Listar QFA_Articles por autoría "ba54d55b-7228-4673-ac29-a362ff9dbe45"
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A Collective Coordinate to Obtain Free Energy Profiles for Complex Reactions in Condensed Phases
Zinovjev, Kirill; Martí Forés, Sergio; Tuñón, Iñaki American Chemical Society (2012)Exploration of chemical reactions in complex explicit environments has become an affordable task with the use of hybrid quantum mechanics/molecular mechanics potentials which allow calculating free energy profiles of ... -
Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase
Aranda, Juan; Zinovjev, Kirill; Roca, Maite; Tuñón, Iñaki American Chemical Society (2014)M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used ... -
Elucidating the Catalytic Reaction Mechanism of Orotate Phosphoribosyltransferase by Means of X‑ray Crystallography and Computational Simulations
Roca, Maite; Navas Yuste, Sergio; Zinovjev, Kirill; López-Estepa, Miguel; Gómez, Sara; Fernández, Francisco J.; Vega, M. Cristina; Tuñón, Iñaki American Chemical Society (2020-01-02)Orotate phosphoribosyltransferase (OPRTase) catalyzes the reaction between the ribose donor α-d-5-phosphoribosyl-1-pyrophosphate (PRPP) and orotate (OA) in the presence of Mg2+ ion to obtain pyrophosphate and pyrimidine ... -
Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase
García Meseguer, Rafael; Zinovjev, Kirill; Roca, Maite; Ruiz-Pernía, José Javier; Tuñón, Iñaki American Chemical Society (2015-08)The role of protein motions in enzymatic catalysis is the subject of a hot scientific debate. We here propose the use of an explicit solvent coordinate to analyze the impact of environmental motions during the reaction ... -
Toward an Automatic Determination of Enzymatic Reaction Mechanisms and Their Activation Free Energies
Zinovjev, Kirill; Ruiz-Pernía, José Javier; Tuñón, Iñaki American Chemical Society (2013)We present a combination of the string method and a path collective variable for the exploration of the free energy surface associated to a chemical reaction in condensed environments. The on-the-fly string method is ... -
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
Aranda, Juan; Zinovjev, Kirill; Świderek, Katarzyna; Roca, Maite; Tuñón, Iñaki American Chemical Society (2016)M.HhaI is a DNA methyltransferase from Haemophilus hemolyticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C5 position of a cytosine. This enzyme is a paradigmatic model for C5 ...