1
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Barragan AM, Ghaby K, Pond MP, Roux B. Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib. J Chem Inf Model 2024; 64:3488-3502. [PMID: 38546820 DOI: 10.1021/acs.jcim.4c00023] [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: 04/23/2024]
Abstract
Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.
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Affiliation(s)
- Angela M Barragan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Kyle Ghaby
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Matthew P Pond
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
- Department of Chemistry, The University of Chicago, 5735 S Ellis Avenue, Chicago, Illinois 60637, United States
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2
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Mihalovits LM, Kollár L, Bajusz D, Knez D, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones. Chemphyschem 2024; 25:e202300596. [PMID: 37888491 DOI: 10.1002/cphc.202300596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS-CoV-2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in-house, cysteine-targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Levente Kollár
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Damijan Knez
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Krištof Bozovičar
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tímea Imre
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Stanislav Gobec
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
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3
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Semelak JA, Zeida A, Foglia NO, Estrin DA. Minimum Free Energy Pathways of Reactive Processes with Nudged Elastic Bands. J Chem Theory Comput 2023; 19:6273-6293. [PMID: 37647166 DOI: 10.1021/acs.jctc.3c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The determination of minimum free energy pathways (MFEP) is one of the most widely used strategies to study reactive processes. For chemical reactions in complex environments, the combination of quantum mechanics (QM) with a molecular mechanics (MM) representation is usually necessary in a hybrid QM/MM framework. However, even within the QM/MM approximation, the affordable sampling of the phase space is, in general, quite restricted. To reduce drastically the computational cost of the simulations, several methods such as umbrella sampling require performing a priori a selection of a reaction coordinate. The quality of the computed results, in an affordable computational time, is intimately related to the reaction coordinate election which is, in general, a nontrivial task. In this work, we provide an approach to model reactive processes in complex environments that does not require the a priori selection of a reaction coordinate. The proposed methodology combines QM/MM simulations with an extrapolation of the nudged elastic bands (NEB) method to the free energy surface (FENEB). We present and apply our own FENEB scheme to optimize MFEP in different reactive processes, using QM/MM frameworks at semiempirical and density functional theory levels. Our implementation is based on performing the FENEB optimization by uncoupling the optimization of the band in a perpendicular and tangential direction. In each step, a full optimization with the spring force is performed, which guarantees that the images remain evenly distributed. The robustness of the method and the influence of sampling on the quality of the optimized MFEP and its associated free energy barrier are studied. We show that the FENEB method provides a good estimation of the reaction barrier even with relatively short simulation times, supporting that its combination with QM/MM frameworks provides an adequate tool to study chemical processes in complex environments.
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Affiliation(s)
- Jonathan A Semelak
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo 11800, Uruguay
- Centro de Investigaciones Biomédicas (CEINBIO), Universidad de la República, Montevideo 11800, Uruguay
| | - Nicolás O Foglia
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), CONICET-Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
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4
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Tooke C, Hinchliffe P, Beer M, Zinovjev K, Colenso CK, Schofield CJ, Mulholland AJ, Spencer J. Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase. J Am Chem Soc 2023; 145:7166-7180. [PMID: 36972204 PMCID: PMC10080687 DOI: 10.1021/jacs.2c12123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/29/2023]
Abstract
