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Query: UNIPROT:P06889 (Mol)
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A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the xo, yo, zo values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < xo and some x > xo where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by "clicking" on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired "pocket" has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein "segment," allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.
J Mol Graph 1992 Dec
PMID:POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. 147 96

The Graphics Command Interpreter (GCI) is an independent server module that can be interfaced to any program that needs interactive three-dimensional (3D) graphics capabilities. The principal advantage of GCI is its simplicity. Only a limited set of powerful features have been implemented, including object management, global and local transformations, rotation, translation, clipping, scaling, viewport operations, window management, menu handling and picking. GCI and the master (client) program it serves run concurrently, communicating over a local or remote TCP/IP network. GCI sets up socket communication and provides a 3D graphics window and a terminal emulator for the master program. Communication between the two programs is via ASCII strings over standard I/O channels. The implied language for messages is very simple. GCI interprets messages from the master program and implements them as changes of graphical objects or as text messages to the user. GCI provides the user with facilities to manipulate the view of the displayed 3D objects interactively, independently of the master program, and to communicate mouse-controlled selection of menu items or 3D points as well as keyboard strings to the master program. The program is written in C and initially implemented using the Silicon Graphics GL graphics library. As the need to link special libraries to the master program is completely avoided, GCI can very easily be interfaced to existing programs written in any language and running on any operating system capable of TCP/IP communication. The program is freely available.
J Mol Graph 1992 Mar
PMID:GCI: a network server for interactive 3D graphics. 150 47

It has been suggested that elevated cytosolic free calcium plays a key role in acetaminophen-induced cell death. The present study has examined the effect of a toxic concentration of acetaminophen on cytosolic free calcium in single mouse hepatocytes, using the dye fura-2 and video imaging fluorescence microscopy. Cytosolic free calcium was calculated from the ratio of emitted fluorescence at greater than 475 nm produced by excitation at 340 and 380 nm, using a double-intensified silicon target camera and digital image processing. In the presence of 5 mM acetaminophen, cell death did not occur for 2 hr, but the toxic lesion that ultimately killed the cells occurred as early as 1 hr. If cytosolic free calcium plays an important role in these toxic events, it would be expected to increase during this period. However, during a 2-hr exposure, cytosolic free calcium concentration in cells exposed to acetaminophen was not different from control. In hepatocytes incubated for longer than 2 hr, the calcium concentration increased shortly before loss of cell viability (i.e., as a late event), consistent with an influx of calcium through a damaged cell membrane. This late increase in calcium occurred well after the appearance of cell surface blebs. The data suggest that there is no sustained change in cytosolic free calcium in acetaminophen injury either before or during the time when irreversible toxic events occur in hepatocytes.
Mol Pharmacol 1992 Apr
PMID:Level of cytosolic free calcium during acetaminophen toxicity in mouse hepatocytes. 156 20

Segment match modeling uses a data base of highly refined known protein X-ray structures to build an unknown target structure from its amino acid sequence and the atomic coordinates of a few of its atoms (generally only the C alpha atoms). The target structure is first broken into a set of short segments. The data base is then searched for matching segments, which are fitted onto the framework of the target structure. Three criteria are used for choosing a matching data base segment: amino acid sequence similarity, conformational similarity (atomic co-ordinates), and compatibility with the target structure (van der Waals' interactions). The new method works surprisingly well: for eight test proteins ranging in size from 46 to 323 residues, the all-atom root-mean-square deviation of the modeled structures is between 0.93 A and 1.73 A (the average is 1.26 A). Deviations of this magnitude are comparable with those found for protein co-ordinates before and after refinement against X-ray data or for co-ordinates of the same protein in different crystal packings. These results are insensitive to errors in the C alpha positions or to missing C alpha atoms: accurate models can be built with C alpha errors of up to 1 A or by using only half the C alpha atoms. The fit to the X-ray structures is improved significantly by building several independent models based on different random choices and then averaging co-ordinates; this novel concept has general implications for other modeling tasks. The segment match modeling method is fully automatic, yields a complete set of atomic co-ordinates without any human intervention and is efficient (14 s/residue on the Silicon Graphics 4D/25 Personal Iris workstation.
J Mol Biol 1992 Jul 20
PMID:Accurate modeling of protein conformation by automatic segment matching. 164 Apr 63

