finally its ability to guide the design of new experiments. Some constructive suggestions for high-resolution structural experiments that have the power to delve into the heart of the matter and throw unprecedented light on the nature of coupled ion translocation in the membrane-bound FO portion of F1FO-ATP synthase are made.
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Affiliation(s)
- Sunil Nath
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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10
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Tichauer RH, Favre G, Cabantous S, Brut M. Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21 N-ras and the Resulting GTP Electronic Density. J Phys Chem B 2019; 123:3935-3944. [PMID: 30991803 DOI: 10.1021/acs.jpcb.9b02660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
p21ras protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 N-ras and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 N-ras Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21ras major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
| | - Gilles Favre
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse , INSERM U1037, Université de Toulouse , 31037 Toulouse , France
| | - Marie Brut
- LAAS-CNRS , Université de Toulouse , CNRS, UPS, Toulouse , France
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11
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Mattioli EJ, Bottoni A, Calvaresi M. DNAzymes at Work: A DFT Computational Investigation on the Mechanism of 9DB1. J Chem Inf Model 2019; 59:1547-1553. [DOI: 10.1021/acs.jcim.8b00815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Edoardo Jun Mattioli
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Andrea Bottoni
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
| | - Matteo Calvaresi
- Dipartimento di Chimica “G. Ciamician”, Alma Mater Studiorum - Università di Bologna, V. F. Selmi 2, 40126 Bologna, Italy
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12
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Wilson KA, Fernandes PA, Ramos MJ, Wetmore SD. Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase η. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4 Canada
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4 Canada
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13
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Cassone G, Pietrucci F, Saija F, Saitta AM. Free Energy Calculations of Electric Field-Induced Chemistry. COMPUTATIONAL APPROACHES FOR CHEMISTRY UNDER EXTREME CONDITIONS 2019. [DOI: 10.1007/978-3-030-05600-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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14
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Prieß M, Göddeke H, Groenhof G, Schäfer LV. Molecular Mechanism of ATP Hydrolysis in an ABC Transporter. ACS CENTRAL SCIENCE 2018; 4:1334-1343. [PMID: 30410971 PMCID: PMC6202651 DOI: 10.1021/acscentsci.8b00369] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Indexed: 05/28/2023]
Abstract
Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO4 2- as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H2PO4 -. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg2+ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved.
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Affiliation(s)
- Marten Prieß
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Hendrik Göddeke
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Gerrit Groenhof
- Department
of Chemistry and Nanoscience Center, University
of Jyväskylä, P.O. Box
35, FI-40014 Jyväskylä, Finland
| | - Lars V. Schäfer
- Theoretical
Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, D-44780 Bochum, Germany
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15
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Chagas MA, Pereira ES, Da Silva JCS, Rocha WR. Theoretical investigation of the neutral hydrolysis of diethyl 4-nitrophenyl phosphate (paraoxon) in aqueous solution. J Mol Model 2018; 24:259. [DOI: 10.1007/s00894-018-3798-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
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16
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Tichauer RH, Favre G, Cabantous S, Landa G, Hemeryck A, Brut M. Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics. Biophys J 2018; 115:1417-1430. [PMID: 30224050 DOI: 10.1016/j.bpj.2018.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022] Open
Abstract
Point mutations in p21ras are associated with ∼30% of human tumors by disrupting its GTP hydrolysis cycle, which is critical to its molecular switch function in cellular signaling pathways. In this work, we investigate the impact of Gln 61 substitutions in the structure of the p21N-ras active site and particularly focus on water reorganization around GTP, which appears to be crucial to evaluate favorable and unfavorable hydration sites for hydrolysis. The NRas-GTP complex is analyzed using a hybrid quantum mechanics/molecular mechanics approach, treating for the first time to our knowledge transient water molecules at the ab initio level and leading to results that account for the electrostatic coupling between the protein complex and the solvent. We show that for the wild-type protein, water molecules are found around the GTP γ-phosphate group, forming an arch extended from residues 12 to 35. Two density peaks are observed, supporting previous results that suggest the presence of two water molecules in the active site, one in the vicinity of residue 35 and a second one stabilized by hydrogen bonds formed with nitrogen backbone atoms of residues 12 and 60. The structural changes observed in NRas Gln 61 mutants result in the drastic delocalization of water molecules that we discuss. In mutants Q61H and Q61K, for which water distribution is overlocalized next to residue 60, the second density peak supports the hypothesis of a second water molecule. We also conclude that Gly 60 indirectly participates in GTP hydrolysis by correctly positioning transient water molecules in the protein complex and that Gln 61 has an indirect steric effect in stabilizing the preorganized catalytic site.
