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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

An algorithm for generation and visualization of a variety of molecular surfaces is described. The algorithm employs center-of-mass or nuclei-centered spherical polar coordinate systems. In the present work, surfaces based on two fundamental molecular scalar fields, viz., the molecular electron density (MED) and the molecular electrostatic potential (MESP), are considered. Four such surfaces are presented: a constant MED surface with rho = 0.002 au; a minimal MESP anionic surface defined recently by Gadre et al.; a molecular covalency surface with a constant MESP value chi (chi being the Mulliken electronegativity value); and the van der Waals (vdW) surface. The MESP is superposed as a "texture" on the first and last surfaces. The color graphics visualization of these surfaces is implemented on a Silicon Graphics IRIS 4D/20 workstation. Several illustrative examples are presented.
J Mol Graph 1994 Mar
PMID:Graphics visualization of molecular surfaces. 801 2

Cigarette smoke is believed to increase the pulmonary retention of many different types of mineral dusts, but the mechanisms of this process are unclear. We have previously shown, using a tracheal organ culture system, that exposure to cigarette smoke directly increases the uptake of asbestos fibers by tracheal epithelial cells, and that this process is mediated by active oxygen species. To determine whether the same effects are seen with other types of mineral dust, we exposed rat tracheal explants to cigarette smoke or air (control) and then to a variety of dusts generally considered "inert" or of low pathogenicity. Explants were maintained in organ culture to allow dust uptake, and segments fixed and prepared for light microscopy at various times up to 1 wk; particle uptake was determined morphometrically. We observed that cigarette smoke significantly increased the epithelial uptake of nonfibrous titanium dioxide and talc, and of fibrous silicon carbide, but not of fibrous or nonfibrous iron oxide, nonfibrous silicon carbide, or fibrous wollastonite. Scavengers of active oxygen species (catalase) or agents that prevent the formation of active oxygen species (deferoxamine) blocked the effects of smoke in enhancing titanium dioxide uptake but did not block the effects of smoke on talc uptake. These observations indicate that cigarette smoke may potentiate the effects of many types of dust, including relatively inert dusts, by directly increasing the numbers of particles entering the tracheobronchial epithelium and eventually reaching the interstitium. However, smoke does not directly enhance the uptake of every dust.(ABSTRACT TRUNCATED AT 250 WORDS)
Am J Respir Cell Mol Biol 1993 Sep
PMID:Effects of cigarette smoke on epithelial uptake of non-asbestos mineral particles in tracheal organ culture. 839 71

Navigator is a molecular database visualization system, designed to support exploratory data analysis and informal structure-activity relationship studies. In addition to the operations commonly found in chemical database systems, it provides new tools that facilitate substituent analysis and help elucidate the relationships among similar molecules and between related assays. Navigator's capabilities include two ways of displaying the relationships between analogs, mouse-sensitive charts of sets of molecules, mouse-sensitive plots of assay relationships, and access to a system for three-dimensional quantitative structure-activity relationship discovery. Navigator's mouse-based user interface provides a one-object/one-window paradigm that makes data manipulation easy even for inexperienced users. Navigator runs on Silicon Graphics workstations.
J Mol Graph 1995 Aug
PMID:Navigator: tools for informal structure-activity relationship discovery. 852 16

MD Display was developed as a means of visualizing molecular dynamic trajectories generated by Amber. The program runs on Silicon Graphics workstations, and features a simple user interface, and convenient display and analysis options. The program has now been extended to accept input from several other molecular dynamics programs.
J Mol Graph 1996 Feb
PMID:MD Display: an interactive graphics program for visualization of molecular dynamics trajectories. 874 71

Eadfrith was written to provide the rapid display of molecules, so that they can be interactively rotated, translated, and scaled, and then rendered in a manner suitable for photography or other high-quality output methods. The program provides support for the display of transparency, electrostatic effects, and the normal vibrational modes of molecules. The compiled version for Silicon Graphics machines is freely available over the World-Wide Web. Eadfrith reads the structures from files in MacroModel format. The aim of the program is to provide a way to display molecular structures quickly and to produce high-quality pictures. Consequently, image-saving routines are not included, and standard utilities must be used in conjunction with Eadfrith to save the images to disk.
J Mol Graph 1996 Apr
PMID:Eadfrith: a molecular rendering program for Silicon Graphics workstations. 883 72

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si(100) - (2 x 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterization of the SW potential. Theoretical and experimental work has demonstrated that the reactive fluorosilyl layer during silicon-fluorine etching is composed of tower-like adspecies of SiF, SiF2 and SiF3 groups. The objective of the simulations is to determine how the chemical composition, mechanism of formation, and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate, the incident kinetic energy, and the parameterization of the potential energy function. Three reactions are simulated: F(g) + SiF3(a), F(g) + SiF2-SiF3(a), and F(g) + SiF2-SiF2-SiF3(a). SiF4 is the major product and Si2F6 and Si3F8 are minor products. In Si2F6 and Si3F8, the silicon-fluorine bond that is formed is stronger than the silicon-silicon bond in the molecule and, therefore, the majority of these products have enough energy to dissociate and will fragment before reaching the detector. An SN2-like mechanism is the primary mechanism responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at higher energies, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon-silicon bond. The results of the simulations with the two potentials differ quite substantially in their prediction of the reactivity of the adsorbates. The SW potential predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section, especially for the SiF4 product. These results are explained in terms of the differences in the potential energy functions used to describe the silicon-fluorine interactions. In addition, the results are compared to experimental data on silicon-fluorine etching.
J Mol Graph 1996 Oct
PMID:Molecular dynamics simulations of silicon-fluorine etching. 909 32

