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Intraperitoneal administration of the nontoxic silicon compound, 1-ethoxysilatrane, to the rat did not cause proliferation of hepatic mitochondria or of endoplasmic reticulum, nor did it affect mitochondrial oxidative phosphorylation. The activities of cholesterol 7 alpha-hydroxylase in hepatic microsomes and of cholesterol oxidase in mitochondria respectively were unaffected by silatrane treatment. The rate of release of bile, whose composition remained unchanged, also was not increased in silatrane-treated animals. The results indicated that the compound did not affect the pathway of cholesterol degradation. A progressive decrease in the activity of hepatic microsomal 3-hydroxy-3-methylglutaryl coenzyme A (HMGCoA) reductase was observed on administration of the compound over a period of three weeks. Consistent with this, cholesterol biosynthesis in liver as measured by incorporation of radioactive precursors, acetate and water but not mevalonate, was significantly decreased in silatrane-treated animals. However, enzyme-linked immunosorbent assay revealed that the concentration of HMGCoA reductase protein was not decreased by the treatment indicating that inactivated enzyme was also present in such microsomes. Addition of silatrane to microsomes in the assay system did not cause inhibition indicating that the inactivation is by an indirect mechanism. It is concluded that the hypocholesterolemic action of the compound rested entirely on the inhibition of cholesterol biosynthesis in vivo by inactivation of the rate-limiting enzyme HMGCoA reductase.
Mol Cell Biochem 1990 Sep 03
PMID:Investigations on the mechanism of the hypocholesterolemic action of 1-ethoxysilatrane. 224 48

We have implemented in TOM/FRODO a protein crystallographic symmetry display and handling package, called CRYStallize. This package is designed as an aid in solving protein structures by molecular replacement methods. It allows the rotation/translation solutions provided by molecular replacement programs to be checked in a fast and easy way. Using CRYStallize, approximate solutions can also be improved by manual modifications. Symmetry-related objects, represented as surfaces, can be generated and handled in the same way as the reference molecules, thus permitting an efficient analysis of crystal packing and site accessibility. This program is available in the TOM/FRODO software release, which runs on the Silicon-Graphics workstations.
J Mol Graph 1990 Jun
PMID:CRYStallize: a crystallographic symmetry display and handling subpackage in TOM/FRODO. 228 56

A comparison of semi-empirical (MNDO) and ab initio (GAUSSIAN) calculations for disiloxane and related molecules is given. The STO-3G* basis set well produced the observed geometries of disiloxane (less than SiOSi observed 144 degrees, calculated 140 degrees), dimethoxy-dimethylsilane (less than OSiO obsd tetrahedral, calc 102 degrees), methyl silyl ether (less than COSi obsd 121 degrees, calc 118 degrees) and correctly predicted the planar geometry found for cyclotrisiloxane. In contrast, more complex basis sets (3-21G(*), DZP, TZVP) gave much poorer agreement with the observed geometries. Comparison of the STO-3G* and the STO-3G basis sets demonstrates the necessity of including d-orbitals on the silicon. However, the semi-empirical MNDO program gave, despite the absence of d-orbitals, a better approximation to the molecular geometry than the complex ab initio basis sets. Force field parameters have been calculated for kSiOSi, kOSiO, 0.089 and 0.73 mdyneA/rad2, and the SiOSiO torsion which has a V1 potential of -0.68 kcal/mol. In addition, the HSiOH torsion is shown to have a three-fold potential of 0.78 kcal/mol. These are profoundly different from the analogous carbon-oxygen force constants, demonstrating that C-O parameters cannot be transferred to the corresponding Si-O systems.
J Comput Aided Mol Des 1989 Jan
PMID:A theoretical study of the Si-O bond in disiloxane and related molecules. 271 89