A cost effective color graphics representation of molecular electrostatic potential surfaces employing the cumulative atomic or bond multipole moments has been described. A general description of the method used to obtain cumulative multipole moments directly from ab-initio wavefunctions is given, along with an outline of the algorithm for generating electrostatic potential surfaces in the molecular graphics programs MOL17 (FORTRAN 77, Silicon Graphics 3130 and 4D series workstations) and PCMCAMM (Turbo Pascal, IBM PC and PS/2 computers). Examples are given that illustrate the convergence of the multiple expansion, the degree of basis-set dependence compensated by the use of higher atomic moments, and the effect of placing additional expansion centers along the bonds.
J Mol Graph 1991 Jun
PMID:Efficient method for the generation and display of electrostatic potential surfaces from ab-initio wavefunctions. 176 44

A general methodology is developed for incorporating accurate electrostatic information from ab initio molecular orbital calculations into molecular mechanics calculations. Examples are given of the method applied to simple aromatic organic molecules. A program has been developed for displaying the results of the ab initio calculations on a Silicon Graphics workstation. The technique developed here provides an alternative method for including electrostatic interactions in molecular mechanics calculations and is compared with other methods for determining atomic charges.
J Mol Graph 1991 Sep
PMID:Calculation and display of electrostatic potentials. 177 41

Rapid, quantitative hybridization assays with good sensitivity are needed in many applications, for example, determining the amount of specific product from PCR. We have developed an assay which relies on the hybridization of a biotinylated oligomer and a fluoresceinated oligomer to a single-stranded target in solution. The hybridized complex is captured by streptavidin to a biotinylated membrane. After capture, the hybridization complex is detected by an antifluorescein-urease conjugate which binds to the fluoresceinated probe. The membrane-bound urease conjugate is exposed to urea and assayed with a pH-sensitive silicon sensor. The total assay time is less than 2 h and the sensitivity limit is 20 x 10(6) molecules with a coefficient of variation, CV, of less than 10%. The assay was applied to the analysis of a model target using PCR. We were able to measure the amount of specific product and the amplification factor during the exponential phase of PCR. Using extrapolation from the measured amounts of amplified product, the initial amounts of target molecules were calculated to be 1.2 x 10(6) and 4.0 x 10(2) when the added quantities were 3 x 10(6) and 3 x 10(3), as determined by serial dilution.
Mol Cell Probes 1991 Oct
PMID:Quantitation of DNA hybridization in a silicon sensor-based system: application to PCR. 179 56

In silicosis, alveolar macrophages (AM) are thought to induce chronic inflammation and fibrosis by release of cytokines. Rats were exposed to aerosols of alpha-quartz and examined 4 to 9 mo later for persistence of silica particles and release of tumor necrosis factor-alpha (TNF-alpha) from macrophages. Silica particles were detected in AM, lung parenchyma, and thoracic lymphoid organs, whereas extrathoracic lymphoid tissues and organs were free of the mineral. When AM were tested functionally, no spontaneous release of TNF-alpha was observed. However, upon in vitro stimulation of AM from silicotic rats with a low concentration of lipopolysaccharide (10 ng/ml), abundant TNF-alpha production was found that was higher and occurred more rapidly than with AM from sham-exposed animals. Peritoneal macrophages, which did not have contact with silica particles, displayed a similarly enhanced TNF-alpha release in response to low doses of lipopolysaccharide. These data demonstrate a state of systemic preactivation ("priming") of macrophages that supports the notion that silicosis is associated with a general immunostimulation.
Am J Respir Cell Mol Biol 1991 Oct
PMID:Systemic macrophage stimulation in rats with silicosis: enhanced release of tumor necrosis factor-alpha from alveolar and peritoneal macrophages. 191 Aug 24

A graphics program, MOLPACK, has been developed on the Silicon Graphics IRIS-4D computer system for displaying the packing of proteins in the crystallographic unit cell. In addition to the normal viewing operations of rotation, translation and scaling, the program has the ability to translate molecules along the cell axes while maintaining their crystallographic equivalent positions within the unit cell. This allows the user to observe the packing of protein molecules generated by molecular replacement, to create a new packing model or to locate an unknown molecule. A special feature of the program is that up to four independent molecules can be manipulated in the asymmetric unit.
J Mol Graph 1991 Mar
PMID:MOLPACK: molecular graphics for studying the packing of protein molecules in the crystallographic unit cell. 201 55

The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples. In substituted methanes (CH3X, CF3X, CCl3X) the effects of varying the electronegativity of the substituents and the alpha- and beta-substituent contributions are clearly illustrated for a variety of substituent groups X. The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges (sigma and pi contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed. The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N'-methylamides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods. The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.
J Comput Aided Mol Des 1991 Feb
PMID:Charge calculations in molecular mechanics. Part 8. Partial atomic charges from classical calculations. 207 23


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