Listar por autoría "483a8f3c-ddf2-41a0-aa46-da4c14cd9023"
Mostrando ítems 1-20 de 131
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A computational study of the phosphoryl transfer reaction between ATP and Dha in Aqueous Solution
Bordes, Isabel; Ruiz-Pernía, José Javier; Castillo, Raquel; Moliner, Vicent Royal Society of Chemistry (2015)Phosphoryl transfer reactions are ubiquitous in biology, being involved in processes ranging from energy and signal transduction to the replication genetic material. Dihydroxyacetone phosphate (Dha-P), an intermediate ... -
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 complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH
Mujika, Jon Iñaki; López, Xabier; Rezabal, Elixabete; Castillo, Raquel; Martí Forés, Sergio; Moliner, Vicent; Ugalde, Jesús M Elsevier (2011-11)Serumtransferrin (sTf) transports iron in serum and internalizes in cells via receptor mediated endocytosis. Additionally, sTf has been identified as the predominant aluminum carrier in serum. Some questions remain unclear ... -
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 QM/MM study on the origin of retro-aldolase activity of a catalytic antibody
de Raffele, daria; Martí, Sergio; Moliner, Vicent The Royal Society of Chemistry (2021-04-26)The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods. The amino acids involved in the reaction ... -
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 ... -
A theoretical study of carbon–carbon bond formation by a Michael-type addition
Świderek, Katarzyna; Pabis, Anna; Moliner, Vicent Royal Society of Chemistry (2012)A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional ... -
A theoretical study of the catalytic mechanism of formate dehydrogenase
Castillo, Raquel; Oliva, Mónica; Martí Forés, Sergio; Moliner, Vicent American Chemical Society (2008-07)A theoretical study of the hydride transfer between formate anion and nicotinamide adenine dinucleotide (NAD+) catalyzed by the enzyme formate dehydrogenase (FDH) has been carried out by a combination of two hybrid quantum ... -
Actitudes frente a las familias homoparentales en el contexto escolar
Ramirez, Sandra; Moliner, Vicent; Vicent, Lidón Universitat Jaume I (2006)Actualmente, en las escuelas conviven cada vez más, niños que provienen de contextos familiares muy diversos. En los últimos tiempos la inmigración ha sido uno de los fenómenos más investigados dentro del contexto escolar. ... -
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 ... -
Assessment of the PETase conformational changes induced bypoly(ethylene terephthalate) binding
Costa, Clauber Henrique Souza da; dos Santos, lberto M.; Nahum Alves, Cláudio; Martí, Sergio; Moliner, Vicent; Santana, Kauê; Lameira, Jerônimo Wiley (2021-06-02)Recently, a bacterium strain of Ideonella sakaiensis was identified with the uncommon ability to degrade the poly(ethylene terephthalate) (PET). The PETase from I. sakaiensis strain 201-F6 (IsPETase) catalyzes the hydrolysis ... -
Benchmarking Quantum Mechanics/Molecular Mechanics (QM/MM) Methods on the Thymidylate Synthase-Catalyzed Hydride Transfer
Świderek, Katarzyna; Arafet Cruz, Kemel; Kohen, Amnon; Moliner, Vicent American Chemical Society (2017-02)Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these ... -
Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT
Krzemińska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Świderek, Katarzyna American Chemical Society (2014-08)The current treatment for HIV-1 infected patients consists of a cocktail of inhibitors, in an attempt to improve the potency of the drugs by adding the possible effects of each supplied compound. In this contribution, nine ... -
Catalytic enantioselective epoxidation of nitroalkenes
Vidal-Albalat, Andreu; Świderek, Katarzyna; Izquierdo Ferrer, Javier; Rodríguez, Santiago; Moliner, Vicent; González, Florenci Royal Society of Chemistry (2016)Nitroepoxides are potentially exploitable as synthons with vicinal electrophilic centers. Nevertheless, although advances have been made in the field, enantioselective epoxidation of nitroalkenes is still a challenging ... -
Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog
Kholodar, Svetlana; Finer-Moore, Janet; Świderek, Katarzyna; Arafet Cruz, Kemel; Moliner, Vicent; Stroud, Robert M.; Kohen, Amnon American Chemical Society (2021-04-08)Methylation of 2-deoxyuridine-5′-monophosphate (dUMP) at the C5 position by the obligate dimeric thymidylate synthase (TSase) in the sole de novo biosynthetic pathway to thymidine 5′-monophosphate (dTMP) proceeds by forming ... -
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 ... -
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes
Galmés, Miquel À; Nödling, Alexander; Luk, Louis Y. P.; Świderek, Katarzyna; Moliner, Vicent American Chemical Society (2021-07-16)Convergent evolution has resulted in nonhomologous enzymes that contain similar active sites that catalyze the same primary and secondary reactions. Comparing how these enzymes achieve their reaction promiscuity can yield ... -
Computational Analysis of Human OGA Structure in Complex with PUGNAc and NAG-Thiazoline Derivatives
De Alencar, Nelson Alberto N.; Sousa, Paulo Robson M.; Silva, José Rogério A.; Lameira, Jerônimo; Nahum Alves, Cláudio; Martí Forés, Sergio; Moliner, Vicent American Chemical Society (2012)The substitution of serine and threonine residues in nucleocytoplasmic proteins with 2-acetamido-2-deoxy-β-d-glucopyranose (O-GlcNAc) residues is an essential post-translational modification found in many multicellular ... -
Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases
Galmes, Miquel Angel; Nödling, Alexander; He, Kaining; Luk, Louis Yu Pan; Świderek, Katarzyna; Moliner, Vicent The Royal Society of Chemistry (2022-03-15)While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics ...