Listar por autoría "071fe0de-4df4-488e-b707-b67ffa3b5a9c"
Mostrando ítems 1-20 de 22
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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 DFT study of the reactivity indexes of ionic [4 + 2+] Diels-Alder cycloaddition to nitrilium and immonium ions
Castillo, Raquel; Andres, Juan Bentham Science Publishers (2011-02)The global electrophilicity index, defined within the conceptual density functional theory (DFT), was used to classify the dienes and dienophiles currently used in Diels-Alder reactions on a unique scale of electrophilicity. ... -
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 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 ... -
A theoretical study on the mechanism of the base-promoted decomposition of N-chloro,N-methylethanolamine
Ramos, Daniel R.; Castillo, Raquel; Canle López, Moisés; García Dopico, María Victoria; Andres, Juan; Santaballa López, J. Arturo Royal Society of Chemistry (2009)The first step of the base-promoted decomposition of N-chloro,N-methylethanolamine in aqueous solution (CH3N(Cl)CH2CH2OH + HO- →imine + Cl- + H2O (+ CH2O)→amine + aldehyde) is investigated at the MP2/6-31++G(d,p) computing ... -
Categorical Variable Mapping Considerations in Classification Problems: Protein Application
Alfonso Perez, Gerardo; Castillo, Raquel MDPI (2023)The mapping of categorical variables into numerical values is common in machine learning classification problems. This type of mapping is frequently performed in a relatively arbitrary manner. We present a series of four ... -
Computational Study of the Phosphoryl Donor Activity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate
Bordes, Isabel; García-Junceda, Eduardo; Sánchez Moreno, Israel; Castillo, Raquel; Moliner, Vicent Wiley (2017-10)Adenosine triphosphate (ATP) is the main biological phosphoryl donor required in many enzymes including dihydroxyacetone kinases (DHAKs) that convert dihydroxyacetone (Dha) into dihydroxyacetone phosphate (Dha-P), a key ... -
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 ... -
Gene Identification in Inflammatory Bowel Disease via a Machine Learning Approach
Alfonso Perez, Gerardo; Castillo, Raquel MDPI (2023-06)Inflammatory bowel disease (IBD) is an illness with increasing prevalence, particularly in emerging countries, which can have a substantial impact on the quality of life of the patient. The illness is rather heterogeneous ... -
Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms
López Canut, Violeta; Ruiz-Pernía, José Javier; Castillo, Raquel; Moliner, Vicent; Tuñón, Iñaki Wiley (2012-07)A theoretical study on the alkaline hydrolysis of paraoxon, one of the most popular organophosphorus pesticides, in aqueous solution and in the active site of Pseudomonas diminuta phosphotriesterase (PTE) is presented. ... -
Identification of Systemic Sclerosis through Machine Learning Algorithms and Gene Expression
Alfonso Perez, Gerardo; Castillo, Raquel MDPI (2022)Systemic sclerosis (SSc) is an autoimmune, chronic disease that remains not well understood. It is believed that the cause of the illness is a combination of genetic and environmental factors. The evolution of the illness ... -
Nonlinear Techniques and Ridge Regression as a Combined Approach: Carcinoma Identification Case Study
Alfonso Perez, Gerardo; Castillo, Raquel MDPI (2023)As more genetic information becomes available, such as DNA methylation levels, it becomes increasingly important to have techniques to analyze such data in the context of cancers such as anal and cervical carcinomas. In ... -
QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)
Viciano Gonzalo, Ignacio; Castillo, Raquel; Martí Forés, Sergio Wiley (2015-09)CYP19A1 aromatase is a member of the Cytochrome P450 family of hemeproteins, and is the enzyme responsible for the final step of the androgens conversion into the corresponding estrogens, via a three-step oxidative process. ... -
Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation of Wild-Type and Seven Mutants of CpNagJ in Complex with PUGNAc
Lameira, Jerônimo; Nahum Alves, Cláudio; Moliner, Vicent; Martí Forés, Sergio; Castillo, Raquel; Tuñón, Iñaki American Chemical Society (2010)The enzyme O-glycoprotein 2-acetamino-2-deoxy-β-d-glucopyranosidase (O-GlcNAcase) is responsible for the removal of N-acetylglucosamine moieties from 2-acetamido-2-deoxy-β-d-glucopyranose (O-GlcNAc) residues of serine/threonine ... -
Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host
Nödling, Alexander; Świderek, Katarzyna; Castillo, Raquel; Hall, Jonathan W.; Angelastro, Antonio; Morrill, Louis; Tsai, Yu-Hsuan; Moliner, Vicent; Luk, Louis Y. P. Wiley (2018-09-17)There has been growing interest in performing organocatalysis within a supramolecular system as a means of controlling reaction reactivity and stereoselectivity. Here, a protein is used as a host for iminium catalysis. A ... -
Synthesis and Biological Evaluation of Small Molecules as Potential Anticancer Multitarget Agents
Pla López, Alberto; Castillo, Raquel; Cejudo Marín, Rocío; García Pedrero, Olaya; Bakir Laso, Mariam; Falomir, Eva; Miguel Carda MDPI (2022-06-24)Twenty-six triazole-based derivatives were designed for targeting both PD-L1 (programmed death receptor ligand 1) and VEGFR-2 (vascular endothelial growth factor receptor 2). These compounds were synthetized and biologically ... -
Temperature dependence of dynamic, tunnelling and kinetic isotope effects in formate dehydrogenase
Roca, Maite; Ruiz-Pernía, José Javier; Castillo, Raquel; Oliva, Mónica; Moliner, Vicent Royal Society of Chemistry (2018)The origin of the catalytic power of enzymes has been a question of debate for a long time. In this regard, the possible contribution of protein dynamics in enzymatic catalysis has become one of the most controversial ... -
The role of streptavidin and its variants in catalysis by biotinylated secondary amines
Nödling, Alexander; Santi, Nicolò; Castillo, Raquel; Lipka-Lloyd, Magdalena; Jin, Yi; Morrill, Louis; Świderek, Katarzyna; Moliner, Vicent; Luk, Louis Yu Pan Royal Society of Chemistry (2021-11-15)Here, we combine the use of host screening, protein crystallography and QM/MM molecular dynamics simulations to investigate how the protein structure affects iminium catalysis by biotinylated secondary amines in a model ... -
Theoretical Study of the Phosphoryl Transfer Reaction from ATP to Dha Catalyzed by DhaK from Escherichia coli
Bordes, Isabel; Castillo, Raquel; Moliner, Vicent American Chemical Society (2017-09)Protein kinases, representing one of the largest protein families involved in almost all aspects of cell life, have become one of the most important targets for the development of new drugs to be used in, for instance, ...