KPC-2 (Klebsiella pneumoniae carbapenemase-2) is a globally disseminated serine-β-lactamase (SBL) responsible for extensive β-lactam antibiotic resistance in Gram-negative pathogens. SBLs inactivate β-lactams via a mechanism involving a hydrolytically labile covalent acyl-enzyme intermediate. Carbapenems, the most potent β-lactams, evade the activity of many SBLs by forming long-lived inhibitory acyl-enzymes; however, carbapenemases such as KPC-2 efficiently deacylate carbapenem acyl-enzymes. We present high-resolution (1.25-1.4 Å) crystal structures of KPC-2 acyl-enzymes with representative penicillins (ampicillin), cephalosporins (cefalothin), and carbapenems (imipenem, meropenem, and ertapenem) obtained utilizing an isosteric deacylation-deficient mutant (E166Q). The mobility of the Ω-loop (residues 165-170) negatively correlates with antibiotic turnover rates (kcat), highlighting the role of this region in positioning catalytic residues for efficient hydrolysis of different β-lactams. Carbapenem-derived acyl-enzyme structures reveal the predominance of the Δ1-(2R) imine rather than the Δ2 enamine tautomer. Quantum mechanics/molecular mechanics molecular dynamics simulations of KPC-2:meropenem acyl-enzyme deacylation used an adaptive string method to differentiate the reactivity of the two isomers. These identify the Δ1-(2R) isomer as having a significantly (7 kcal/mol) higher barrier than the Δ2 tautomer for the (rate-determining) formation of the tetrahedral deacylation intermediate. Deacylation is therefore likely to proceed predominantly from the Δ2, rather than the Δ1-(2R) acyl-enzyme, facilitated by tautomer-specific differences in hydrogen-bonding networks involving the carbapenem C-3 carboxylate and the deacylating water and stabilization by protonated N-4, accumulating a negative charge on the Δ2 enamine-derived oxyanion. Taken together, our data show how the flexible Ω-loop helps confer broad-spectrum activity upon KPC-2, while carbapenemase activity stems from efficient deacylation of the Δ2-enamine acyl-enzyme tautomer.
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Affiliation(s)
- Catherine
L. Tooke
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Michael Beer
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Kirill Zinovjev
- School
of Biochemistry, Biomedical Sciences Building, University
Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Departamento
de Química Física, Universitat
de València, Burjassot 46100, Comunitat Valenciana, Spain
| | - Charlotte K. Colenso
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, Mansfield Road, University of Oxford, Oxford OX1 3TA United
Kingdom
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, Cantock’s
Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - James Spencer
- School
of Cellular and Molecular Medicine, Biomedical Sciences
Building, University Walk, University of Bristol, Bristol BS8 1TD, United Kingdom
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5
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Kulshrestha A, Punnathanam SN, Ayappa KG. Finite temperature string method with umbrella sampling using path collective variables: application to secondary structure change in a protein. SOFT MATTER 2022; 18:7593-7603. [PMID: 36165347 DOI: 10.1039/d2sm00888b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in biomolecular systems. Due to long time scales involved in the transition, it is challenging to study such protein conformational changes using direct molecular dynamics simulations. This limitation is typically overcome using an indirect approach wherein one computes the free energy landscape associated with the transition. Computation of free energy landscapes, however, requires a suitable set of collective variables that describe the transition. In this work, we demonstrate the use of path collective variables [D. Branduardi, F. L. Gervasio and M. Parrinello, J. Chem. Phys., 2007, 126, 054103] and combine it with the finite temperature string (FTS) method [E. Weinan, W. Ren and E. Vanden-Eijnden, J. Phys. Chem. B, 2005, 109, 6688-6693] to determine the molecular mechanisms involved during the structural transition of the mini G-protein from an α-helix to a β-hairpin. The transition from the α-helix proceeds via unfolding of the terminal residues, giving rise to a β-turn unfolded intermediate to eventually form the β-hairpin. Our proposed algorithm uses umbrella sampling simulations to simulate images along the string and the weighted histogram analysis to compute the free energy along the computed transition path. This work demonstrates that the string method in combination with path collective variables can be exploited to study complex protein conformational changes such as a complete change in the secondary structure.
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Affiliation(s)
- Avijeet Kulshrestha
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - Sudeep N Punnathanam
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, 560012, India.
| | - K Ganapathy Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, 560012, India.
