Browsing QFA_Articles by Keyword "Molecular dynamics"
Now showing items 1-11 of 11
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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. ... -
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 ... -
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 ...