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Best matches for Tuñón I[au]:

Adaptive Finite Temperature String Method in Collective Variables. Zinovjev K et al. J Phys Chem A. (2017)

Quantifying the limits of transition state theory in enzymatic catalysis. Zinovjev K et al. Proc Natl Acad Sci U S A. (2017)

Computational strategies for the design of new enzymatic functions. Świderek K et al. Arch Biochem Biophys. (2015)

Search results

Items: 1 to 50 of 111

1.

Why are some Enzymes Dimers? Flexibility and Catalysis in Thermotoga Maritima Dihydrofolate Reductase.

Ruiz-Pernía JJ, Tuñón I, Moliner V, Allemann RK.

ACS Catal. 2019 Jul 5;9(7):5902-5911. doi: 10.1021/acscatal.9b01250. Epub 2019 May 13.

2.

Convergence of theory and experiment on the role of preorganization, quantum tunneling and enzyme motions into flavoenzyme-catalyzed hydride transfer.

Delgado M, Görlich S, Longbotham JE, Scrutton NS, Hay S, Moliner V, Tuñón I.

ACS Catal. 2019 May 15;7(5):3190-3198. doi: 10.1021/acscatal.7b00201. Epub 2017 Apr 3.

3.

A first peek into sub-picosecond dynamics of spin energy levels in magnetic biomolecules.

Rosaleny LE, Zinovjev K, Tuñón I, Gaita-Ariño A.

Phys Chem Chem Phys. 2019 Jun 7;21(21):10908-10913. doi: 10.1039/c9cp01909j. Epub 2019 May 13.

PMID:
31080970
4.

Translocation of enzymes into a mesoporous MOF for enhanced catalytic activity under extreme conditions.

Navarro-Sánchez J, Almora-Barrios N, Lerma-Berlanga B, Ruiz-Pernía JJ, Lorenz-Fonfria VA, Tuñón I, Martí-Gastaldo C.

Chem Sci. 2019 Feb 28;10(14):4082-4088. doi: 10.1039/c9sc00082h. eCollection 2019 Apr 14.

5.

Heavy Enzymes and the Rational Redesign of Protein Catalysts.

Scott AF, Luk LY, Tuñón I, Moliner V, Allemann RK.

Chembiochem. 2019 Apr 24. doi: 10.1002/cbic.201900134. [Epub ahead of print]

PMID:
31016852
6.

Studying the phosphoryl transfer mechanism of the E. coli phosphofructokinase-2: from X-ray structure to quantum mechanics/molecular mechanics simulations.

Murillo-López J, Zinovjev K, Pereira H, Caniuguir A, Garratt R, Babul J, Recabarren R, Alzate-Morales J, Caballero J, Tuñón I, Cabrera R.

Chem Sci. 2019 Jan 28;10(10):2882-2892. doi: 10.1039/c9sc00094a. eCollection 2019 Mar 14.

7.

Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design.

Ramos-Guzmán CA, Zinovjev K, Tuñón I.

Eur J Med Chem. 2019 May 1;169:159-167. doi: 10.1016/j.ejmech.2019.02.064. Epub 2019 Feb 27.

PMID:
30875506
8.

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA.

Francés-Monerris A, Gattuso H, Roca-Sanjuán D, Tuñón I, Marazzi M, Dumont E, Monari A.

Chem Sci. 2018 Sep 18;9(41):7902-7911. doi: 10.1039/c8sc03252a. eCollection 2018 Nov 7.

9.

Catalytic Reaction Mechanism in Native and Mutant Catechol- O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis.

Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E.

J Phys Chem B. 2018 Sep 27;122(38):8861-8871. doi: 10.1021/acs.jpcb.8b07339. Epub 2018 Sep 12.

PMID:
30157632
10.

Insights on the Origin of Catalysis on Glycine N-Methyltransferase from Computational Modeling.

Świderek K, Tuñón I, Williams IH, Moliner V.

J Am Chem Soc. 2018 Mar 28;140(12):4327-4334. doi: 10.1021/jacs.7b13655. Epub 2018 Feb 26.

11.