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6
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Douglas-Gallardo OA, Murillo-López JA, Oller J, Mulholland AJ, Vöhringer-Martinez E. Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oscar A. Douglas-Gallardo
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Juliana A. Murillo-López
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Javier Oller
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380000, Chile
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
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7
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Kim B, Snyder R, Nagaraju M, Zhou Y, Ojeda-May P, Keeton S, Hege M, Shao Y, Pu J. Reaction Path-Force Matching in Collective Variables: Determining Ab Initio QM/MM Free Energy Profiles by Fitting Mean Force. J Chem Theory Comput 2021; 17:4961-4980. [PMID: 34283604 PMCID: PMC9064116 DOI: 10.1021/acs.jctc.1c00245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
First-principles determination of free energy profiles for condensed-phase chemical reactions is hampered by the daunting costs associated with configurational sampling on ab initio quantum mechanical/molecular mechanical (AI/MM) potential energy surfaces. Here, we report a new method that enables efficient AI/MM free energy simulations through mean force fitting. In this method, a free energy path in collective variables (CVs) is first determined on an efficient reactive aiding potential. Based on the configurations sampled along the free energy path, correcting forces to reproduce the AI/MM forces on the CVs are determined through force matching. The AI/MM free energy profile is then predicted from simulations on the aiding potential in conjunction with the correcting forces. Such cycles of correction-prediction are repeated until convergence is established. As the instantaneous forces on the CVs sampled in equilibrium ensembles along the free energy path are fitted, this procedure faithfully restores the target free energy profile by reproducing the free energy mean forces. Due to its close connection with the reaction path-force matching (RP-FM) framework recently introduced by us, we designate the new method as RP-FM in collective variables (RP-FM-CV). We demonstrate the effectiveness of this method on a type-II solution-phase SN2 reaction, NH3 + CH3Cl (the Menshutkin reaction), simulated with an explicit water solvent. To obtain the AI/MM free energy profiles, we employed the semiempirical AM1/MM Hamiltonian as the base level for determining the string minimum free energy pathway, along which the free energy mean forces are fitted to various target AI/MM levels using the Hartree-Fock (HF) theory, density functional theory (DFT), and the second-order Møller-Plesset perturbation (MP2) theory as the AI method. The forces on the bond-breaking and bond-forming CVs at both the base and target levels are obtained by force transformation from Cartesian to redundant internal coordinates under the Wilson B-matrix formalism, where the linearized FM is facilitated by the use of spline functions. For the Menshutkin reaction tested, our FM treatment greatly reduces the deviations on the CV forces, originally in the range of 12-33 to ∼2 kcal/mol/Å. Comparisons with the experimental and benchmark AI/MM results, tests of the new method under a variety of simulation protocols, and analyses of the solute-solvent radial distribution functions suggest that RP-FM-CV can be used as an efficient, accurate, and robust method for simulating solution-phase chemical reactions.
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Affiliation(s)
- Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Ryan Snyder
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Seth Keeton
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Mellisa Hege
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of
Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana
University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN
46202
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8
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Recabarren R, Zinovjev K, Tuñón I, Alzate-Morales J. How a Second Mg 2+ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodrigo Recabarren
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
| | - Kirill Zinovjev
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, Valencia 46010, Spain
| | - Jans Alzate-Morales
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente, 1141 Talca, Chile
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9
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Murillo-López J, Zinovjev K, Pereira H, Caniuguir A, Garratt R, Babul J, Recabarren R, Alzate-Morales J, Caballero J, Tuñón I, Cabrera R. Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations. Chem Sci 2019; 10:2882-2892. [PMID: 30996866 PMCID: PMC6429617 DOI: 10.1039/c9sc00094a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/24/2019] [Indexed: 12/31/2022] Open
Abstract
Phosphofructokinases catalyze the ATP-dependent phosphorylation of fructose-6-phosphate and they are highly regulated.
Phosphofructokinases (Pfks) catalyze the ATP-dependent phosphorylation of fructose-6-phosphate (F6P) and they are regulated in a wide variety of organisms. Although numerous aspects of the kinetics and regulation have been characterized for Pfks, the knowledge about the mechanism of the phosphoryl transfer reaction and the transition state lags behind. In this work, we describe the X-ray crystal structure of the homodimeric Pfk-2 from E. coli, which contains products in one site and reactants in the other, as well as an additional ATP molecule in the inhibitory allosteric site adjacent to the reactants. This complex was previously predicted when studying the kinetic mechanism of ATP inhibition. After removing the allosteric ATP, molecular dynamic (MD) simulations revealed conformational changes related to domain packing, as well as stable interactions of Lys27 and Asp256 with donor (ATP) and acceptor (fructose-6-) groups, and of Asp166 with Mg2+. The phosphoryl transfer reaction mechanism catalyzed by Pfk-2 was investigated through Quantum Mechanics/Molecular Mechanics (QM/MM) simulations using a combination of the string method and a path-collective variable for the exploration of its free energy surface. The calculated activation free energies showed that a dissociative mechanism, occurring with a metaphosphate intermediate formation followed by a proton transfer to Asp256, is more favorable than an associative one. The structural analysis reveals the role of Asp256 acting as a catalytic base and Lys27 stabilizing the transition state of the dissociative mechanism.
