Search results for "molecular dynamics"
showing 10 items of 1075 documents
Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.
2014
M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex where the target adenine is flipped out into the active site. Key protein–DNA interactions established by the target adenine in the active site are described in detail. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. According to our free energy calculations the reaction takes…
Theoretical study of phosphodiester hydrolysis in nucleotide pyrophosphatase/phosphodiesterase. Environmental effects on the reaction mechanism.
2010
We here present a theoretical study of the alkaline hydrolysis of methyl p-nitrophenyl phosphate (MpNPP(-)) in aqueous solution and in the active site of nucleotide pyrophosphatase/phosphodiesterase (NPP). The analysis of our simulations, carried out by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods, shows that the reaction takes place through different reaction mechanisms depending on the environment. Thus, while in aqueous solution the reaction occurs by means of an A(N)D(N) mechanism, the enzymatic process takes place through a D(N)A(N) mechanism. In the first case, we found associative transition-state (TS) structures, while in the enzyme TS structures have dissoc…
Enzyme Promiscuity in Enolase Superfamily. Theoretical Study of o-Succinylbenzoate Synthase Using QM/MM Methods
2015
The promiscuous activity of the enzyme o-succinylbenzoate synthase (OSBS) from the actinobacteria Amycolatopsis is investigated by means of QM/MM methods, using both density functional theory and semiempirical Hamiltonians. This enzyme catalyzes not only the dehydration of 2-succinyl-6R-hydroxy-2,4-cyclohexadiene-1R-carboxylate but also catalyzes racemization of different acylamino acids, with N-succinyl-R-phenylglycine being the best substrate. We investigated the molecular mechanisms for both reactions exploring the potential energy surface. Then, molecular dynamics simulations were performed to obtain the free energy profiles and the averaged interaction energies of enzymatic residues wi…
A QM/MM study of the reaction mechanism for the 3′-processing step catalyzed by HIV-1 integrase
2009
Integrase (IN) is one of the three human immunodeficiency virus type 1 enzymes (HIV-1) essential for effective viral replication. This viral enzyme is involved in the integration of HIV DNA into host chromosomal DNA. In this work we have carried out molecular dynamics simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach to study the reaction mechanism for the 3′-processing step of DNA integration using a model substrate. The results obtained by QM(AM1)/MM and QM(PM3)/MM simulations have been improved by single-point corrections using an ab initio method to describe the quantum subsystem. The results obtained within this computational model can be used to obtain …
Analysis of the Decarboxylation Step in Mammalian Histidine Decarboxylase
2008
We report a hybrid quantum mechanics/molecular mechanics theoretical study on the reaction mechanism of mammalian histidine decarboxylase that allows us to obtain valuable insights on the structure of the cofactor-substrate adduct (external aldimine) in the active site of rat histidine decarboxylase. By means of molecular dynamics simulations, we traced the potential of mean force corresponding to the decarboxylation reaction of the adduct both in the active site of the enzyme and in aqueous solution. By comparing this process in both media, we have identified the key electrostatic interactions that explain the lowering of the free energy barrier in the enzyme. Our analysis also offers a va…
Theoretical Elucidation of β-O-4 Bond Cleavage of Lignin Model Compound Promoted by Sulfonic Acid-Functionalized Ionic Liquid
2019
While the depolymerization of lignin to chemicals catalyzed by ionic liquids has attracted significant attention, the relevant molecular mechanism, especially the cleavage of specific bonds related to efficient depolymerization, still needs to be deeply understood for the complexity of this natural aromatic polymer. This work presents a detailed understanding of the cleavage of the most abundant β-O-4 bond in the model system, guaiacylglycerol β-guaiacyl ether, by a Brønsted acidic IL (1-methyl-3-(propyl-3-sulfonate) imidazolium bisulfate ([C3SO3Hmim][HSO4]) using density functional theory calculation and molecular dynamics simulation. It has been found that [C3SO3Hmim][HSO4] generates zwit…
Applicability of solid state fast field cycling NMR relaxometry in understanding relaxation properties of leaves and leaf-litters
2011
Abstract Inversion recovery high field solid state (SS) 1H NMR spectroscopy and fast field cycling (FFC) NMR relaxometry have been applied on dried leaves and leaf-litters from a reafforestated area in central Sicily (Italy) in order to evaluate relaxation properties in both slow ( 1 ≪ ω 0 2 τ C 2 ) and fast ( 1 ≫ ω 0 2 τ C 2 ) motion regimes. Namely, SS 1H NMR spectroscopy (i.e. slow motion regime conditions) revealed that two relaxation components (a fast and a slow one) can be identified in all the leaves and leaf-litter samples. The fast component was assigned to small sized plant metabolites, whereas the slow one was attributed to slowly tumbling macropolymeric molecules. FFC NMR relax…
Nuclear Magnetic Resonance with Fast Field-Cycling Setup: A Valid Tool for Soil Quality Investigation
2020
Nuclear magnetic resonance (NMR) techniques are largely employed in several fields. As an example, NMR spectroscopy is used to provide structural and conformational information on pure systems, while affording quantitative evaluation on the number of nuclei in a given chemical environment. When dealing with relaxation, NMR allows understanding of molecular dynamics, i.e., the time evolution of molecular motions. The analysis of relaxation times conducted on complex liquid–liquid and solid–liquid mixtures is directly related to the nature of the interactions among the components of the mixture. In the present review paper, the peculiarities of low resolution fast field-cycling (FFC) NMR rela…
ChemInform Abstract: Environmental NMR: Fast-Field-Cycling Relaxometry
2016
Fast-field-cycling (FFC) NMR relaxometry deals with the variation of the spin–lattice relaxation times (T1) in a complex system, as the strength of the applied magnetic field is changed. Information about molecular dynamics can be achieved. Until now, only model theories for FFC NMR relaxometry have been developed for polymer and material sciences. Just a few applications have been performed in the environmental sciences. These mainly deal with soil porosity, rock permeability, biomass transformations, and natural organic matter dynamics. Further, FFC NMR relaxometry can also be applied to monitor the environmental fate of contaminants, to understand the dynamics of nutrients at the soil–pl…
Environmental NMR: Fast-field-cycling Relaxometry
1996
Fast-field-cycling (FFC) NMR relaxometry deals with the variation of the spin–lattice relaxation times (T1) in a complex system, as the strength of the applied magnetic field is changed. Information about molecular dynamics can be achieved. Until now, only model theories for FFC NMR relaxometry have been developed for polymer and material sciences. Just a few applications have been performed in the environmental sciences. These mainly deal with soil porosity, rock permeability, biomass transformations, and natural organic matter dynamics. Further, FFC NMR relaxometry can also be applied to monitor the environmental fate of contaminants, to understand the dynamics of nutrients at the soil–pl…