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Affiliation(s)
- Ruth H Tichauer
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Stéphanie Cabantous
- Cancer Research Center of Toulouse, INSERM U1037, Toulouse, France; Université de Toulouse, Toulouse, France
| | - Georges Landa
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne Hemeryck
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Brut
- LAAS-CNRS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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18
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Fatima T, Rani S, Fischer S, Efferth T, Kiani FA. The hydrolysis of 6-phosphogluconolactone in the second step of pentose phosphate pathway occurs via a two-water mechanism. Biophys Chem 2018; 240:98-106. [PMID: 30014892 DOI: 10.1016/j.bpc.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 11/28/2022]
Abstract
Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown. We report three mechanisms of hydrolysis of δ-6-phosphogluconolactone based on density functional computations. In the energetically most favorable mechanism, two water molecules participate in the hydrolysis reaction and the mechanism is sequential, i.e., activation of the attacking water molecule (OH bond breaking) precedes that of the cleavage of the CO bond of the C-O-C linkage. The rate-limiting energy barrier of this mechanism is comparable to the reported experimental free energy barrier. This mechanism has similarities with the mechanism of triphosphate hydrolysis and that of hydrolytic cleavage of DNA in EcoRV enzyme. This two-water sequential hydrolysis mechanism could be the unified mechanism required for the hydrolysis of other hydrolysable species in living cells.
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Affiliation(s)
- Tabeer Fatima
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Biotechnology, University of Sialkot, 51310 Sialkot, Pakistan
| | - Sadaf Rani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing, The University of Heidelberg, D-69120 Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Farooq Ahmad Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, 02118 Boston, MA, United States.
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Kiani FA, Fischer S. Comparing the catalytic strategy of ATP hydrolysis in biomolecular motors. Phys Chem Chem Phys 2018; 18:20219-33. [PMID: 27296627 DOI: 10.1039/c6cp01364c] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
ATP-driven biomolecular motors utilize the chemical energy obtained from the ATP hydrolysis to perform vital tasks in living cells. Understanding the mechanism of enzyme-catalyzed ATP hydrolysis reaction has substantially progressed lately thanks to combined quantum/classical molecular mechanics (QM/MM) simulations. Here, we present a comparative summary of the most recent QM/MM results for myosin, kinesin and F1-ATPase motors. These completely different motors achieve the acceleration of ATP hydrolysis through a very similar catalytic mechanism. ATP hydrolysis has high activation energy because it involves the breaking of two strong bonds, namely the Pγ-Oβγ bond of ATP and the H-O bond of lytic water. The key to the four-fold decrease in the activation barrier by the three enzymes is that the breaking of the Pγ-Oβγ bond precedes the deprotonation of the lytic water molecule, generating a metaphosphate hydrate complex. The resulting singly charged trigonal planar PγO3(-) metaphosphate is a better electrophilic target for attack by an OaH(-) hydroxyl group. The formation of this OaH(-) is promoted by a strong polarization of the lytic water: in all three proteins, this water is forming a hydrogen-bond with a backbone carbonyl group and interacts with the carboxylate group of glutamate (either directly or via an intercalated water molecule). This favors the shedding of one proton by the attacking water. The abstracted proton is transferred to the γ-phosphate via various proton wires, resulting in a H2PγO4(-)/ADP(3-) product state. This catalytic strategy is so effective that most other nucleotide hydrolyzing enzymes adopt a similar approach, as suggested by their very similar triphosphate binding sites.
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Affiliation(s)
- Farooq Ahmad Kiani
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany. and Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000, Islamabad, Pakistan.
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany.
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20
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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21
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Phosphoryl Transfer Reaction in RNA: Is the Substrate-Assisted Catalysis a Possible Mechanism in Certain Solvents? J Phys Chem A 2017; 121:8525-8534. [PMID: 29039953 DOI: 10.1021/acs.jpca.7b09156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A proton shuttle mechanism for the phosphoryl transfer reaction in RNA, in which a proton is transferred from the nucleophile to the leaving group through a nonbridged oxygen atom of the phosphate, was explored using the MO6-2X density functional method and the solvent continuum model. This reaction is the initial step of the RNA hydrolysis. We used different solvents characterized by their dielectric constant, and, for each of them, we studied the nuclear and electronic relaxation, produced by the solvent reaction field, for the stationary points. Given that RNA has a poor leaving group, the bond breaking corresponds to the rate-determining step. If the O atom is substituted by a S atom, the leaving group is now good, and the rate-determining step is now the nucleophilic attack concerted with the proton transfer. The most relevant result we found is that none of the solvents we studied has a free energy of activation that is smaller than the one in water. This suggests that the enzyme catalysis following this mechanism must be due to the permanent electric field that is created by a preorganized charge distribution but not to the solvent reaction field.