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Affiliation(s)
- Juliana Murillo-López
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Kirill Zinovjev
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Humberto Pereira
- Instituto de Física de São Carlos , Universidade de São Paulo , São Paulo , Brazil
| | - Andres Caniuguir
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
| | - Richard Garratt
- Instituto de Física de São Carlos , Universidade de São Paulo , São Paulo , Brazil
| | - Jorge Babul
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
| | - Rodrigo Recabarren
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Jans Alzate-Morales
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM) , Facultad de Ingeniería , Universidad de Talca , 1 Poniente 1141 , Talca , Chile .
| | - Iñaki Tuñón
- Departament de Química Física , Universitat de València , 46100 Burjassot , Spain .
| | - Ricardo Cabrera
- Departamento de Biología , Facultad de Ciencias , Universidad de Chile , Santiago , Chile .
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10
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Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method. Molecules 2018; 23:molecules23102652. [PMID: 30332773 PMCID: PMC6222333 DOI: 10.3390/molecules23102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022] Open
Abstract
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
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Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
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11
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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12
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Zinovjev K, Tuñón I. Adaptive Finite Temperature String Method in Collective Variables. J Phys Chem A 2017; 121:9764-9772. [DOI: 10.1021/acs.jpca.7b10842] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kirill Zinovjev
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
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13
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Abstract
Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.
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14
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Zinovjev K, Tuñón I. Reaction coordinates and transition states in enzymatic catalysis. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1329] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kirill Zinovjev
- Departament de Química FísicaUniversitat de València Valencia Spain
| | - Iñaki Tuñón
- Departament de Química FísicaUniversitat de València Valencia Spain
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15
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Aranda J, Attana F, Tuñón I. Molecular Mechanism of Inhibition of DNA Methylation by Zebularine. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Juan Aranda
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Fedaa Attana
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departamento Química
Física, Universitat de València, 46100 Burjassot, Spain
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16
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Smyrnova D, Zinovjev K, Tuñón I, Ceulemans A. Thermal Isomerization Mechanism in Dronpa and Its Mutants. J Phys Chem B 2016; 120:12820-12825. [PMID: 28002952 DOI: 10.1021/acs.jpcb.6b10859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoswitching speed of the reversibly switchable fluorescent proteins (RSFPs) from the family of green fluorescent proteins (GFPs) changes upon mutation which is of direct importance for various high-resolution techniques. Dronpa is one of the most used RSFPs. Its point mutants rsFastLime (Dronpa V157G) and rsKame (Dronpa V157L) exhibit a striking difference in their photoswitching speed. Here the QM/MM on-the-fly string method is used in order to explore the details of the thermal isomerization mechanism. The four principal ways in which isomerization may occur have been scrutinized for each of the three proteins. It has been shown that thermal isomerization occurs via a one-bond-flip mechanism in all three proteins, although, in rsKame, where the chromophore is constrained more, the activation free energy difference between hula-twist and one-bond-flip is significantly smaller. Functional mode analysis has been applied to examine the motions of the amino acids during the isomerization. It clearly identifies the importance of Val/Leu 157 as well as the amino acids in the α-helix during the isomerization.
