Search results for "QM"
showing 10 items of 284 documents
QM/MM Determination of Kinetic Isotope Effects for COMT-Catalyzed Methyl Transfer Does Not Support Compression Hypothesis
2004
Secondary alpha-D3 kinetic isotope effects calculated by the hybrid AM1/TIP3P/CHARMM method for the reaction of S-adenosylmethionine with catecholate anion in aqueous solution and catalyzed by rat liver catechol O-methyltransferase at 298 K are 0.94 and 0.85, respectively, in good accord with experiment. The large inverse effect for the enzymatic reaction is not due to compression but arises from significant increases in the stretching and bending force constants involving the isotopically substituted atoms of the transferring methyl group as between the reactant complex and the transition structure, larger than for the reaction in water.
Identification and characterisation of the dopamine receptor II from the cat flea Ctenocephalides felis (CfDopRII)
2006
International audience; G protein-coupled receptors (GPCRs) represent a protein family with a wide range of functions. Approximately 30% of human drug targets are GPCRs, illustrating their pharmaceutical relevance. In contrast, the knowledge about invertebrate GPCRs is limited and is mainly restricted to model organisms like Drosophila melanogaster and Caenorhabditis elegans. Especially in ectoparasites like ticks and fleas, only few GPCRs are characterised. From the cat flea Ctenocephalides felis, a relevant parasite of cats and dogs, no GPCRs are known so far. Thus, we performed a bioinformatic analysis of available insect GPCR sequences from the honeybee Apis mellifera, the mosquito Anop…
Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses.
2014
There is epidemiological evidence that patients with certain Central Nervous System (CNS) disorders have a lower than expected probability of developing some types of Cancer. We tested here the hypothesis that this inverse comorbidity is driven by molecular processes common to CNS disorders and Cancers, and that are deregulated in opposite directions. We conducted transcriptomic meta-analyses of three CNS disorders (Alzheimer's disease, Parkinson's disease and Schizophrenia) and three Cancer types (Lung, Prostate, Colorectal) previously described with inverse comorbidities. A significant overlap was observed between the genes upregulated in CNS disorders and downregulated in Cancers, as wel…
Taopatch® combined with home-based training protocol to prevent sedentary lifestyle and biochemical changes in MS patients during COVID-19 pandemic
2021
In Multiple sclerosis (MS) it is important to preserve the residual physiological functions of subjects. The aim of the present study was to investigate the influence of nanotechnological device treatment combined with home-based training program (TP) on lactate level, hand grip strength and cervical mobility on MS patients. Seventeen MS patients were enrolled in the study and randomly assigned to an experimental group (EG) in which the Taopatch® nanotechnological device was applied or to a control group (CG). All the participants carried out a cervical range of motion (1) assessment and the hand grip test at baseline (T0) and after TP (T1), also investigating the lactate levels to figure o…
World Influence of Infectious Diseases from Wikipedia Network Analysis
2019
AbstractWe consider the network of 5 416 537 articles of English Wikipedia extracted in 2017. Using the recent reduced Google matrix (REGOMAX) method we construct the reduced network of 230 articles (nodes) of infectious diseases and 195 articles of world countries. This method generates the reduced directed network between all 425 nodes taking into account all direct and indirect links with pathways via the huge global network. PageRank and CheiRank algorithms are used to determine the most influential diseases with the top PageRank diseases being Tuberculosis, HIV/AIDS and Malaria. From the reduced Google matrix we determine the sensitivity of world countries to specific diseases integrat…
Improving the QM/MM Description of Chemical Processes: A Dual Level Strategy To Explore the Potential Energy Surface in Very Large Systems.
2005
Potential energy surfaces are fundamental tools for the analysis of reaction mechanisms. The accuracy of these surfaces for reactions in very large systems is often limited by the size of the system even if hybrid quantum mechanics/molecular mechanics (QM/MM) strategies are employed. The large number of degrees of freedom of the system requires hundreds or even thousands of optimization steps to reach convergence. Reactions in condensed media (such as enzymes or solutions) are thus usually restricted to be analyzed using low level quantum mechanical methods, thus introducing a source of error in the description of the QM region. In this paper, an alternative method is proposed, coupled to t…
Exploring Chemical Reactivity in Enzyme Catalyzed Processes Using QM/MM Methods: An Application to Dihydrofolate Reductase
2015
Enzymes are the catalysts used by living organisms to accelerate chemical processes under physiological conditions. In this chapter, we illustrate the current view about the origin of their extraordinary rate enhancement based on molecular simulations and, in particular, on methods based on the combination of Quantum Mechanics and Molecular Mechanics potentials which provide a solution to treat the chemical reactivity of these large and complex molecular systems. Computational studies on Dihydrofolate Reductase have been selected as a conductor wire to present the evolution and difficulties to model chemical reactivity in enzymes. The results discussed here show that experimental observatio…
Insights on the origin of catalysis on glycine N-methyltransferase from computational modeling.
2018
The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three mutants to test whether recent experimental observations of rate-constant reductions and variations in inverse secondary α-3H kinetic isotope effects (KIEs) should be attributed to changes in the methyl donor−acceptor distance (DAD): is catalysis due to a compression effect? Semiempirical (AM1) and DFT (M06-2X) methods were used to describe the QM subset of atoms, while OPLS-AA and TIP3P classical force fields were used for the protein and water molecules, respectively. The …
Computational strategies for the design of new enzymatic functions
2015
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, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful desig…
Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water
2011
2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-…