Search results for "SIMULATION"
showing 10 items of 5095 documents
Electron Microscopy of Human Erythrocyte Catalase: New Two-Dimensional Crystal Forms
1993
Abstract Using the mica-spreading "negative staining-carbon film" procedure, human erythrocyte catalase has been shown to create a number of different periodic or crystalline two-dimensional (2-D) arrays which differ in the arrangement of molecules in the repeating units and the lattice type. Digital image processing has been performed with a 2-D array which contains regularly arranged "undulating" rows of molecules and also with a 2-D crystal form, exhibiting pgg (p22 1 2 1 ) symmetry and lattice parameters of a = 12.7 nm, b = 44 nm, and γ= 92°. The data are compared with our previous analysis of a different human erythrocyte catalase 2-D crystal, and the effect of partial-depth negative s…
Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects
2013
Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from dif…
Structural and magnetic characterization of a 1D chain of [Co(II)2(mu-aqua)(mu-carboxylate)2] strung cores.
2009
A novel 1D chain built up from stringing of [Co2(μ-OH 2)(μ-O2CC(CH3)3)2] units with the bridging 2,2′-bipyrimidine ligand has been synthesized and structurally characterized. The chains are well isolated from each other by the bulky tert-butyl groups of the carboxlyates and show an alternating zigzag configuration for the Co(II) metallic centres. DC magnetic measurements show anti-ferromagnetic coupling, Jca.-3 cm-1 between adjacent Co(II) ions along the chain. Noticeably, good data fitting was obtained by means of simple models that neglect any kind of first order orbital contribution to the spin ground state, which is normally observed in Co(II) complexes. These results were further confi…
Characterizing cavities in model inclusion molecules: a comparative study
1998
We have selected fullerene-60 and -70 cavities as model systems in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecule taken as a unitary sphere, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and a cubic lattice approach to a molecular space. Accurate measures of the molecular volume and surface area have been performed with the pseudo-random Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the…
Ionic conduction, rectification, and selectivity in single conical nanopores
2006
Modern track-etching methods allow the preparation of membranes containing a single charged conical nanopore that shows high ionic permselectivity due to the electrical interactions of the surface pore charges with the mobile ions in the aqueous solution. The nanopore has potential applications in electrically assisted single-particle detection, analysis, and separation of biomolecules. We present a detailed theoretical and experimental account of the effects of pore radii and electrolyte concentration on the current-voltage and current-concentration curves. The physical model used is based on the Nernst-Planck and Poisson equations. Since the validity of continuum models for the descriptio…
Molecular dynamics studies on HIV-1 protease: a comparison of the flap motions between wild type protease and the M46I/G51D double mutant
2007
The emergence of drug-resistant mutants of HIV-1 is a tragic effect associated with conventional long-treatment therapies against acquired immunodeficiency syndrome. These mutations frequently involve the aspartic protease encoded by the virus; knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lasting treatment regimes. The flap regions of the protease are the target of a particular type of mutations occurring far from the active site. These mutations modify the affinity for both substrate and ligands, thus conferring resistance. In this work, molecular dynamics simulations were perform…
A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation
2015
International audience; Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukary- otic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is du…
Computational and experimental studies of size and shape related physical properties of hydroxyapatite nanoparticles
2011
In this work, the properties of hydroxyapatite (HAP) nanoparticles (NPs) have been studied both theoretically and experimentally focusing on computational analysis. HAP is widely used to fabricate implants, for drug delivery, etc. The physical properties of the nanosized HAP particles play an important role in the interaction with cells in the human body and are of great interest. Computer simulation was employed to understand the properties of HAP clusters (Ca(5)(PO(4))(3)OH) including formation energies, dipole moments and polarization (surface charges) by molecular mechanics (MM + , OPLS) and mostly by quantum semi-empirical Hartree-Fock (PM3) methods. The size of the simulated cluster i…
On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study
2012
The mechanism of the intramolecular Diels#8211;Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition stat…
Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin
2005
We performed a room temperature molecular dynamics (MD) simulation on a system containing 1 carboxy-myoglobin (MbCO) molecule in a sucrose–water matrix of identical composition (89% [sucrose/(sucrose + water)] w/w) as for a previous trehalose–water–MbCO simulation (Cottone et al., Biophys J 2001;80:931–938). Results show that, as for trehalose, the amplitude of protein atomic mean-square fluctuations, on the nanosecond timescale, is reduced with respect to aqueous solutions also in sucrose. A detailed comparison as a function of residue number evidences mobility differences along the protein backbone, which can be related to a different efficacy in bioprotection. Different heme pocket struc…