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Affiliation(s)
- Daryna Smyrnova
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València , 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València , 46100 Burjassot, Spain
| | - Arnout Ceulemans
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven , Celestijnenlaan 200F, 3001 Heverlee, Belgium
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17
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Cao L, Cheng L, Tang T, Liu J, Zhang D, Xu P, Li G. Understanding enzyme reactions using enhanced sampling techniques. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1132316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Wu D, Fajer MI, Cao L, Cheng X, Yang W. Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways. Methods Enzymol 2016; 577:57-74. [PMID: 27498634 PMCID: PMC4978182 DOI: 10.1016/bs.mie.2016.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this minipresentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study.
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Affiliation(s)
- D Wu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - M I Fajer
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; Florida State University, Tallahassee, FL, United States
| | - L Cao
- Florida State University, Tallahassee, FL, United States
| | - X Cheng
- UT-ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, United States; The University of Tennessee, Knoxville, TN, United States.
| | - W Yang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States; Florida State University, Tallahassee, FL, United States.
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19
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Aranda J, Zinovjev K, Świderek K, Roca M, Tuñón I. Unraveling the Reaction Mechanism of Enzymatic C5-Cytosine Methylation of DNA. A Combined Molecular Dynamics and QM/MM Study of Wild Type and Gln119 Variant. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00394] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Juan Aranda
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Katarzyna Świderek
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Maite Roca
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Quı́mica Fı́sica, Universitat de València, 46100 Burjassot, Spain
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20
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He X, Shen Y, Hung FR, Santiso EE. Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt. J Chem Phys 2015; 143:124506. [PMID: 26429023 DOI: 10.1063/1.4931654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The homogeneous nucleation of crystals of the ionic liquid [dmim(+)][Cl(-)] from its supercooled liquid phase in the bulk (P = 1 bar, T = 340 K, representing a supercooling of 58 K) was studied using molecular simulations. The string method in collective variables [Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] was used in combination with Markovian milestoning with Voronoi tessellations [Maragliano et al., J. Chem. Theory Comput. 5, 2589-2594 (2009)] and order parameters for molecular crystals [E. E. Santiso and B. L. Trout, J. Chem. Phys. 134, 064109 (2011)] to sketch a minimum free energy path connecting the supercooled liquid and the monoclinic crystal phases, and to determine the free energy and the rates involved in the homogeneous nucleation process. The physical significance of the configurations found along this minimum free energy path is discussed with the help of calculations based on classical nucleation theory and with additional simulation results obtained for a larger system. Our results indicate that, at a supercooling of 58 K, the liquid has to overcome a free energy barrier of the order of 60 kcal/mol and to form a critical nucleus with an average size of about 3.6 nm, before it reaches the thermodynamically stable crystal phase. A simulated homogeneous nucleation rate of 5.0 × 10(10) cm(-3) s(-1) was obtained for our system, which is in reasonable agreement with experimental and simulation rates for homogeneous nucleation of ice at similar degrees of supercooling. This study represents our first step in a series of studies aimed at understanding the nucleation and growth of crystals of organic salts near surfaces and inside nanopores.
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Affiliation(s)
- Xiaoxia He
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Yan Shen
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Francisco R Hung
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Erik E Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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21
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Manna RN, Zinovjev K, Tuñón I, Dybala-Defratyka A. Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study. J Phys Chem B 2015; 119:15100-9. [DOI: 10.1021/acs.jpcb.5b07538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rabindra Nath Manna
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
| | - Kirill Zinovjev
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament
de Química Física, Universitat de Valéncia, 46100 Burjassot, Spain
| | - Agnieszka Dybala-Defratyka
- Institute
of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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22
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Zinovjev K, Tuñón I. Transition state ensemble optimization for reactions of arbitrary complexity. J Chem Phys 2015; 143:134111. [DOI: 10.1063/1.4931596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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23
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Sousa SF, Ramos MJ, Lim C, Fernandes PA. Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sérgio F. Sousa
- 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
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - 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
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24
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Fujisaki H, Moritsugu K, Matsunaga Y, Morishita T, Maragliano L. Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review. Front Bioeng Biotechnol 2015; 3:125. [PMID: 26389113 PMCID: PMC4558547 DOI: 10.3389/fbioe.2015.00125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/10/2015] [Indexed: 01/12/2023] Open
Abstract
Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.