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Affiliation(s)
- Carles Acosta-Silva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Joan Bertran
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Antoni Oliva
- Department of Chemistry, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
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22
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Salvio R, Casnati A. Guanidinium Promoted Cleavage of Phosphoric Diesters: Kinetic Investigations and Calculations Provide Indications on the Operating Mechanism. J Org Chem 2017; 82:10461-10469. [DOI: 10.1021/acs.joc.7b01925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Riccardo Salvio
- Dipartimento
di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185 Roma, Italy
| | - Alessandro Casnati
- Dipartimento
di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Viale delle Scienze 17/A, 43124 Parma, Italy
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23
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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24
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Hassan HA, Rani S, Fatima T, Kiani FA, Fischer S. Effect of protonation on the mechanism of phosphate monoester hydrolysis and comparison with the hydrolysis of nucleoside triphosphate in biomolecular motors. Biophys Chem 2017; 230:27-35. [PMID: 28941815 DOI: 10.1016/j.bpc.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/31/2017] [Accepted: 08/13/2017] [Indexed: 11/25/2022]
Abstract
Hydrolysis of phosphate groups is a crucial reaction in living cells. It involves the breaking of two strong bonds, i.e. the OaH bond of the attacking water molecule, and the POl bond of the substrate (Oa and Ol stand for attacking and leaving oxygen atoms). Mechanism of the hydrolysis reaction can proceed either by a concurrent or a sequential mechanism. In the concurrent mechanism, the breaking of OaH and POl bonds occurs simultaneously, whereas in the sequential mechanism, the OaH and POl bonds break at different stages of the reaction. To understand how protonation affects the mechanism of hydrolysis of phosphate monoester, we have studied the mechanism of hydrolysis of protonated and deprotonated phosphate monoester at M06-2X/6-311+G**//M06-2X/6-31+G*+ZPE level of theory (where ZPE stands for zero point energy). Our calculations show that in both protonated and deprotonated cases, the breaking of the water OaH bond occurs before the breaking of the POl bond. Because the two events are not separated by a stable intermediate, the mechanism can be categorized as semi-concurrent. The overall energy barrier is 41kcalmol-1 in the unprotonated case. Most (5/6th) of this is due to the initial breaking of the water OaH bond. This component is lowered from 34 to 25kcalmol-1 by adding one proton to the phosphate. The rest of the overall energy barrier comes from the subsequent breaking of the POl bond and is not sensitive to protonation. This is consistent with previous findings about the effect of triphosphate protonation on the hydrolysis, where the equivalent protonation (on the γ-phosphate) was seen to lower the barrier of breaking the water OaH bond and to have little effect on the POl bond breaking. Hydrolysis pathways of phosphate monoester with initial breaking of the POl bond could not be found here. This is because the leaving group in phosphate monoester cannot be protonated, unlike in triphosphate hydrolysis, where protonation of the β- and γ-phosphates had been shown to promote a mechanism where the POl bond breaks before the OaH bond does. We also point out that the charge shift due to POl bond breaking during sequential ATP hydrolysis in bio-molecular motors onsets the week unbinding of hydrolysis product that finally leads to the product release during power stroke.
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Affiliation(s)
- Hammad Ali Hassan
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Sadaf Rani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Tabeer Fatima
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan; Department of Biotechnology, University of Gujrat Sialkot Sub Campus, 51310 Sialkot, Pakistan
| | - Farooq Ahmad Kiani
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan; Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany street, 02118 Boston, MA, United States.
| | - Stefan Fischer
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 205, D-69120 Heidelberg, Germany
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25
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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26
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metallfluoride als Analoga für Studien an Phosphoryltransferenzymen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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27
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Hsu WL, Furuta T, Sakurai M. ATP Hydrolysis Mechanism in a Maltose Transporter Explored by QM/MM Metadynamics Simulation. J Phys Chem B 2016; 120:11102-11112. [PMID: 27712074 DOI: 10.1021/acs.jpcb.6b07332] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Translocation of substrates across the cell membrane by adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporters depends on the energy provided by ATP hydrolysis within the nucleotide-binding domains (NBDs). However, the detailed mechanism remains unclear. In this study, we focused on maltose transporter NBDs (MalK2) and performed a quantum mechanical/molecular mechanical (QM/MM) well-tempered metadynamics simulation to address this issue. We explored the free-energy profile along an assigned collective variable. As a result, it was determined that the activation free energy is approximately 10.5 kcal/mol, and the reaction released approximately 3.8 kcal/mol of free energy, indicating that the reaction of interest is a one-step exothermic reaction. The dissociation of the ATP γ-phosphate seems to be the rate-limiting step, which supports the so-called dissociative model. Moreover, Glu159, located in the Walker B motif, acts as a base to abstract the proton from the lytic water, but is not the catalytic base, which corresponds to an atypical general base catalysis model. We also observed two interesting proton transfers: transfer from the His192 ε-position nitrogen to the dissociated inorganic phosphate, Pi, and transfer from the Lys42 side chain to adenosine 5'-diphosphate β-phosphate. These proton transfers would stabilize the posthydrolysis state. Our study provides significant insight into the ATP hydrolysis mechanism in MalK2 from a dynamical viewpoint, and this insight would be applicable to other ABC transporters.