Smectites, members of the 2:1 layer silicate family, share the common feature that two tetrahedral sheets sandwich a sheet of octahedrally coordinated metal ion. The diversity of the members of the 2:1 layer silicates occurs because of their capacity for isomorphous substitution of various cations in the octahedral or tetrahedral sheets. Substitution of a divalent metal ion (such as Mg2+) for the trivalent Al3+ or a trivalent metal ion (such as Al3+) for the tetravalent silicon results in a net negative charge, which then undergoes interaction with positive ions (the exchangeable cations) to form an interlayer hydrated phase. Local density functional (LDF) calculations were employed to model isomorphous substitution of Al3+ by Na+, K+, Mg2+, Fe2+, and Fe3+ in the octahedral layer of a dioctahedral smectite clay such as montmorillonite. The energies of the isomorphous substitution were then compared with the experimental observation. The ordering for successful substitution is Al3+ > Fe3+ > Mg2+ > Fe2+ > Na+ < K+. This ordering is consistent with experimental observation. The vibrational frequencies for the isomorphous substituted systems were calculated by LDF calculation and were compared with the experimental IR results. The results match very well with experiment. This understanding will help in successful prediction of the catalytic activity of smectite clays.
J Mol Graph 1996 Oct
PMID:Relationship between infrared spectra and isomorphous substitution in smectites: a computer simulation study. 909 37

The adsorption of low density lipoprotein (LDL) and human serum albumin (HSA) to model surfaces of different hydrophobicities has been studied using two, surface-sensitive, real-time, in situ techniques: total internal reflection fluorescence (TIRF) and scanning force microscopy (SFM). The model surfaces used were: (1) hydrophilic negatively charged silica (TIRF) and mica (SFM) surfaces, (2) hydrophobic octadecyldimethylsilyl-(ODS)-modified silica (TIRF) and ODS-modified oxidized silicon (SFM) surfaces and (3) amphiphilic ODS-silica gradient surfaces (TIRF). The kinetics of fluorescein isothiocyanate-LDL adsorption onto the ODS-silica gradient surface from FITC-LDL solution and from a solution mixture of LDL and HSA showed that a transport-limited process on the clean silica changed into an adsorption-limited process with increasing surface coverage of ODS chains. SFM analysis of the in situ adsorption of LDL on hydrophilic mica demonstrated a steady increase in surface coverage with time which was somewhat lower than determined by TIRF for FITC-LDL adsorption on silica. The adsorption behavior of a binary mixture of HSA and LDL suggested that lateral interactions between HSA and LDL affect the adsorption process. The diameter of LDL adsorbed on mica and ODS-modified silicon has been determined using SFM to be approximately 55 nm. Tetrameric LDL aggregates were observed on all of the surfaces in addition to some dimers and trimers. Imaging LDL and HSA adsorption on clean oxidized silicon surfaces using "contact mode' SFM techniques was hindered by probe manipulation of the proteins.
J Mol Recognit
PMID:Human low density lipoprotein and human serum albumin adsorption onto model surfaces studied by total internal reflection fluorescence and scanning force microscopy. 917 22

A modular immunosensor device based on silicon technology with electrochemical detection is presented. The sensor surface is functionalized with the antigen estradiol using the streptavidin-biotin system. The immobilized antigen is recognized by ferrocene-labeled antibody molecules in a competitive assay format. The ferrocene redox centers can be detected electrochemically. In order to facilitate the electron transfer, a gold layer structured in nanometer dimensions is used as an electrode. The functionalized silicon chip will be integrated into a micromachined fluid transport system. The resulting immunosensor device for estradiol represents a prototype allowing easy adaptation to other biotinylated analytes since the immobilized streptavidin serves as a universal anchor.
J Mol Recognit
PMID:Immobilization of streptavidin for immunosensors on nanostructured surfaces. 917 28

Charcoal filters impregnated with triethylenediamine (TEDA) are known to be efficient for the collection of volatile methyl iodide, which may be released under a hypothetical loss-of-coolant accident in a nuclear generating station. The structure and thermodynamic stability of the products of the TEDA-methyl iodide reaction have thus been studied using semi-empirical techniques. The reaction of TEDA with two molecules of methyl iodide leads to a quaternization reaction at each of the nitrogens. Moreover, it is shown that substitution of the hydrogens on TEDA with electron-donating groups can lead to enhanced stability of the quaternary ammonium reaction products. The semi-empirical method PM3 (Parametric Method 3) was used as the basis for all calculations. Molecular systems and simulations were constructed using HyperChem 4.5 for Silicon Graphics workstations. Enthalpy determination and geometry optimization were some of the calculations performed on a system.
J Mol Graph Model 1997 Apr
PMID:Applications of the PM3 semi-empirical method to the study of triethylenediamine. 938 56


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