1
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Affiliation(s)
- M. Roca
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - V. Moliner
- Departament
de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - I. Tuñón
- Departament
de Química Física, Universitat de València, 46100 Burjassot, Spain
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2
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
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Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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4
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Affiliation(s)
- S Martí
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, Castellón, Spain
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Martí S, Andrés J, Silla E, Moliner V, Tuñón I, Bertrán J. Computer-Aided Rational Design of Catalytic Antibodies: The 1F7 Case. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Tortonda F, Pascual-Ahuir J, Silla E, Tuñón I. A theoretical study of solvent effects on the conformational equilibria of neutral glycine in aqueous solution. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(02)00697-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Martí S, Andrés J, Moliner V, Silla E, Tuñón I, Bertrán J, Field MJ. A hybrid potential reaction path and free energy study of the chorismate mutase reaction. J Am Chem Soc 2001; 123:1709-12. [PMID: 11456771 DOI: 10.1021/ja003522n] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We present a combination of two techniques--QM/MM statistical simulation methods and QM/MM internal energy minimizations--to get a deeper insight into the reaction catalyzed by the enzyme chorismate mutase. Structures, internal energies and free energies, taken from the paths of the reaction in solution and in the enzyme have been analyzed in order to estimate the relative importance of the reorganization and preorganization effects. The results we obtain for this reaction are in good agreement with experiment and show that chorismate mutase achieves its catalytic efficiency in two ways; first, it preferentially binds the active conformer of the substrate and, second, it reduces the free energy of activation for the reaction relative to that in solution by providing an environment which stabilizes the transition state.
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Affiliation(s)
- S Martí
- Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castellón, Spain
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Collado JA, Tuñón I, Silla E, Ramírez FJ. Vibrational Dynamics of Histamine Monocation in Solution: an Experimental (FT-IR, FT-Raman) and Theoretical (SCRF-DFT) Study. J Phys Chem A 2000. [DOI: 10.1021/jp994084d] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- J. A. Collado
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia) Spain
| | - I. Tuñón
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia) Spain
| | - E. Silla
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia) Spain
| | - F. J. Ramírez
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia) Spain
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Ruiz-López MF, Oliva A, Tuñón I, Bertrán J. Self-Consistent Reaction Field Calculations of Nonequilibrium Solvent Effects on Proton Transfer Processes through Low-Barrier Hydrogen Bonds. J Phys Chem A 1998. [DOI: 10.1021/jp983288b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. F. Ruiz-López
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - A. Oliva
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - I. Tuñón
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
| | - J. Bertrán
- Laboratoire de Chimie Théorique, UMR CNRS-UHP 7565, Université Henri Poincaré, Nancy I, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Unitat de Química Física, Universitat Autónoma de Barcelona, 08193 Bellaterra (Barcelona), Spain, and Departamento de Química Física, Universidad de Valencia, 46100 Burjasot, Spain
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Ramírez FJ, Tuñón I, Silla E. Amino Acid Chemistry in Solution: Structural Study and Vibrational Dynamics of Glutamine in Solution. An ab Initio Reaction Field Model. J Phys Chem B 1998. [DOI: 10.1021/jp981831i] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- F. J. Ramírez
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia), Spain
| | - I. Tuñón
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia), Spain
| | - E. Silla
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, 29071-Málaga, Spain, and Departamento de Química Física, Universidad de Valencia, 46100-Burjassot (Valencia), Spain
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Tuñón I, Martins-Costa MTC, Millot C, Ruiz-López MF. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. I. Proton transfer in strongly H-bonded complexes. J Chem Phys 1997. [DOI: 10.1063/1.473457] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Strnad M, Martins-Costa MTC, Millot C, Tuñón I, Ruiz-López MF, Rivail JL. Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes. J Chem Phys 1997. [DOI: 10.1063/1.473458] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Moliner V, Castillo R, Safont VS, Oliva M, Bohn S, Tuñón I, Andrés J. A Theoretical Study of the Favorskii Rearrangement. Calculation of Gas-Phase Reaction Paths and Solvation Effects on the Molecular Mechanism for the Transposition of the α-Chlorocyclobutanone. J Am Chem Soc 1997. [DOI: 10.1021/ja962571q] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- V. Moliner
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - R. Castillo
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - V. S. Safont
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - M. Oliva
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - S. Bohn
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - I. Tuñón
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - J. Andrés
- Contribution from the Departament de Ciències Experimentals, Universitat Jaume I, Box 224, 12080 Castelló, Spain, Departament de Química Física, Universitat de València, 46100 Burjassot, València, Spain, and Department of Organic Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
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14
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Affiliation(s)
- I Tuñón
- Department of Physical Chemistry, University of Valencia, Spain
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