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Affiliation(s)
- Wei-Lin Hsu
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , 4259-B-62, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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28
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Zhang F, Chen N, Zhou J, Wu R. Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02096] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People’s Republic of China
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29
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Duarte F, Barrozo A, Åqvist J, Williams NH, Kamerlin SCL. The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis. J Am Chem Soc 2016; 138:10664-73. [PMID: 27471914 PMCID: PMC4999962 DOI: 10.1021/jacs.6b06277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Despite the numerous
experimental and theoretical studies on phosphate
monoester hydrolysis, significant questions remain concerning the
mechanistic details of these biologically critical reactions. In the
present work we construct a linear free energy relationship for phosphate
monoester hydrolysis to explore the effect of modulating leaving group
pKa on the competition between solvent-
and substrate-assisted pathways for the hydrolysis of these compounds.
Through detailed comparative electronic-structure studies of methyl
phosphate and a series of substituted aryl phosphate monoesters, we
demonstrate that the preferred mechanism is dependent on the nature
of the leaving group. For good leaving groups, a strong preference
is observed for a more dissociative solvent-assisted pathway. However,
the energy difference between the two pathways gradually reduces as
the leaving group pKa increases and creates
mechanistic ambiguity for reactions involving relatively poor alkoxy
leaving groups. Our calculations show that the transition-state structures
vary smoothly across the range of pKas
studied and that the pathways remain discrete mechanistic alternatives.
Therefore, while not impossible, a biological catalyst would have
to surmount a significantly higher activation barrier to facilitate
a substrate-assisted pathway than for the solvent-assisted pathway
when phosphate is bonded to good leaving groups. For poor leaving
groups, this intrinsic preference disappears.
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Affiliation(s)
- Fernanda Duarte
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
| | - Nicholas H Williams
- Department of Chemistry, Sheffield University , Sheffield S3 7HF, United Kingdom
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, SE-751 24 Uppsala, Sweden
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30
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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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31
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Pereira ES, Da Silva JCS, Brandão TAS, Rocha WR. Phosphorane lifetime and stereo-electronic effects along the alkaline hydrolysis of phosphate esters. Phys Chem Chem Phys 2016; 18:18255-67. [DOI: 10.1039/c6cp01536k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio molecular dynamics simulations revealed that phosphorane, an important intermediate in the hydrolysis of phosphate diesters, has a lifetime of ∼1 ps in aqueous solution. QTAIM and EDA analyses along the reaction coordinate show that the hydrolysis reaction of phosphate esters is driven mainly by electrostatic interactions.
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Affiliation(s)
- Eufrásia S. Pereira
- Laboratório de Química Computacional e Modelagem Molecular
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Campus Universitário Pampulha
| | - Júlio C. S. Da Silva
- Biomaterial Modeling Group
- Departamento de Química Fundamental
- CCEN
- Universidade Federal de Pernambuco
- Cidade Universitária
| | - Tiago A. S. Brandão
- Laboratório de Catálise e Mecanismos de Reações
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Campus Universitário Pampulha
| | - Willian R. Rocha
- Laboratório de Química Computacional e Modelagem Molecular
- Departamento de Química
- ICEX
- Universidade Federal de Minas Gerais
- Campus Universitário Pampulha
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32
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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33
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He X, Lin M, Guo J, Qu Z, Xu F. Experimental and simulation studies of polyarginines across the membrane of giant unilamellar vesicles. RSC Adv 2016. [DOI: 10.1039/c6ra02420c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cell-penetrating peptides have widespread applications in biomedicine because of their capability to translocate across cell membranes alone or with cargos.
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Affiliation(s)
- XiaoCong He
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - Min Lin
- Bioinspired Engineering and Biomechanics Center (BEBC)
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
| | - Jun Guo
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - ZhiGuo Qu
- Key Laboratory of Thermo-Fluid Science and Engineering of Ministry of Education
- School of Energy and Power Engineering
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
| | - Feng Xu
- Bioinspired Engineering and Biomechanics Center (BEBC)
- Xi'an Jiaotong University
- Xi'an 710049
- P.R. China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education
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34
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Formamide reaction network in gas phase and solution via a unified theoretical approach: Toward a reconciliation of different prebiotic scenarios. Proc Natl Acad Sci U S A 2015; 112:15030-5. [PMID: 26598679 DOI: 10.1073/pnas.1512486112] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Increasing experimental and theoretical evidence points to formamide as a possible hub in the complex network of prebiotic chemical reactions leading from simple precursors like H2, H2O, N2, NH3, CO, and CO2 to key biological molecules like proteins, nucleic acids, and sugars. We present an in-depth computational study of the formation and decomposition reaction channels of formamide by means of ab initio molecular dynamics. To this aim we introduce a new theoretical method combining the metadynamics sampling scheme with a general purpose topological formulation of collective variables able to track a wide range of different reaction mechanisms. Our approach is flexible enough to discover multiple pathways and intermediates starting from minimal insight on the systems, and it allows passing in a seamless way from reactions in gas phase to reactions in liquid phase, with the solvent active role fully taken into account. We obtain crucial new insight into the interplay of the different formamide reaction channels and into environment effects on pathways and barriers. In particular, our results indicate a similar stability of formamide and hydrogen cyanide in solution as well as their relatively facile interconversion, thus reconciling experiments and theory and, possibly, two different and competing prebiotic scenarios. Moreover, although not explicitly sought, formic acid/ammonium formate is produced as an important formamide decomposition byproduct in solution.