Isotope Substitution of Promiscuous Alcohol Dehydrogenase Reveals the Origin of Substrate Preference in the Transition State.

Behiry EM, Ruiz-Pernia JJ, Luk L, Tuñón I, Moliner V, Allemann RK.

Angew Chem Int Ed Engl. 2018 Mar 12;57(12):3128-3131. doi: 10.1002/anie.201712826. Epub 2018 Feb 19.

12.

Adaptive Finite Temperature String Method in Collective Variables.

Zinovjev K, Tuñón I.

J Phys Chem A. 2017 Dec 28;121(51):9764-9772. doi: 10.1021/acs.jpca.7b10842. Epub 2017 Dec 18.

PMID:
29190105
13.

Quantifying the limits of transition state theory in enzymatic catalysis.

Zinovjev K, Tuñón I.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12390-12395. doi: 10.1073/pnas.1710820114. Epub 2017 Nov 3.

14.

Insights into the inhibited form of the redox-sensitive SufE-like sulfur acceptor CsdE.

Peña-Soler E, Aranda J, López-Estepa M, Gómez S, Garces F, Coll M, Fernández FJ, Tuñon I, Vega MC.

PLoS One. 2017 Oct 18;12(10):e0186286. doi: 10.1371/journal.pone.0186286. eCollection 2017.

15.

Regioselectivity of the OH Radical Addition to Uracil in Nucleic Acids. A Theoretical Approach Based on QM/MM Simulations.

Aranda J, Francés-Monerris A, Tuñón I, Roca-Sanjuán D.

J Chem Theory Comput. 2017 Oct 10;13(10):5089-5096. doi: 10.1021/acs.jctc.7b00610. Epub 2017 Sep 28.

PMID:
28901132
16.

Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA.

Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E.

Phys Chem Chem Phys. 2017 Jun 7;19(22):14695-14701. doi: 10.1039/c6cp07966k.

PMID:
28537602
17.

Revealing the Origin of the Efficiency of the De Novo Designed Kemp Eliminase HG-3.17 by Comparison with the Former Developed HG-3.

Świderek K, Tuñón I, Moliner V, Bertran J.

Chemistry. 2017 Jun 1;23(31):7582-7589. doi: 10.1002/chem.201700807. Epub 2017 May 15.

PMID:
28334464
18.

Thermal Isomerization Mechanism in Dronpa and Its Mutants.

Smyrnova D, Zinovjev K, Tuñón I, Ceulemans A.

J Phys Chem B. 2016 Dec 22;120(50):12820-12825. doi: 10.1021/acs.jpcb.6b10859. Epub 2016 Dec 8.

PMID:
28002952
19.
20.

Singlet Oxygen Attack on Guanine: Reactivity and Structural Signature within the B-DNA Helix.

Dumont E, Grüber R, Bignon E, Morell C, Aranda J, Ravanat JL, Tuñón I.

Chemistry. 2016 Aug 22;22(35):12358-62. doi: 10.1002/chem.201601287. Epub 2016 Jul 21.

PMID:
27440482
21.

Minimization of dynamic effects in the evolution of dihydrofolate reductase.

Ruiz-Pernía JJ, Behiry E, Luk LYP, Loveridge EJ, Tuñón I, Moliner V, Allemann RK.

Chem Sci. 2016 May 1;7(5):3248-3255. doi: 10.1039/c5sc04209g. Epub 2016 Feb 3.

22.

Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study.

Manna RN, Zinovjev K, Tuñón I, Dybala-Defratyka A.

J Phys Chem B. 2015 Dec 10;119(49):15100-9. doi: 10.1021/acs.jpcb.5b07538. Epub 2015 Nov 25.

PMID:
26561208
23.

Publisher's Note: "Transition state ensemble optimization for reactions of arbitrary complexity" [J. Chem. Phys. 143, 134111 (2015)].

Zinovjev K, Tuñón I.

J Chem Phys. 2015 Nov 7;143(17):179902. doi: 10.1063/1.4935109. No abstract available.

PMID:
26547187
24.

Transition state ensemble optimization for reactions of arbitrary complexity.

Zinovjev K, Tuñón I.

