Search results for "Dynamic"
showing 10 items of 12329 documents
The dynamic orientation of membrane-bound peptides: bridging simulations and experiments.
2007
AbstractThe structural organization in a peptide/membrane supramolecular complex is best described by knowledge of the peptide orientation plus its time-dependent and spatial fluctuations. The static orientation, defined by the peptide tilt and a rotation about its molecular axis, is accessible through a number of spectroscopic methods. However, peptide dynamics, although relevant to understand the functionality of these systems, remains largely unexplored. Here, we describe the orientation and dynamics of Trp-flanked and Lys-flanked hydrophobic peptides in a lipid bilayer from molecular dynamics simulations. A novel view is revealed, where collective nontrivial distributions of time-evolvi…
Self-Assembling of Peptide/Membrane Complexes by Atomistic Molecular Dynamics Simulations
2007
Abstract Model biological membranes consisting of peptide/lipid-bilayer complexes can nowadays be studied by classical molecular dynamics (MD) simulations at atomic detail. In most cases, the simulation starts with an assumed state of a peptide in a preformed bilayer, from which equilibrium configurations are difficult to obtain due to a relatively slow molecular diffusion. As an alternative, we propose an extension of reported work on the self-organization of unordered lipids into bilayers, consisting of including a peptide molecule in the initial random configuration to obtain a membrane-bound peptide simultaneous to the formation of the lipid bilayer. This strategy takes advantage of the…
A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.
2007
Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…
Volumes and heat capacities of the aqueous sodium dodecanoate/sodium perfluorooctanoate mixtures in the presence of β-cyclodextrin
2003
Apparent molar volumes (VΦ) and heat capacities (CΦ) of the sodium dodecanoate (NaL)/sodium perfluorooctanoate (NaPFO) mixtures in the water/β-cyclodextrin (β-CD) solvent as functions of the surfactant total molality (mt) were determined at 25°C. For a given surfactant mixture, VΦ decreases with mt to ca. 0.05 mol kg−1 thereafter it increases tending to a constant value. CΦ displays a behaviour opposite to VΦ. The mt values where the apparent molar properties exhibit extrema are nearly coincident with the critical micellar concentrations determined by conductivity. An equation correlating VΦ to mt was derived by assuming that the equilibria for the 1∶1 surfactant/cyclodextrin complex format…
Polyelectrolytes in dilute solution: viscometric access to coil dimensions and salt effects
2015
Copolymers of acrylamide (AM) and diallyldimethylammonium chloride (DADMAC), differing in molar masses M (52.3 to 227 kDa) and degrees of charging y (0.2 to 0.6), were studied with respect to their viscometric behavior in dilute aqueous solutions containing variable amounts of NaCl. Complementary measurements were performed on a Brookhaven 90 plus particle size analyzer. M dominates the intrinsic viscosities [η]. For the viscometric interaction parameters B this is only true for large concentrations of extra salt. [η] and B as a function of solvent salinity follow Boltzmann laws. Coil dimensions, determined either via dynamic light scattering or viscometry, agree well. For low salt contents…
Chain Stiffness of Elastin-Like Polypeptides
2010
The hydrodynamic radii of a series of genetically engineered monodisperse elastin like polypeptides (ELP) was determined by dynamic light scattering in aqueous solution as function of molar mass. Utilizing the known theoretical expression for the hydrodynamic radius of wormlike chains, the Kuhn statistical segment length was determined to be lk = 2.1 nm, assuming that the length of the peptide repeat unit was b = 0.365 nm, a value derived for a coiled conformation of ELP. The resulting chain stiffness is significantly larger than previously reported by force-distance curve analysis (lk < 0.4 nm). The possible occurrence of superstructures, such as hairpins or helices, would reduce the conto…
Cellulose/Water: Liquid/Gas and Liquid/Liquid Phase Equilibria and Their Consistent Modeling
2007
Liquid/liquid and liquid/gas equilibria were measured for the water/cellulose system at 80 °C using three different polymer samples. For these experiments we prepared cellulose films of approximately 20−25 μm in thickness and determined their equilibrium swelling in water. Thereafter the polymer concentration in the mixed phase was increased by means of a stepwise removal of the volatile component, and the equilibrium vapor pressures were measured using an automated combination of head space sampling and gas chromatography. Contrary to the usual behavior of polymers, the swelling of cellulose increases as its molar mass becomes larger. The Flory−Huggins interaction parameters calculated fro…
Entanglement Transition in Hyperbranched Polyether-Polyols
2010
Are hyperbranched polymers capable of forming entanglements? This is the central issue of this contribution. Hyperbranched polyglycerol (hbPG) samples with different molecular weights (600-106 000 g · mol(-1) ), narrow polydispersities (1.2-1.8) and high degrees of branching (≈0.6) were prepared by anionic ring-opening polymerization. The viscoelastic properties of these polymers with respect to molecular architecture and molar mass were investigated. At low molecular weights "classical" scaling behavior between zero shear viscosity and molecular weight can be observed, whereas between 3 000 and 10 000 g · mol(-1) a plateau-like area is found. The results indicate entanglement dynamics when…
Viscometry of polyelectrolyte solutions: Star-like versus linear poly[[2-(methacryloyloxy)ethyl] trimethylammonium iodide] and specific salt effects
2017
Abstract The intrinsic viscosities, [η], of the 3-arm star polyelectrolyte in pure water are for a given molar mass considerably lower than for the linear product because of the higher monomer concentration and charge density in isolated coils. These effects are much more pronounced than in the case of uncharged macromolecules. Extra salt (NaCl, NaI, CaCl2) reduces the solution viscosities of the 3-arm star polymer less than of the linear product. The transition of [η] from the value in pure water to the minimum saturation value at high salt concentrations follows a Boltzmann sigmoid. In saline solvents the changes of the viscosities with rising polymer concentration depend strongly on the …
Polymer-polymer interaction, in the presence of a solvent as measured by viscometry
2001
Dilute solution viscometry experiments have been carried out in five ternary polymer systems solvent(1)/polymer(2)/polymer(3). Values of the specific viscosity of polymer (3) in a ‘binary solvent’ formed by polymer(2) + solvent(1) have been used to determine the compatibility of the polymer blends. Krigbaum and Wall formalism has been used to predict compatibility which relies on an interaction parameter that depends on the concentration, weight fraction and molar mass of each polymer. To reduce the dependences and to clarify the criterion of compatibility, a parameter independent of polymer (3) composition and molar mass has been deduced. This parameter shows the same behaviour with polyme…