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35
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Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. J Struct Biol 2015; 192:76-87. [DOI: 10.1016/j.jsb.2015.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/04/2015] [Accepted: 08/17/2015] [Indexed: 02/01/2023]
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36
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. SP20 Phosphorylation Reaction Catalyzed by Protein Kinase A: QM/MM Calculations Based on Recently Determined Crystallographic Structures. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Mireia Garcia-Viloca
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Àngels González-Lafont
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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37
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Huang M, York DM. Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations. Phys Chem Chem Phys 2015; 16:15846-55. [PMID: 24961771 DOI: 10.1039/c4cp01050g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
RNA cleavage transesterification is of fundamental reaction in biology that is catalyzed by both protein and RNA enzymes. In this work, a series of RNA transesterification model reactions with a wide range of leaving groups are investigated with density-functional calculations in an aqueous solvation environment in order to study linear free energy relationships (LFERs) and their connection to transition state structure and bonding. Overall, results obtained from the polarizable continuum solvation model with UAKS radii produce the best linear correlations and closest overall agreement with experimental results. Reactions with a poor leaving group are predicted to proceed via a stepwise mechanism with a late transition state that is rate controlling. As leaving group becomes more acidic and labile, the barriers of both early and late transition states decrease. LFERs for each transition state are computed, with the late transition state barrier showing greater sensitivity to leaving group pKa. For sufficiently enhanced leaving groups, the reaction mechanism transits to a concerted mechanism characterized by a single early transition state. Further linear relationships were derived for bond lengths and bond orders as a function of leaving group pKa and rate constant values that can be used for prediction. This work provides important benchmark linear free energy data that allows a molecular-level characterization of the structure and bonding of the transition states for this important class of phosphoryl transfer reactions. The relations reported herein can be used to aid in the interpretation of data obtained from experimental studies of non-catalytic and catalytic mechanisms.
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Affiliation(s)
- Ming Huang
- Scientific Computation, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455-0431, USA
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38
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Explore the reaction mechanism of the Maillard reaction: a density functional theory study. J Mol Model 2015; 21:132. [PMID: 25934157 DOI: 10.1007/s00894-015-2674-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/01/2015] [Indexed: 01/07/2023]
Abstract
The mechanism of Maillard reaction has been investigated by means of density functional theory calculations in the gaseous phase and aqueous solution. The Maillard reaction is a cascade of consecutive and parallel reaction. In the present model system study, glucose and glycine were taken as the initial reactants. On the basis of previous experimental results, the mechanisms of Maillard reaction have been proposed, and the possibility for the formation of different compounds have been evaluated through calculating the relative energy changes for different steps of reaction under different pH conditions. Our calculations reveal that the TS3 in Amadori rearrangement reaction is the rate-determining step of Maillard reaction with the activation barriers of about 66.7 and 68.8 kcal mol(-1) in the gaseous phase and aqueous solution, respectively. The calculation results are in good agreement with previous studies and could provide insights into the reaction mechanism of Maillard reaction, since experimental evaluation of the role of intermediates in the Maillard reaction is quite complicated.
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39
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Wang C, Huang W, Liao JL. QM/MM investigation of ATP hydrolysis in aqueous solution. J Phys Chem B 2015; 119:3720-6. [PMID: 25658024 DOI: 10.1021/jp512960e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Adenosine-5'-triphosphate (ATP) hydrolysis represents a most important reaction in biology. Despite extensive research efforts, the mechanism for ATP hydrolysis in aqueous solution still remains under debate. Previous theoretical studies often predefined reaction coordinates to characterize the mechanism for ATP hydrolysis in water with Mg(2+) by evaluating free energy profiles through these preassumed reaction paths. In the present work, a nudged elastic band method is applied to identify the minimum energy path calculated with a hybrid quantum mechanics and molecular mechanics approach. Along the reaction path, the free energy profile was obtained to have a single transition state and the activation energy of 32.5 kcal/mol. This transition state bears a four-centered structure that describes a concerted nature of the reaction. In the More-O'Ferrall-Jencks diagram, the results show that the reaction proceeds through a concerted path before the system reaches the transition state and along an associative path after the transition state. In addition, the calculated reaction free energy is -7.0 kcal/mol, in good agreement with experiment, capturing the exothermic feature of MgATP(2-) hydrolysis in aqueous solution, whereas the reaction was often shown to be endothermic in the previous theoretical studies. As Mg(2+) is required for ATP hydrolysis in cells, its role in the reaction is also elucidated.
