Browsing by Author "ba54d55b-7228-4673-ac29-a362ff9dbe45"
Now showing items 1-9 of 9
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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 ... -
Elucidation of the Active Form and Reaction Mechanism in Human Asparaginase Type III Using Multiscale Simulations
Anđelković, Milorad; Zinovjev, Kirill; Ramos Guzmán, Carlos Alberto; Ruiz-Pernía, José Javier; Tuñón, Iñaki American Chemical Society (2023-08-27)l-asparaginases catalyze the asparagine hydrolysis to aspartate. These enzymes play an important role in the treatment of acute lymphoblastic leukemia because these cells are unable to produce their own asparagine. Due to ... -
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 ... -
The impact of SARS-CoV-2 3CL protease mutations on nirmatrelvir inhibitory efficiency. Computational insights into potential resistance mechanisms
Ramos Guzmán, Carlos Alberto; Anđelković, Milorad; Zinovjev, Kirill; Ruiz-Pernía, José Javier; Tuñón, Iñaki The Royal Society of Chemistry (2023-02-14)The use of antiviral drugs can promote the appearance of mutations in the target protein that increase the resistance of the virus to the treatment. This is also the case of nirmatrelvir, a covalent inhibitor of the 3CL ... -
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 ... -
Unveiling the Mechanistic Singularities of Caspases: A Computational Analysis of the Reaction Mechanism in Human Caspase-1
Ramos Guzmán, Carlos Alberto; Ruiz-Pernía, José Javier; Zinovjev, Kirill; Tuñón, Iñaki American Chemical Society (2023-04-07)Caspases are cysteine proteases in charge of breaking a peptide bond next to an aspartate residue. Caspases constitute an important family of enzymes involved in cell death and inflammatory processes. A plethora of diseases, ...