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PubMed1989

Electron transport in sulfate-reducing bacteria. Molecular modeling and NMR studies of the rubredoxin--tetraheme-cytochrome-c3 complex.

A hypothetical model of the complex formed between the iron-sulfur protein rubredoxin and the tetraheme cytochrome c3 from the sulfate-reducing bacteria Desulfovibrio vulgaris (Hildenborough) has been proposed utilizing computer graphic modeling, computational methods and NMR spectroscopy. The proposed complex appears feasible on the basis of complementary electrostatic interaction and steric factors and is consistent with the data from NMR experiments. In this model, the non-heme iron atom of rubredoxin is in close proximity to heme 1 of cytochrome c3. The complex is stabilized by charge-pair interactions and hydrogen bonds. This complex is compared to the flavodoxin-cytochrome c3 complex previously proposed [Stewart, D. E., LeGall, J., Moura, I., Moura, J. J. G., Peck, H. D. Jr, Xavier, A. V., Weiner, P. K. & Wampler, J. E. (1988) Biochemistry 27, 2444-2450] and new NMR data shows that both proteins interact with the same heme group of the cytochrome as postulated.

Binding Sites↗
PubMed1990

Computer applications in orthopaedics.

With the rapid developments in microprocessors, the widespread availability of computers has brought about broad applications in the field of orthopaedics. The present technology enables large quantities of data to be logically processed in a very short span of time. This has led to the development of information management database systems where relevant medical information may be retrieved very quickly and effectively. The analytical power of the computer has also been utilised in expert systems to assist in clinical-decision making process. Computer graphics have revolutionised the visualisation of physical features of internal and external body parts, providing new and improved modalities of diagnosis. In some centres, surgical planning and rehearsals are already being carried out at the computer terminal with the use of animation and computer graphics. Computer technology has also played an active role in the field of prosthetics and rehabilitation. Intelligent robotic systems and microprocessor with functional neuromuscular stimulation have been applied to benefit, and in some cases restore some motor functions to the physically disabled. With more collaboration between engineers, scientists and the medical community, several prototypes of computer-controlled prostheses and prosthesis designed and manufactured by Computer-Aided Design/Computer-Aided Manufacturing (CAD/CAM) technology are available today to assist the amputees in their daily living and ambulatory activities.

Computer Graphics↗
PubMed1992

Radioimmunoassay data handling and calculations with a graphics-statistics computer program.

This paper discusses the application of the data handling-graphics-statistics program Stata (Computing Resources Center, Santa Monica, CA) to radioimmunoassay. We have found that this program is more powerful and easier to use than a spreadsheet for analyzing various kinds of laboratory data generated from chromatography, radiolabeling experiments, enzyme-linked immunosorbent assays, and radioimmunoassays, to name several examples. Data from a radioimmunoassay procedure, originally analyzed using a spreadsheet, Lotus 1-2-3, have been processed with Stata. Simple programs (batch files) have been devised for computations and graphics. The original data and a comparison of results are presented.

Radioimmunoassay↗
PubMed1978

Interactive computer surface graphics approach to study of the active site of bovine trypsin.

A descriptive medium for the presentation of protein structure has been developed and used to evaluate the structure of the active site of bovine trypsin (EC 3.4.21.4). This technique, involving advanced computer graphics technology, permits the facile display of a representation of the molecular surface of proteins of known structure and employs color to code the structural or chemical features of this surface. Benzamidine derivatives were inserted into the benzamidine-binding site of trypsin and the binary inhibitor-trypsin complex was evaluated by using the computer-generated structure. On the basis of qualitative assessments of the contribution of electrostatic and hydrophobic forces to the binding energy associated with complex formation, we made predictions concerning the effects of interaction of benzamidine substituents and amino acid side chains upon the binding energy associated with inhibitor-protein binding. The computer display of the molecular surfaces of the binary complex of substituted benzamidines and trypsin permitted unique insight into the identity and chemical properties of the atoms that participate at the interface of the molecular surfaces of the inhibitor and the protein. The computer-generated molecular surface display can potentially be combined with quantitative definition of the physical forces involved in the interaction of molecular surfaces. This technology should facilitate the study of the structure-activity relationship of substrates, inhibitors, and drugs that bind to proteins of known three-dimensional structure.

Animals↗
PubMed1992

[Comparison of fingerprints using a personal computer and graphic software sold on market].

We compared the fingerprint images using a personal computer and a graphic software sold on market. The fingerprints of thumb of left hand recorded by pressing and rolling on paper were input in computer using image scanner. These two fingerprint images were overlapped by moving and rotation on the computer screen, and were fitted well. This result showed that the fingerprints recorded by any way from one person were fitted. Latent and accused's fingerprints were also input in computer using image scanner. These images were analyzed by the same procedure. These two fingerprints were part by unfitting. It was decided these two fingerprints were not derived from one person. We also considered the possibility that the latent fingerprint was the reversed one. Then, the image was reversed of its color on the screen of computer (black to white and white to black) and compared by the same procedure. In this experiment, two fingerprint images were not fitted in a part. This showed that the reversed fingerprint was also able to be analyzed by this procedure. For the comparison of fingerprints, this report showed the ability of the personal computer and software which can be obtained easily from market. Following the improvement of the hardware and software used in this examination in near future, the computerized identification of fingerprints like this study will become more accurate and convenient.

Computer Graphics↗
PubMed1991

Two-dimensional computer color graphics of gastric mucosal blood distribution in normal subjects and ulcer patients.

