Listar por tema "Molecular dynamics"
Mostrando ítems 1-16 de 16
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A historical/epistemological account of the foundation of the key ideas supporting chemical equilibrium theory
Springer (2019-07)In this paper it is performed a historical account of the theoretical roots that grounded the following four key basic ideas of chemical equilibrium: ‘incomplete reaction’, ‘reversibility’, ‘equilibrium constant’ and ... -
A QM/MM study of the complexes formed by aluminum and iron with serum transferrin at neutral and acidic pH
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 ... -
Computational Analysis of Human OGA Structure in Complex with PUGNAc and NAG-Thiazoline Derivatives
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
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 ... -
Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformatión for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases
Royal Society of Chemistry (2009)Molecular dynamics simulations have been performed for non-covalent complexes of phenyl b-xylobioside with the retaining endo-b-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. ... -
Computational strategies for the design of new enzymatic functions
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, ... -
Dynamic correlation networks in human peroxisome proliferator-activated receptor-γ nuclear receptor protein
Springer-Verlag (2010)Peroxisome proliferator-activated receptor-γ nuclear receptor (PPAR-γ) belongs to the superfamily of nuclear receptor proteins that function as ligand-dependent transcription factors and plays a specific physiological role ... -
Ensemble-Averaged QM/MM Kinetic Isotope Effects for the SN2 Reaction of Cyanide Anions with Chloroethane in DMSO Solution
Wiley (2012-07)The existence of solvent fluctuations leads to populations of reactant-state (RS) and transition-state (TS) configurations and implies that property calculations must include appropriate averaging over distributions of ... -
Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms
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. ... -
Mechanism of glycoside hydrolysis: a comparative QM/MM molecular dynamics analysis for wild type and Y69F mutant retaining xylanases
Royal Society of Chemistry (2009)Computational simulations have been performed using hybrid quantum-mechanical/ molecular-mechanical potentials to investigate the catalytic mechanism of the retaining endo-b-1, 4-xylanase (BCX) from B. circulans. ... -
Molecular dynamics simulations of concentrated aqueous electrolyte solutions
Taylor & Francis (2011)Transport properties of concentrated electrolytes have been analysed using classical molecular dynamics simulations with the algorithms and parameters typical of simulations describing complex electrokinetic phenomena. ... -
Origin of the absorption maxima of the photoactive yellow protein resolved via ab initio multiconfigurational methods
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 ... -
Protein Flexibility and Preorganization in the Design of Enzymes. The Kemp Elimination Catalyzed by HG3.17
ACS Publications (2015)A recently designed enzyme, HG3.17, obtained by directed evolution, has shown a catalytic activity close to natural enzymes. Hybrid QM/MM molecular dynamics simulations for the Kemp elimination in this new enzyme have ... -
Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism
Springer (2021-08-25)Ribozymes are huge complex biological catalysts composed of a combination of RNA and proteins. Nevertheless, there is a reduced number of small ribozymes, the self-cleavage ribozymes, that are formed just by RNA and, ... -
Tripodal halogen bonding iodo-azolium receptors for anion recognition
Royal Society of Chemistry (2017)The synthesis, characterization and anion binding properties of 1,3,5-tri-substituted benzene platform-based tripodal receptors containing halogen bonding (XB) iodo-imidazolium and iodo-triazolium motifs, and hydrogen ... -
Using Grote-Hynes theory to quantify dynamical effects on the reaction rate of enzymatic processes. The case of Methyltransferases
American Chemical Society (2008)Dynamical effects have recently received much attention in the context of the theoretical investigation of enzymatic catalysis. In this paper we use a combination of Grote−Hynes theory with quantum mechanical/molecular ...