J Chem Phys. 2015 Oct 7;143(13):134111. doi: 10.1063/1.4931596. Erratum in: J Chem Phys. 2015 Nov 7;143(17):179902.

PMID:
26450296
25.

Peptide Bond Formation Mechanism Catalyzed by Ribosome.

Świderek K, Marti S, Tuñón I, Moliner V, Bertran J.

J Am Chem Soc. 2015 Sep 23;137(37):12024-34. doi: 10.1021/jacs.5b05916. Epub 2015 Sep 10.

26.

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.

Tuñón I, Laage D, Hynes JT.

Arch Biochem Biophys. 2015 Sep 15;582:42-55. doi: 10.1016/j.abb.2015.06.004. Epub 2015 Jun 15.

27.

Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase.

Luk LY, Ruiz-Pernía JJ, Adesina AS, Loveridge EJ, Tuñón I, Moliner V, Allemann RK.

Angew Chem Int Ed Engl. 2015 Jul 27;54(31):9016-20. doi: 10.1002/anie.201503968. Epub 2015 Jun 16.

28.

Computational strategies for the design of new enzymatic functions.

Świderek K, Tuñón I, Moliner V, Bertran J.

Arch Biochem Biophys. 2015 Sep 15;582:68-79. doi: 10.1016/j.abb.2015.03.013. Epub 2015 Mar 19. Review.

29.
30.

Enzyme promiscuity in enolase superfamily. Theoretical study of o-succinylbenzoate synthase using QM/MM methods.

Sánchez-Tarín M, Swiderek K, Roca M, Tuñón I.

J Phys Chem B. 2015 Feb 5;119(5):1899-911. doi: 10.1021/jp511147b. Epub 2015 Jan 22.

PMID:
25556698
31.

Protein isotope effects in dihydrofolate reductase from Geobacillus stearothermophilus show entropic-enthalpic compensatory effects on the rate constant.

Luk LY, Ruiz-Pernía JJ, Dawson WM, Loveridge EJ, Tuñón I, Moliner V, Allemann RK.

J Am Chem Soc. 2014 Dec 10;136(49):17317-23. doi: 10.1021/ja5102536. Epub 2014 Nov 26.

PMID:
25396728
32.

Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.

Aranda J, Zinovjev K, Roca M, Tuñón I.

J Am Chem Soc. 2014 Nov 19;136(46):16227-39. doi: 10.1021/ja5077124. Epub 2014 Nov 7.

PMID:
25347783
33.

Linking electrostatic effects and protein motions in enzymatic catalysis. A theoretical analysis of catechol o-methyltransferase.

García-Meseguer R, Zinovjev K, Roca M, Ruiz-Pernía JJ, Tuñón I.

J Phys Chem B. 2015 Jan 22;119(3):873-82. doi: 10.1021/jp505746x. Epub 2014 Sep 10.

PMID:
25159911
34.

The catalytic mechanism of carboxylesterases: a computational study.

Aranda J, Cerqueira NM, Fernandes PA, Roca M, Tuñon I, Ramos MJ.

Biochemistry. 2014 Sep 16;53(36):5820-9. doi: 10.1021/bi500934j. Epub 2014 Sep 4.

PMID:
25101647
35.

Exploring chemical reactivity of complex systems with path-based coordinates: role of the distance metric.

Zinovjev K, Tuñón I.

J Comput Chem. 2014 Sep 5;35(23):1672-81. doi: 10.1002/jcc.23673. Epub 2014 Jul 1.

PMID:
24986052
36.

Heavy enzymes--experimental and computational insights in enzyme dynamics.

Swiderek K, Ruiz-Pernía JJ, Moliner V, Tuñón I.

Curr Opin Chem Biol. 2014 Aug;21:11-8. doi: 10.1016/j.cbpa.2014.03.005. Epub 2014 Apr 5.

PMID:
24709164
37.

Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase.

Ruiz-Pernia JJ, Luk LY, García-Meseguer R, Martí S, Loveridge EJ, Tuñón I, Moliner V, Allemann RK.

J Am Chem Soc. 2013 Dec 11;135(49):18689-96. doi: 10.1021/ja410519h. Epub 2013 Nov 26.