We have monitored the growth of domains of sickle hemoglobin polymers by using temporally and spatially resolved light scattering and birefringence measured pseudosimultaneously on a 50-microns square area. Polymerization was induced and indefinitely maintained by photolysis of the carbonmonoxy derivative using an argon ion laser. Intensity of scattering and birefringence (measured as intensity transmitted through crossed polarizers) were measured using a silicon-intensified target vidicon interfaced to a computer. Polymer concentration, as inferred by light scattering, grew with primarily circular symmetry, with approximately 20% of the signal initially in a twofold symmetric pattern. In time the circular symmetry increased. A distinct decrease in the scattering signal developed which spread outward from the center of the domain. Birefringence lagged the scattering and initially grew in a twofold pattern, with the formation of a characteristic Maltese cross only appearing much later, and well after the scattering signal had peaked. Radial profiles of the domain scattering and birefringence were both approximately gaussian. We successfully modeled the decrease in scattering by fitting the profiles to a large gaussian from which a second smaller gaussian was subtracted. This second gaussian had the width of the birefringence gaussian. The width of the birefringence gaussian grew linearly in time, while the width of the scattering gaussian showed a notable acceleration. We conclude that domains form primarily as disordered arrays which align at later times. We explain the above observations, including the shape of the birefringence progress curves, as the result of an alignment transition which is solely due to a redistribution of monomers from short to long, and from entangled to radial, polymers. We present a theoretical justification for this process in an appendix. In a separate paper (Zhou, H. X., and F. A. Ferrone, manuscript submitted for publication) we show that the gaussian shapes and acceleration of the width naturally arise from a generalization of the double nucleation mechanism for sickle hemoglobin gelation (Ferrone, F. A., J. Hofrichter, H. Sunshine, and W. A. Eaton 1980. Biophys. J. 32:361-377; Ferrone, F. A., J. Hofrichter, and W. A. Eaton. 1985. J. Mol. Biol. 183:611-631).
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PMID:Kinetics of domain formation by sickle hemoglobin polymers. 324 32

The degradation of glucose by Trypanosoma cruzi leads to the excretion of succinate. Malate dehydrogenase (MDH) participates in this process by reducing to malate the oxaloacetate synthesized by the glycosomal enzyme, phosphoenolpyruvate carboxykinase. The best coupling for these two sequential reactions would be attained if both enzymes were placed in the same subcellular compartment. The intracellular distribution of the MDH activity in epimastigotes of T. cruzi was studied by two methods. Selective disruption of cellular membranes with increasing concentrations of digitonin, indicated that trypanosomal MDH is particulate. Isopycnic centrifugation in a sucrose gradient of a large granule fraction, obtained by grinding the cells with silicon carbide, showed the presence of two MDH activities: one banding together with the glycosomal marker phosphoenolpyruvate carboxykinase, the other with the mitochondrial marker citrate synthase. Isoelectrofocusing of cell-free extracts led to the separation of two enzyme forms, with pI values of about 3.5 (MDHa) and 9.4 (MDHb). These forms had similar molecular weights (approx. 60 000) and apparent Km values, but showed a small but consistent difference in their pH optima (9.23 for MDHa and 9.05 for MDHb), and in their activation by inorganic phosphate (apparent Ka values of 33 mM and 87 mM, for MDHa and MDHb, respectively). Determination of the pH optima of the enzyme forms separated by isopycnic centrifugation suggests that the glycosomal enzyme form is MDHa, and the mitochondrial one is MDHb.
Mol Biochem Parasitol 1984 Apr
PMID:Glycosomal and mitochondrial malate dehydrogenases in epimastigotes of Trypanosoma cruzi. 637 51

