Listar por autoría "6b7ee591-3a9b-4bf9-a5ce-5fe4392a2512"
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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 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 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 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 ... -
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 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 study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi
De Farias Silva, Natália; Lameira, Jerônimo; Nahum Alves, Cláudio; Martí Forés, Sergio Royal Society of Chemistry (2013)Chagas' disease is considered to be a health problem affecting millions of people in Latin America. This disease is caused by the parasite Trypanosoma cruzi. Recently dihydroorotate dehydrogenase class 1A from Trypanosoma ... -
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 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 ... -
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 ... -
Increased Dynamic Effects in a Catalytically Compromised Variant of Escherichia coli Dihydrofolate Reductase
Ruiz-Pernía, José Javier; Luk, Louis Y. P.; García Meseguer, Rafael; Martí Forés, Sergio; Loveridge, E. Joel; Tuñón, Iñaki; Moliner, Vicent; Allemann, Rudolf K. American Chemical Society (2013)Isotopic substitution (15N, 13C, 2H) of a catalytically compromised variant of Escherichia coli dihydrofolate reductase, EcDHFR-N23PP/S148A, has been used to investigate the effect of these mutations on catalysis. The ... -
Joint Use of Bonding Evolution Theory and QM/MM Hybrid Method for Understanding the Hydrogen Abstraction Mechanism via Cytochrome P450 Aromatase
Viciano Gonzalo, Ignacio; González Navarrete, Patricio; Andres, Juan; Martí Forés, Sergio Copyright © 2015 American Chemical Society (2015-02)Bonding evolution theory (BET), as a combination of the electron localization function (ELF) and Thom’s catastrophe theory (CT), has been coupled with quantum mechanics/molecular mechanics (QM/MM) method in order to study ... -
Mechanism and plasticity of isochorismate pyruvate lyase: a computational study
Martí Forés, Sergio; Andres, Juan; Moliner, Vicent; Silla, Estanislao; Tuñón, Iñaki; Bertrán, Juan American Chemical Society (2009)The isochorismate pyruvate lyase (IPL) from Pseudomonas aeruginosa, designated as PchB, catalyzes the transformation of isochorismate into pyruvate and salicylate, but it also catalyzes the rearrangement of chorismate into ... -
Molecular mechanism of chorismate mutase activity of promiscuos MbtI
Andres, Juan; Ferrer Castillo, Silvia; Martí Forés, Sergio; Moliner, Vicent; Tuñón, Iñaki; Bertrán, Juan Springer (2010-06-15)Salicylate synthase from Mycobacterium tuberculosis, MbtI, initiates the biosynthesis of siderophores by converting chorismate to salicylate. Nevertheless, three more distinct activities for wild-type MbtI have been detected ... -
Molecular Mechanism of the site-specific self-cleavage of the RNA phosphodiester backbone by a Twister Ribozyme
Świderek, Katarzyna; Martí Forés, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertrán, Juan Springer (2017-02)The catalytic activity of some classes of natural RNA, named as ribozymes, has been discovered just in the past decades. In this paper, the cleavage of the RNA phosphodiester backbone has been studied in aqueous solution ... -
New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis
Viciano Gonzalo, Ignacio; Berski, Slawomir; Martí Forés, Sergio; Andres, Juan John Wiley & Sons (2013-02)The electronic structure of iron-oxo porphyrin π-cation radical complex Por·+FeIV[DOUBLE BOND]O (S[BOND]H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology ... -
Origin of the absorption maxima of the photoactive yellow protein resolved via ab initio multiconfigurational methods
Coto, Pedro B.; Martí Forés, Sergio; Oliva, Mónica; Olivucci, Massimo; Merchán, Manuela; Andres, Juan American Chemical Society (2008)We discuss the role of the protein in controlling the absorption spectra of photoactive yellow protein (PYP), the archetype xanthopsin photoreceptor, using quantum mechanics/molecular mechanics (QM/MM) methods based on ab ... -
Peptide Bond Formation Mechanism Catalyzed by Ribosome
Świderek, Katarzyna; Martí Forés, Sergio; Tuñón, Iñaki; Moliner, Vicent; Bertran, Joan American Chemical Society (2015)In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, ...