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Affiliation(s)
- Cui Wang
- Department of Chemical Physics, University of Science and Technology of China , 96 Jinzhai Road, 230026 Hefei, Anhui Province, People's Republic of China
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40
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. A QM/MM study of Kemptide phosphorylation catalyzed by protein kinase A. The role of Asp166 as a general acid/base catalyst. Phys Chem Chem Phys 2014; 17:3497-511. [PMID: 25535906 DOI: 10.1039/c4cp03579h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this work a theoretical study of the γ-phosphoryl group transfer from ATP to Ser17 of the synthetic substrate Kemptide (LRRASLG) in protein kinase A (PKA) has been carried out with a solvated model of the PKA-Mg2ATP-Kemptide system based on the X-ray crystallographic structure. We have used high levels (B3LYP/MM and MP2/MM) of theory to determine the overall reaction paths of the so-called concerted loose mechanism trying to clarify some aspects of that mechanism still under debate. Our calculations demonstrate for the first time in a complete model of the ternary system the viability of the final step of the catalytic mechanism in which the protonation of the phosphokemptide product by Asp166 takes place. Asp166 is a base catalyst that abstracts the HγSer17 of Kemptide thus facilitating the phosphoryl transfer, but it also acts as an acid catalyst by donating the proton just accepted from Ser17 to the O2γATP atom of the phosphoryl group.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Institut de Biotecnologia i de Biomedicina and Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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41
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Kale S, Sode O, Weare J, Dinner AR. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. J Chem Theory Comput 2014; 10:5467-5475. [PMID: 25516726 PMCID: PMC4263463 DOI: 10.1021/ct500852y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Indexed: 11/28/2022]
Abstract
Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys.2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.
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Affiliation(s)
- Seyit Kale
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
| | - Olaseni Sode
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Computing, Environment, and Life Sciences, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Jonathan Weare
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
| | - Aaron R Dinner
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States
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42
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Khrenova MG, Mironov VA, Grigorenko BL, Nemukhin AV. Modeling the role of G12V and G13V Ras mutations in the Ras-GAP-catalyzed hydrolysis reaction of guanosine triphosphate. Biochemistry 2014; 53:7093-9. [PMID: 25339142 DOI: 10.1021/bi5011333] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cancer-associated point mutations in Ras, in particular, at glycine 12 and glycine 13, affect the normal cycle between inactive GDP-bound and active GTP-bound states. In this work, the role of G12V and G13V replacements in the GAP-stimulated intrinsic GTP hydrolysis reaction in Ras is studied using molecular dynamics (MD) simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. A model molecular system was constructed by motifs of the relevant crystal structure (Protein Data Bank entry 1WQ1 ). QM/MM optimization of geometry parameters in the Ras-GAP-GTP complex and QM/MM-MD simulations were performed with a quantum subsystem comprising a large fraction of the enzyme active site. For the system with wild-type Ras, the conformations fluctuated near the structure ready to be involved in the efficient chemical reaction leading to the cleavage of the phosphorus-oxygen bond in GTP upon approach of the properly aligned catalytic water molecule. Dynamics of the system with the G13V mutant is characterized by an enhanced flexibility in the area occupied by the γ-phosphate group of GTP, catalytic water, and the side chains of Arg789 and Gln61, which should somewhat hinder fast chemical steps. Conformational dynamics of the system with the G12V mutant shows considerable displacement of the Gln61 side chain and catalytic water from their favorable arrangement in the active site that may lead to a marked reduction in the reaction rate. The obtained computational results correlate well with the recent kinetic measurements of the Ras-GAP-catalyzed hydrolysis of GTP.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, M. V. Lomonosov Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russian Federation
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43
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McCullagh M, Saunders MG, Voth GA. Unraveling the mystery of ATP hydrolysis in actin filaments. J Am Chem Soc 2014; 136:13053-8. [PMID: 25181471 PMCID: PMC4183606 DOI: 10.1021/ja507169f] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Actin
performs its myriad cellular functions by the growth and
disassembly of its filamentous form. The hydrolysis of ATP in the
actin filament has been shown to modulate properties of the filament,
thus making it a pivotal regulator of the actin life cycle. Actin
has evolved to selectively hydrolyze ATP in the filamentous form,
F-actin, with an experimentally observed rate increase over the monomeric
form, G-actin, of 4.3 × 104. The cause of this dramatic
increase in rate is investigated in this paper using extensive QM/MM
simulations of both G- and F-actin. To compute the free energy of
hydrolysis in both systems, metadynamics is employed along two collective
variables chosen to describe the reaction coordinates of hydrolysis.
F-actin is modeled as a monomer with restraints applied to coarse-grained
variables enforced to keep it in a filament-like conformation. The
simulations reveal a barrier height reduction for ATP hydrolysis in
F-actin as compared to G-actin of 8 ± 1 kcal/mol, in good agreement
with the experimentally measured barrier height reduction of 7 ±
1 kcal/mol. The barrier height reduction is influenced by an enhanced
rotational diffusion of water in F-actin as compared to G-actin and
shorter water wires between Asp154 and the nucleophilic water in F-actin,
leading to more rapid proton transport.
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Affiliation(s)
- Martin McCullagh
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago , Chicago, Illinois 60637, United States
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44
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Pérez-Gallegos A, Garcia-Viloca M, González-Lafont À, Lluch JM. A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant. J Comput Aided Mol Des 2014; 28:1077-91. [PMID: 25129483 DOI: 10.1007/s10822-014-9786-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
Here we analyze in detail the possible catalytic role of the associative mechanism in the γ-phosphoryl transfer reaction in the catalytic subunit of the mammalian cyclic AMP-dependent protein kinase (PKA) enzyme and its D166A mutant. We have used a complete solvated model of the ATP-Mg2-Kemptide/PKA system and good levels of theory (B3LYP/MM and MP2/MM) to determine several potential energy paths from different MD snapshots, and we present a deep analysis of the interaction distances and energies between ligands, metals and enzyme residues. We have also tested the electrostatic stabilization of the transition state structures localized herein with the charge balance hypothesis. Overall, the results obtained in this work reopen the discussion about the plausibility of the associative reaction pathway and highlight the proposed role of the catalytic triad Asp166-Lys168-Thr201.
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Affiliation(s)
- Ayax Pérez-Gallegos
- Departament de Química, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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45
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Prakash P, Gorfe AA. Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras. MOLECULAR SIMULATION 2014; 40:839-847. [PMID: 26491216 DOI: 10.1080/08927022.2014.895000] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Over the last 40 years, we have learnt a great deal about the Ras onco-proteins. These intracellular molecular switches are essential for the function of a variety of physiological processes, including signal transduction cascades responsible for cell growth and proliferation. Molecular simulations and free energy calculations have played an essential role in elucidating the conformational dynamics and energetics underlying the GTP hydrolysis reaction catalysed by Ras. Here we present an overview of the main lessons from molecular simulations on the GTPase reaction and conformational dynamics of this important anti-cancer drug target. In the first part, we summarise insights from quantum mechanical and combined quantum mechanical/molecular mechanical simulations as well as other free energy methods and highlight consensus viewpoints as well as remaining controversies. The second part provides a very brief overview of new insights emerging from large-scale molecular dynamics simulations. We conclude with a perspective regarding future studies of Ras where computational approaches will likely play an active role.
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Affiliation(s)
- Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
| | - Alemayehu A Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Medical School at Houston, 6431 Fannin St, Houston, TX 77030, USA
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46
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Elsässer B, Fels G, Weare JH. QM/MM simulation (B3LYP) of the RNase A cleavage-transesterification reaction supports a triester A(N) + D(N) associative mechanism with an O2' H internal proton transfer. J Am Chem Soc 2014; 136:927-36. [PMID: 24372083 DOI: 10.1021/ja406122c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) AN + DN mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10(11) difference in rate strongly supporting the less accepted triester mechanism.
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Affiliation(s)
- Brigitta Elsässer
- Department of Chemistry, University of Paderborn , Warburgerstr. 100, D-33098 Paderborn, Germany
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47
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Quantum mechanical modeling: a tool for the understanding of enzyme reactions. Biomolecules 2013; 3:662-702. [PMID: 24970187 PMCID: PMC4030948 DOI: 10.3390/biom3030662] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 01/16/2023] Open
Abstract
Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.
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48
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DeYonker NJ, Webster CE. Phosphoryl transfers of the phospholipase D superfamily: a quantum mechanical theoretical study. J Am Chem Soc 2013; 135:13764-74. [PMID: 24007383 DOI: 10.1021/ja4042753] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The HKD-containing Phospholipase D superfamily catalyzes the cleavage of the headgroup of phosphatidylcholine to produce phosphatidic acid and choline. The mechanism of this cleavage process is studied theoretically. The geometric basis of our models is the X-ray crystal structure of the five-coordinate phosphohistidine intermediate from Streptomyces sp . Strain PMF (PDB Code = 1V0Y ). Hybrid ONIOM QM:QM methodology with Density Functional Theory (DFT) and semiempirical PM6 (DFT:PM6) is used to acquire thermodynamic and kinetic data for the initial phosphoryl transfer, subsequent hydrolysis, and finally, the formation of the experimentally observed ″dead-end″ phosphohistidine product (PDB Code = 1V0W ). The model contains nineteen amino acid residues (including the two highly conserved HKD-motifs), four explicit water molecules, and the substrate. Via computations, the persistence of the short-lived five-coordinate phosphorane intermediate on the minutes times scale is rationalized. This five-coordinate phosphohistidine intermediate energetically exists between the hydrolysis event and ″substrate reorganization″ (the reorganization of the in vitro model substrate within the active site). Computations directly support the thermodynamic favorability of the in vitro four-coordinate phosphohistidine product. In vivo, the activation energy of substrate reorganization is too high, perhaps due to a combination of substrate immobility when embedded in the lipid bilayer, as well as its larger steric bulk compared to the compound used in the in vitro substrate soaks. On this longer time scale, the enzyme will migrate along the lipid membrane toward its next substrate target, rather than promote the formation of the dead-end product.
