Listar por autoría "8e6d277b-277e-450a-a356-e4ec33461c44"
Mostrando ítems 1-20 de 29
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Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease
Movilla Núñez, Santiago; Martí, Sergio; Roca, Maite; Moliner, Vicent American Chemical Society (2023-01-17)Alzheimer’s disease represents one of the most ambitious challenges for biomedical sciences due to the growing number of cases worldwide in the elderly population and the lack of efficient treatments. One of the recent ... -
Critical evaluation of anharmonicity and configurational averaging in QM/MM modelling of equilibrium isotope effects
Roca, Maite; Upfold, Catherine M.; Williams, Ian Royal Society of Chemistry (2020)Anharmonic effects upon vibrational frequencies and isotopic partition function ratios are modelled computationally by means of quantum mechanics/molecular mechanics (QM/MM) methods for two systems. First, the methyl ... -
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 ... -
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 ... -
Effective approach for calculations of absolute stability of proteins using focused dielectric constants
Vicatos, Spyridon; Roca, Maite; Warshel, Arieh John Wiley & Sons, Inc. (2009-11)The ability to predict the absolute stability of proteins based on their corresponding sequence and structure is a problem of great fundamental and practical importance. In this work, we report an extensive, refinement and ... -
Electrostatic Contributions to Protein Stability and Folding Energy
Roca, Maite; Messer, Benjamin; Warshel, Arieh Federation of European Biochemical Societies (2007-05-15)The ability to predict the thermal stability of proteins based on their corresponding sequence is a problem of great fundamental and practical importance. Here we report an approach for calculating the electrostatic ... -
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 Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods
Sánchez-Tarín, María; Świderek, Katarzyna; Roca, Maite; Tuñón, Iñaki American Chemical Society (2015)The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. ... -
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 ... -
Modeling methods for studying post-translational and transcriptional modifying enzymes
Roca, Maite; Aranda, Juan; Moliner, Vicent; Tuñón, Iñaki Elsevier (2012)Biological catalysis is a complex chemical process that involves not only electronic reorganization in the substrate but also the reorganization of the catalyst. This complexity is even larger in the case of post-transcriptional ... -
Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases
Movilla Núñez, Santiago; Roca, Maite; Moliner, Vicent; Magistrato, Alessandra American Chemical Society (2023-03-29)The spliceosome machinery catalyzes precursor messenger (pre-m)RNA splicing. In each cycle, the spliceosome experiences massive compositional and conformational remodeling fueled by the concerted action of specific ... -
On the relationship between folding and chemical landscapes in enzyme catalysis
Roca, Maite; Messer, Benjamin; Hilvert, Donald; Warshel, Arieh National Academy of Sciences (2008-09-16)Elucidating the relationship between the free energy landscape of enzymes and their catalytic power has been one of the challenges of modern enzymology. The present work explores this issue by using a simplified folding ... -
On the relationship between thermal stability and catalytic power of enzymes
Roca, Maite; Liu, Hanbin; Messer, Benjamin; Warshel, Arieh ACS Publications (2007-12-25)The possible relationship between the thermal stability and the catalytic power of enzymes is of great current interest. In particular, it has been suggested that thermophilic or hyperthermophilic ... -
Origin of Enzymatic Kinetic Isotope Effects in Human Purine Nucleoside Phosphorylase
Roca, Maite; Moliner, Vicent; Tuñón, Iñaki American Chemical Society (2017)Here we report a study of the effect of heavy isotope labeling on the reaction catalyzed by human purine nucleoside phosphorylase (hPNP) to elucidate the origin of its catalytic effect and of the enzymatic kinetic isotope ... -
Promiscuity in alkaline phosphatase superfamily: unraveling evolution through molecular simulations
Moliner, Vicent; Roca, Maite; Bertrán, Juan; Tuñón, Iñaki; López Canut, Violeta American Chemical Society (2011-08)We here present a theoretical study of the alkaline hydrolysis of a phosphodiester (methyl p-nitrophenyl phosphate or MpNPP) in the active site of Escherichia coli alkaline phosphatase (AP), a monoesterase that also presents ... -
Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions
Roca, Maite; Pascual Ahuir, Juan Luis; Tuñón, Iñaki American Chemical Society (2012-06)Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, ... -
Selective oxidation of alkyl and aryl glyceryl monoethers catalysed by an engineered and immobilised glycerol dehydrogenase
Velasco-Lozano, Susana; Roca, Maite; Leal-Duaso, Alejandro; Mayoral, José A.; Pires, Elisabet; Moliner, Vicent; López Gallego, Fernando Royal Society of Chemistry (2020-12-07)Enzymes acting over glyceryl ethers are scarce in living cells, and consequently biocatalytic transformations of these molecules are rare despite their interest for industrial chemistry. In this work, we have engineered ... -
Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight
Aranda, Juan; Roca, Maite; Tuñón, Iñaki Royal Society of Chemistry (2012)M.PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes methylation of cytosine at the N4 position. This enzyme also displays promiscuous activity catalyzing methylation of adenine at the N6 ...