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Affiliation(s)
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Tetsuya Morishita
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Luca Maragliano
- Center for Synaptic Neuroscience, Istituto Italiano di Tecnologia, Genova, Italy
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25
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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26
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Branduardi D, Marinelli F, Faraldo-Gómez JD. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method. J Comput Chem 2015; 37:575-86. [PMID: 26149527 DOI: 10.1002/jcc.23991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 01/28/2023]
Abstract
The atomic mechanisms of isomerization of ATP-Mg(2+) in solution are characterized using the recently developed String Method with Optimal Molecular Alignment (SOMA) and molecular-dynamics simulations. Bias-Exchange Metadynamics simulations are first performed to identify the primary conformers of the ATP-Mg(2+) complex and their connectivity. SOMA is then used to elucidate the minimum free-energy path (MFEP) for each transition, in a 48-dimensional space. Analysis of the per-atom contributions to the global free-energy profiles reveals that the mechanism of these transitions is controlled by the Mg(2+) ion and its coordinating oxygen atoms in the triphosphate moiety, as well as by the ion-hydration shell. Metadynamics simulations in path collective variables based on the MFEP demonstrate these isomerizations proceed across a narrow channel of configurational space, thus validating the premise underlying SOMA. This study provides a roadmap for the examination of conformational changes in biomolecules, based on complementary enhanced-sampling techniques with different strengths. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Davide Branduardi
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, Frankfurt-am-Main, DE 60438, Germany
| | - Fabrizio Marinelli
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland, 20892
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, Frankfurt-am-Main, DE 60438, Germany.,Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health, Building 5635FL, Suite T-800, Bethesda, Maryland, 20892
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27
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Aranda J, Zinovjev K, Roca M, Tuñón I. Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase. J Am Chem Soc 2014; 136:16227-39. [DOI: 10.1021/ja5077124] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Aranda
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Kirill Zinovjev
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Maite Roca
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química
Física, Universitat de València, 46100 Burjassot, Spain
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28
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Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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29
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Zinovjev K, Tuñón I. Exploring chemical reactivity of complex systems with path-based coordinates: Role of the distance metric. J Comput Chem 2014; 35:1672-81. [DOI: 10.1002/jcc.23673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/16/2014] [Accepted: 06/18/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Kirill Zinovjev
- Departament de Química Física; Universitat de València; 46100 Burjassot Spain
| | - Iñaki Tuñón
- Departament de Química Física; Universitat de València; 46100 Burjassot Spain
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30
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Swiderek K, Ruiz-Pernía JJ, Moliner V, Tuñón I. Heavy enzymes--experimental and computational insights in enzyme dynamics. Curr Opin Chem Biol 2014; 21:11-8. [PMID: 24709164 DOI: 10.1016/j.cbpa.2014.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/14/2014] [Indexed: 11/18/2022]
Abstract
The role of protein motions in the chemical step of enzyme-catalyzed reactions is the subject of an open debate in the scientific literature. The systematic use of isotopically substituted enzymes has been revealed as a useful tool to quantify the role of these motions. According to the Born-Oppenheimer approximation, changing the mass of the protein does not change the forces acting on the system but alters the frequencies of the protein motions, which in turn can affect the rate constant. Experimental and theoretical studies carried out in this field are presented in this article and discussed in the framework of Transition State Theory.
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Affiliation(s)
- Katarzyna Swiderek
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - J Javier Ruiz-Pernía
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Departamento de Química Física y Analítica, Universitat Jaume I, 12071 Castellón, Spain.
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain.
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31
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Świderek K, Tuñón I, Moliner V. Predicting enzymatic reactivity: from theory to design. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1173] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katarzyna Świderek
- Departamento de Química FísicaUniversidad de ValenciaValenciaSpain
- Institute of Applied Radiation ChemistryLodz University of TechnologyLodzPoland
| | - Iñaki Tuñón
- Departamento de Química FísicaUniversidad de ValenciaValenciaSpain
| | - Vicent Moliner
- Departament de Química Física i AnalíticaUniversitat Jaume ICastellónSpain
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