Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
On the Importance of Carbohydrate-Aromatic Interactions for the Molecular Recognition of Oligosaccharides by Proteins: NMR Studies of the Structure a…
2005
The specific interaction of a variety of modified hevein domains to chitooligosaccharides has been studied by NMR spectroscopy in order to assess the importance of aromatic-carbohydrate interactions for the molecular recognition of neutral sugars. These mutant AcAMP2-like peptides, which have 4-fluoro-phenylalanine, tryptophan, or 2-naphthylalanine at the key interacting positions, have been prepared by solid-phase synthesis. Their three-dimensional structures, when bound to the chitin-derived trisaccharide, have been deduced by NMR spectroscopy. By using DYANA and restrained molecular dynamics simulations with the AMBER 5.0 force field, the three-dimensional structures of the protein-sugar…
Tritopic phenanthroline and pyridine tail-tied aza-scorpiands
2010
The synthesis of two new tritopic double-scorpiand receptors in which two equivalent 5-(2-aminoethyl)-2,5,8-triaza[9]-(2,6)-pyridinophane moieties have been linked with 2,6-dimethylpyridine (L1) or 2,9-dimethylphenanthroline (L2) units is reported for the first time. Their acid-base behaviour and Zn(2+) coordination chemistry have been studied by pH-metric titrations, molecular dynamic calculations, NMR, UV-Vis and steady-state fluorescence techniques. L1 and L2 behave, respectively, as hexaprotic and heptaprotic bases in the experimental conditions used (298.1 +/- 0.1 K, 0.15 mol dm(-3) NaCl, pH range under study 2.0-11.0). These ligands are able to form mono-, bi- and trinuclear Zn(2+) co…
Molecular modeling studies of interactions between styrene–butadiene latex and sodium polyacrylate polymer surface
2010
Abstract The interaction between two important paper coating ingredients, sodium polyacrylate polymer dispersing agent and styrene–butadiene latex binder, was studied using classical force field and quantum chemical methods. The objective was to understand the adsorption of styrene–butadiene latex on the sodium polyacrylate polymer model surfaces at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the above interactions. In addition, the effect of moisture was investigated. Calculations showed that the conformation and orientation of styrene–butadiene latex, the number of carboxylate groups in t…
Impact of surface state on polyethylene glycol conformation confined inside a nanopore.
2021
Solid-state nanopores are a promising platform for characterizing proteins. In order to improve their lifetime and prevent fouling, Polyethylene Glycol (PEG) grafting is one of the most efficient and low-cost solutions. Different models to calculate the PEG thickness do not consider their interaction with the nanopore inner surface nor the effect of confinement. Here, we investigate by molecular dynamic simulation the PEG conformation inside a nanopore in the case of hydrophobic and hydrophilic nanopores. Our results reveal that the nanopore inner surface plays a role in the PEG organization and, thus, in the speed of the salt constituent. The resulting pair interaction between PEG and its …
Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions
2020
AbstractHuman telomeric DNA (h-Telo), in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics (MD) simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.
Computer simulations of undercooled fluids and the glass transition
2000
Abstract Two model studies are presented that attempt to describe the static and dynamic properties of glass-forming fluids via molecular dynamics simulations: The first model is an atomistically realistic model of SiO 2 , the second model provides a coarse-grained description of polymer liquids, i.e., typical `fragile' glassformers, while SiO 2 is the prototype of a `strong glassformer'. For both models, attention is given to the questions as to which range of temperatures are properties in equilibrium, and whether such simulations can help to interpret experiments and/or check theoretical predictions. While in the simulation of SiO 2 using the potential of van Beest, Kramer and van Santen…
Dynamics of macromolecules grafted in spherical brushes under good solvent conditions
2013
Spherical polymer brushes have a structure intermediate between star polymers and polymer brushes on flat substrates, and are important building blocks of polymer nanoparticles. Molecular dynamics simulations are presented for isolated spherical polymer brushes under good solvent conditions, varying the grafting density as well as the chain length, using a coarse-grained bead-spring model of flexible chains. We complement previous work on the static properties of the same model by analyzing the chain dynamics, studying the motions of monomers in relation to their position along the grafted chains, and extract suitable relaxation times. A qualitative discussion in terms of the Rouse model is…
Blood Proteins and Their Interactions with Nanoparticles Investigated Using Molecular Dynamics Simulations
2018
Blood proteins play a fundamental role in determining the response of the organism to the injection of drugs or, more in general, of therapeutic preparations in the blood stream. Some of these proteins are responsible for mediating immune response and coagulation. Nanoparticles, which are being intensely investigated as possible drug nanocarriers, heavily interact with blood proteins and their ultimate fate is determined by these interactions. Here we report the results of molecular dynamics simulations of several blood proteins aimed to determining their possible behavior at the nanoparticle surface. On one hand we investigated the behavior of fibrinogen, a glycoprotein, which polymerizes …
Polymers films with indandione derivatives as alternatives to azobenzene polymers for optical patterning
2008
Surface relief gratings (SRGs) on organic thin films are studied extensively for both scientific interest and in relevance to the applications. Among the chromophores being used the azobenzenes showed the best performance, but the use of alternative photo-sensitive groups provides better general understanding of the phenomena. A thermodynamic theory and molecular dynamics simulations of photoinduced effects are discussed. In this study we use indandione derivatives, known as promising materials for photonics applications, as an alternative to the azobenzenes. We consider their photoreactions when incorporated into a polymer film. One of interesting features is the spectral dependence of the…
Interplay between Chain Collapse and Microphase Separation in Bottle-Brush Polymers with Two Types of Side Chains
2010
Conformations of a bottle-brush polymer with two types (A,B) of grafted side chains are studied by molecular dynamics simulations, using a coarse-grained bead−spring model with side chains of up to...