38.

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis.

Luk LY, Javier Ruiz-Pernía J, Dawson WM, Roca M, Loveridge EJ, Glowacki DR, Harvey JN, Mulholland AJ, Tuñón I, Moliner V, Allemann RK.

Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16344-9. doi: 10.1073/pnas.1312437110. Epub 2013 Sep 24.

39.

Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies.

Zinovjev K, Ruiz-Pernía JJ, Tuñón I.

J Chem Theory Comput. 2013 Aug 13;9(8):3740-9. doi: 10.1021/ct400153r. Epub 2013 Jul 5.

PMID:
26584125
40.

Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates.

García-Meseguer R, Martí S, Ruiz-Pernía JJ, Moliner V, Tuñón I.

Nat Chem. 2013 Jul;5(7):566-71. doi: 10.1038/nchem.1660. Epub 2013 May 26.

PMID:
23787745
41.

Role of solvent on nonenzymatic peptide bond formation mechanisms and kinetic isotope effects.

Świderek K, Tuñón I, Martí S, Moliner V, Bertrán J.

J Am Chem Soc. 2013 Jun 12;135(23):8708-19. doi: 10.1021/ja403038t. Epub 2013 May 29.

PMID:
23679067
42.

The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach.

Reis M, Alves CN, Lameira J, Tuñón I, Martí S, Moliner V.

Phys Chem Chem Phys. 2013 Mar 21;15(11):3772-85. doi: 10.1039/c3cp43968b.

PMID:
23389436
43.

Modeling methods for studying post-translational and transcriptional modifying enzymes.

Roca M, Aranda J, Moliner V, Tuñón I.

Curr Opin Chem Biol. 2012 Dec;16(5-6):465-71. doi: 10.1016/j.cbpa.2012.10.014. Epub 2012 Nov 2. Review.

PMID:
23127358
44.

Do zwitterionic species exist in the non-enzymatic peptide bond formation?

Świderek K, Tuñón I, Martí S, Moliner V, Bertrán J.

Chem Commun (Camb). 2012 Nov 25;48(91):11253-5. doi: 10.1039/c2cc35409h.

PMID:
23070359
45.

Hydrolysis of phosphotriesters: a theoretical analysis of the enzymatic and solution mechanisms.

López-Canut V, Ruiz-Pernía JJ, Castillo R, Moliner V, Tuñón I.

Chemistry. 2012 Jul 27;18(31):9612-21. doi: 10.1002/chem.201103615. Epub 2012 Jun 28.

PMID:
22745111
46.

Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight.

Aranda J, Roca M, Tuñón I.

Org Biomol Chem. 2012 Jul 28;10(28):5395-400. doi: 10.1039/c2ob07021a. Epub 2012 Jun 15.

PMID:
22699309
47.

Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution.

Meliá C, Ferrer S, Moliner V, Tuñón I, Bertrán J.

J Comput Chem. 2012 Sep 15;33(24):1948-59. doi: 10.1002/jcc.23030. Epub 2012 Jun 7.

PMID:
22674452
48.

Reversibility and diffusion in mandelythiamin decarboxylation. Searching dynamical effects in decarboxylation reactions.

Roca M, Pascual-Ahuir JL, Tuñón I.

J Am Chem Soc. 2012 Jun 27;134(25):10509-14. doi: 10.1021/ja3026455. Epub 2012 Jun 19.

PMID:
22668129
49.

A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases.

Zinovjev K, Martí S, Tuñón I.

J Chem Theory Comput. 2012 May 8;8(5):1795-801. doi: 10.1021/ct300070b. Epub 2012 Apr 5.

PMID:
26593670
50.

A Novel Strategy to Study Electrostatic Effects in Chemical Reactions: Differences between the Role of Solvent and the Active Site of Chalcone Isomerase in a Michael Addition.

Ruiz-Pernía JJ, Martí S, Moliner V, Tuñón I.

J Chem Theory Comput. 2012 May 8;8(5):1532-5. doi: 10.1021/ct300064f. Epub 2012 Apr 10.

PMID:
26593647

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