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Affiliation(s)
- Nathan J DeYonker
- The Department of Chemistry, The University of Memphis , 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
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49
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McGrath MJ, Kuo IFW, Hayashi S, Takada S. Adenosine triphosphate hydrolysis mechanism in kinesin studied by combined quantum-mechanical/molecular-mechanical metadynamics simulations. J Am Chem Soc 2013; 135:8908-19. [PMID: 23751065 DOI: 10.1021/ja401540g] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Kinesin is a molecular motor that hydrolyzes adenosine triphosphate (ATP) and moves along microtubules against load. While motility and atomic structures have been well-characterized for various members of the kinesin family, not much is known about ATP hydrolysis inside the active site. Here, we study ATP hydrolysis mechanisms in the kinesin-5 protein Eg5 by using combined quantum mechanics/molecular mechanics metadynamics simulations. Approximately 200 atoms at the catalytic site are treated by a dispersion-corrected density functional and, in total, 13 metadynamics simulations are performed with their cumulative time reaching ~0.7 ns. Using the converged runs, we compute free energy surfaces and obtain a few hydrolysis pathways. The pathway with the lowest free energy barrier involves a two-water chain and is initiated by the Pγ-Oβ dissociation concerted with approach of the lytic water to PγO3-. This immediately induces a proton transfer from the lytic water to another water, which then gives a proton to the conserved Glu270. Later, the proton is transferred back from Glu270 to HPO(4)2- via another hydrogen-bonded chain. We find that the reaction is favorable when the salt bridge between Glu270 in switch II and Arg234 in switch I is transiently broken, which facilitates the ability of Glu270 to accept a proton. When ATP is placed in the ADP-bound conformation of Eg5, the ATP-Mg moiety is surrounded by many water molecules and Thr107 blocks the water chain, which together make the hydrolysis reaction less favorable. The observed two-water chain mechanisms are rather similar to those suggested in two other motors, myosin and F1-ATPase, raising the possibility of a common mechanism.
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Affiliation(s)
- Matthew J McGrath
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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50
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Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A. Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces. J Phys Chem B 2013; 117:12807-19. [PMID: 23601038 DOI: 10.1021/jp4020146] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Understanding the nature of the free-energy surfaces for phosphate hydrolysis is a prerequisite for understanding the corresponding key chemical reactions in biology. Here, the challenge has been to move to careful ab initio QM/MM (QM(ai)/MM) free-energy calculations, where obtaining converging results is very demanding and computationally expensive. This work describes such calculations, focusing on the free-energy surface for the hydrolysis of phosphate monoesters, paying special attention to the comparison between the one water (1W) and two water (2W) paths for the proton-transfer (PT) step. This issue has been explored before by energy minimization with implicit solvent models and by nonsystematic QM/MM energy minimization, as well as by nonsystematic free-energy mapping. However, no study has provided the needed reliable 2D (3D) surfaces that are necessary for reaching concrete conclusions. Here we report a systematic evaluation of the 2D (3D) free-energy maps for several relevant systems, comparing the results of QM(ai)/MM and QM(ai)/implicit solvent surfaces, and provide an advanced description of the relevant energetics. It is found that the 1W path for the hydrolysis of the methyl diphosphate (MDP) trianion is 6-9 kcal/mol higher than that the 2W path. This difference becomes slightly larger in the presence of the Mg(2+) ion because this ion reduces the pKa of the conjugated acid form of the phosphate oxygen that accepts the proton. Interestingly, the BLYP approach (which has been used extensively in some studies) gives a much smaller difference between the 1W and 2W activation barriers. At any rate, it is worth pointing out that the 2W transition state for the PT is not much higher that the common plateau that serves as the starting point of both the 1W and 2W PT paths. Thus, the calculated catalytic effects of proteins based on the 2W PT mechanistic model are not expected to be different from the catalytic effects predicted using the 1W PT mechanistic model, which was calibrated on the observed barrier in solution and in which the TS charge distribution was similar to the that of the plateau (as was done in all of our previous EVB studies).
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Affiliation(s)
- Nikolay V Plotnikov
- Department of Chemistry, University of Southern California , SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, United States
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