Listar QFA_Articles por autoría "c79ceb3f-9b76-4354-8fd2-0fd65054c686"
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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 ... -
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, José Javier; Martí Forés, Sergio; Moliner, Vicent; Tuñón, Iñaki American Chemical Society (2012)The electrostatic behavior of active site residues in enzyme catalysis is quite different from that of water molecules in solution. To highlight the electrostatic differences between both environments, we propose a QM/MM ... -
A QM/MM study of the reaction mechanism for the 3′-processing step catalyzed by HIV-1 integrase
Ruiz-Pernía, José Javier; Nahum Alves, Cláudio; Moliner, Vicent; Silla, Estanislao; Tuñón, Iñaki Elsevier (2009)Integrase (IN) is one of the three human immunodeficiency virus type 1 enzymes (HIV-1) essential for effective viral replication. This viral enzyme is involved in the integration of HIV DNA into host chromosomal DNA. In ... -
A quantum mechanic/molecular mechanic study of the wild-type and N155S mutant HIV-1 integrase complexed with diketo acid
Nahum Alves, Cláudio; Martí Forés, Sergio; Castillo, Raquel; Andres, Juan; Moliner, Vicent; Tuñón, Iñaki; Silla, Estanislao (2008)Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. Recently, mutation studies have been reported that have shown that a certain degree of viral ... -
A Quantum Mechanics / Molecular Mechanics Study of the Protein-Ligand Interaction of two potent inhibitors of human O-GlcNAcase: PUGNAc and NAG-thiazoline
Moliner, Vicent; Nahum Alves, Cláudio; Lameira, Jerônimo; Martí Forés, Sergio; Kanaan Izquierdo, Natalia; Tuñón, Iñaki American Chemical Society (2008)O-glycoprotein 2-acetamino-2-deoxy-β-D-glucopyranosidase (O-GlcNAcase) hydrolyzes 2-acetamido-2-deoxy-β-D-glucopyranose (O-GlcNAc) residues of serine/threonine residues of modified proteins. O-GlcNAc is present in many ... -
Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase
Martí, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Joan American Chemical Society (2020-09-03)The design of biocatalysts is a goal to improve the rate, selectivity and environmental friendship of chemical processes in biotechnology. In this regard, the use of computational techniques has provided valuable assistance ... -
Chemical Ligation and Isotope Labeling to Locate Dynamic Effects during Catalysis by Dihydrofolate Reductase
Luk, Louis Y. P.; Ruiz-Pernía, José Javier; Adesina, Aduragbemi S.; Loveridge, E. Joel; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K. Wiley (2015-07-27)Experimental and computational approaches have long been employed to define the role of protein motions in en- zyme catalysis, but a refined experimental method for locating the origin of dynamic effects has not previously ... -
Computational design of biological catalysts
Martí Forés, Sergio; Andres, Juan; Moliner, Vicent; Silla, Estanislao; Tuñón, Iñaki; Bertrán, Juan Royal Society of Chemistry (2008)The purpose of this tutorial review is to illustrate the way to design new and powerful catalysts. The first possibility to get a biological catalyst for a given chemical process is to use existing enzymes that catalyze ... -
Computational strategies for the design of new enzymatic functions
Świderek, Katarzyna; Tuñón, Iñaki; Moliner, Vicent; Bertrán, Juan Elsevier (2015-09-15)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, ... -
Computational study on hydrolysis of Cefotaxime in gas phase and in aqueous solution
Meliá, Conchín; Ferrer, Silvia; Moliner, Vicent; Tuñón, Iñaki; Beltrán, Juan Wiley-Blackwell (2012)We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy ... -
Convergence of Theory and Experiment on the Role of Preorganization, Quantum Tunneling, and Enzyme Motions into Flavoenzyme-Catalyzed Hydride Transfer
Delgado, Manuel; Görlich, Stefan; Scrutton, Nigel; Hay, Sam; Moliner, Vicent; Tuñón, Iñaki American Chemical Society (2017)Hydride transfer is one of the most common reactions catalyzed by enzymatic systems, and it has become an object of study because of possible significant quantum tunneling effects. In the present work, we provide a combination ... -
Diseño computacional de catalizadores biológicos
Martí Forés, Sergio; Moliner, Vicent; Andres, Juan; Roca, Maite; López Canut, Violeta; Silla, Estanislao; Tuñón, Iñaki; Bertrán, Juan Real Sociedad Española de Química (2011)Enzymes are a source of inspiration for the design of new and powerful industrial catalysts able to work, in principle, in mild conditions of pressure, temperature and solvents. The Transition State of the reaction is the ... -
Do Dynamic Effects Play a Significant Role in Enzymatic Catalysis? A Theoretical Analysis of Formate Dehydrogenase
Roca, Maite; Oliva, Mónica; Castillo, Raquel; Moliner, Vicent; Tuñón, Iñaki Wiley-VCH (2010)A theoretical study of the protein dynamic effects on the hydride transfer between the formate anion and nicotinamide adenine dinucleotide (NAD+), catalyzed by formate dehydrogenase (FDH), is presented in this paper. The ... -
Do zwitterionic species exist in the non-enzymatic peptide bond formation?
Świderek, Katarzyna; Tuñón, Iñaki; Martí Forés, Sergio; Moliner, Vicent; Bertrán, Juan The Royal Society of Chemistry (2012-09-30)The use of proper computational methods and models has allowed answering the controversial question of whether zwitterionic species exist in the mechanism of peptide bond synthesis in aqueous solution. In fact, the different ... -
Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water
Williams, Ian H.; Ruiz-Pernía, José Javier; Tuñón, Iñaki International Union of Pure and Applied Chemistry (2011)2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of ... -
Dynamic effects on reaction rates in a Michael Addition catalyzed by Chalcone Isomerase. Beyond the frozen environment approach
Ruiz-Pernía, José Javier; Tuñón, Iñaki; Moliner, Vicent; Hynes, James T.; Roca, Maite American Chemical Society (2008)We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6′-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction ... -
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 ... -
Electrostatics as a Guiding Principle in Understanding and Designing Enzymes
Ruiz-Pernía, José Javier; Świderek, Katarzyna; Bertran, Joan; Moliner, Vicent; Tuñón, Iñaki American Chemical Society (2024-03-12)Enzyme design faces challenges related to the implementation of the basic principles that govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic concepts that have been shown to ... -
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 ... -
Enzyme Molecular Mechanism as a Starting Point to Design New Inhibitors: A Theoretical Study of O-GlcNAcase
Lameira, Jerônimo; Nahum Alves, Cláudio; Tuñón, Iñaki; Martí Forés, Sergio; Moliner, Vicent ACS (2011-05)O-Glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) hydrolyzes O-linked 2-acetamido-2-deoxy-β-d-glucopyranoside (O-GlcNAc) residues from post-translationally modified serine/threonine residues of ...