Particulate fractions obtained from Trypanosoma cruzi and Crithidia fasciculata by different procedures were subjected to isopycnic centrifugation in sucrose gradients, in order to determine the subcellular localization of phosphoenolpyruvate carboxykinase (PEPCK) in both organisms, and of malic enzyme (ME) I in T. cruzi. The more clear-cut results were obtained with T. cruzi by breaking the cells by grinding in a mortar with silicon carbide and using a gradient from 0.4 to 2.0 M sucrose, whereas with C. fasciculata, the best procedure was disruption of the cells by digitonin treatment and potter homogenization and use of a gradient from 1.1 to 2.0 M sucrose. PEPCK banded together with the glycosomal marker hexokinase in both organisms; there was a clear separation from the mitochondrial markers, oligomycin-sensitive Mg2+-APTase and citrate synthase. PEPCK showed a latency of 24% in the enriched 'glycosoma' fraction of T. cruzi. ME I from T. cruzi, on the other hand, banded together with the mitochondrial markers. These results indicate that PEPCK and ME are present in different subcellular compartments, a fact significant for the prevention of a futile cycle between C4-dicarboxylic acids and C3-monocarboxylic acids, which might take place if both enzymes functioned in the same compartment.
Mol Biochem Parasitol 1982 Sep
PMID:Subcellular localization of phosphoenolpyruvate carboxykinase in the trypanosomatids Trypanosoma cruzi and Crithidia fasciculata. 675 7

Proteins in the molecular weight range of 10 000-170 000 were separated by high performance gel permeation chromatography. Silica particles with 30 nm or 50 nm pores were derivatized with glycidoxypropyltrimethoxysilane and used as support. The proteins were eluted with 50% formic acid. A protein fraction which induces endodermal and mesodermal tissues in amphibian gastrula ectoderm was purified by this method.
Mol Biol Rep 1981 Nov 30
PMID:High performance gel permeation chromatography of proteins. Application to embryonic inducing factors. 732 17

Nucleic acid probe-based assays are now widely used in genetic research, human identification, forensics and in a broad spectrum of clinical assays in the fields of microbiology, haematology/oncology and virology. Labelled probes are used in a variety of assay formats including dot-blots, Southern blots (DNA target), Northern blots (RNA target), Western blots (protein target), in situ hybridization, plaque or colony screening and immobilized arrays on silicon or glass surfaces. Traditionally, the probes used in these assays have a radioactive 32phosphorous label that has a short shelf-life, is dangerous, has high disposal costs and, when labelled to high specific-activity, may be unstable. Extensive efforts to develop alternative labelling techniques have resulted in colorimetric, chemiluminescent and fluorescent assay formats. This review summarizes the properties desired in a probe, describes the advantages and disadvantages of the different non-radioactive labelling strategies, and illustrates examples of probe-based assays in which detection is facilitated by imaging samples using a general purpose fluorescence scanner.
Mol Cell Probes 1995 Jun
PMID:Nucleic acid detection using non-radioactive labelling methods. 747 6

A program for drawing automatically exact and schematic views of nucleic acids is described. The program is written in C ANSI and uses the Silicon Graphics GL and Xirisw libraries within the X11/Motif environment. Through menus, the user can choose, specify, and manipulate in real time the three-dimensional views to be displayed. Drawing options include partitioning of structures into differently colored or shaped fragments, representation of backbones as flat or with conic-section ribbons, display of paired or free bases as rods, and display of surfaces as filled or outlined and stereo or depth-cued views.
J Mol Graph 1994 Sep
PMID:DRAWNA: a program for drawing schematic views of nucleic acids. 752 57

QMView is designed to facilitate the visualization and interpretation of quantum mechanical data. Capabilities include display of chemical structure, animation of quantum mechanically determined vibrational modes, and depiction of electronic properties and three-dimensional molecular orbitals. QMView has a user-friendly interface that allows users to interactively manipulate many features of the molecular structure and/or property, including positioning and structure representation, via mouse-activated dialog boxes. Although the interface allows input from results of any of the popularly used quantum mechanical software, we have focused on GAMESS, a widely distributed quantum chemistry code. QMView has been designed with the special feature of working in distributed mode with GAMESS, the latter running on a supercomputer, the former running on a Silicon Graphics platform. Ancillary programs provide a method of obtaining output of graphic images in various media, including hardcopy, PostScript files, slide, and/or video. These and other original features discussed in this article provide a graphic interface that is unique compared to others that are currently available. Examples of images produced by QMView are presented.
J Mol Graph 1995 Feb
PMID:QMView: a computational chemistry three-dimensional visualization tool at the interface between molecules and mankind. 779 35


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