The mucosal blood volume in 20 to 24 different regions of stomach was estimated by reflectance spectrophotometry during endoscopy, and an image showing mucosal blood distribution was made by two-dimensional computer color graphics with the aid of a personal computer. In 55 normal controls, the estimated mucosal blood volume (EMBV) was greater in the corpus mucosa than in the antral mucosa, and less in the lesser curvature than in the greater curvature. The volume in the anterior and posterior walls was almost the same. In 15 patients with active gastric ulcers in the angular region, the EMBV was decreased in all regions in the stomach. In 37 patients with healing ulcers, the EMBV increased, resuming the same levels as in normal controls. However, the EMBV around the ulcer increased remarkably at this stage. In 35 patients with ulcers in the scarring stage, the distribution of the EMBV was similar to that in the normal controls. These hemodynamic changes were shown clearly in a color display with the aid of a personal computer. This method could offer new possibilities in endoscopic research.

Adult↗
PubMed1991

Model for the structure of formaldehyde dehydrogenase based on alcohol dehydrogenase.

The three-dimensional structure of rat liver formaldehyde dehydrogenase (FALDH), previously known as class III alcohol dehydrogenase, was constructed using computer graphics and computer programs developed for model building. The construction is based on horse liver alcohol dehydrogenase (EE-ADH), whose structure has been elucidated by X-ray crystallography. The high sequence homology between the two enzymes makes knowledge-based modelling feasible in this case. The model shows a remarkable similarity to horse liver alcohol dehydrogenase especially in the NAD-binding domain. Certain mutations, and the one insertion in FALDH compared to EE-ADH in particular, have cause important changes in the substrate binding site, and thus aliphatic alcohols have been replaced by hemi-thioacetals as favourable substrates.

Alcohol Dehydrogenase↗
PubMed1986

Modeling complex molecular interactions involving proteins and DNA.

We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Base Sequence↗
PubMed1987

Comparison of computer modelling and X-ray results of the binding of a pyrazole derivative to liver alcohol dehydrogenase.

The binding to liver alcohol dehydrogenase of the inhibitor 2,4-(4-pyrazolyl)-butylisothiourea has been studied both by modelling experiments using computer graphics with interactive energy minimization and by X-ray crystallographic structure determination. For the modelling experiments, we used the program system TOM, which was developed in our laboratory as an extension of the program FRODO. Different strategies for using computer graphics with interactive energy minimization were tested. Two essentially different binding modes were found. One of these was favoured from energy minimizations using a potential energy function which was the sum of a Coulomb interaction term and two different van der Waals' interaction terms for non-bonded and torsional interactions. This binding mode was close to the crystallographic observed structure. The results show that flexibility of both ligand and receptor side-chains as well as main-chain conformations are important for docking to the active site of liver alcohol dehydrogenase.

Alcohol Dehydrogenase↗
PubMed1991

Displaying inter-main chain hydrogen bond patterns in proteins.

Two computer graphics techniques for displaying hydrogen bonds between the main chains of different proteins are described, and illustrated for two thiol proteases. (The X-ray crystallography was performed by Kamphuis et al. in 1984, and by Baker and Dodson in 1980.) One is a three-dimensional model that can be manipulated in space; the hydrogen bonds are represented with the smoothed alpha-carbon plot of the polypeptide chain. In the other type of display, hydrogen bonds are viewed in relation to the one-dimensional sequence. Both types of picture facilitate visualization of hydrogen bond patterns, such that loop motifs, as well as alpha-helices and beta-sheets, can be examined easily. We suggest that such displays are useful as a general means of displaying whole proteins and whole domains because they reveal more information than do conventional simplified pictures of proteins, which focus exclusively on alpha-helices and beta-sheets. These techniques can be implemented on a UNIX-based computer graphics workstation. (UNIX is a trademark of Bell Telephone laboratories.)

Computer Graphics↗
PubMed1976

Morphological correlates of synaptic transmission in lamprey spinal cord.

The dye Procion brown was used to identify in the light and electron microscope, synaptic contacts made between monosynaptically coupled neurons in the lamprey spinal cord whose synaptic interaction had been recorded. Synaptic contacts were made on different dendrites of the postsynaptic cell at different distances from the soma. Some of the contacts were made on dentritic spines and some on the smooth shaft of the dentrites. Serial sections through synaptic contacts made on dendritic processess of the postsynaptic cells were used for three-dimensional reconstruction of the synapses using computer graphics techniques. The computer reconstructions and detailed examination of the serial EM micrographs revealed the large proliferation of membrane involved in making these en passant synapses as well as the morphological changes due to stimulation of the presynaptic axon. These changes include depletion of synaptic vesicles and formation of complex vesicles and synaptic cisternae. Besides chemical synaptic contacts, four electrotonic contacts were located, confirming the mixed electrochemical synaptic response recorded from the postsynaptic cell. The mean quantum content was estimated and compared with the estimate of the available transmitter pool, assuming the quantal release hypothesis applies at these synapses. The total transmitter pool was estimated by counting all synaptic vesicles in all synaptic contacts. It was estimated that about 6% of the total transmitter pool is available for release at these synapses. This compares with less than 1% at the neuromuscular junction and about 20% at sympathetic synapses. These results support the hypothesis that synaptic vesicles may be recycled as described by Heuser and Reese (22) at the neuromuscular junction. Ongoing studies are investigating the effect on a variety of synaptic junctions to stimulation for different periods of time of presynaptic axons. The methods described in this study can also be used to test the models of synaptic interaction on dendritic trees described by Rall (39) and Jack and Redman (24).

Action Potentials↗
PubMed1989

[Development of a system for ultrasonic three-dimensional reconstruction of fetus].

We have developed a system for ultrasonic three-dimensional (3-D) fetus reconstruction using computers. Either a real-time linear array probe or a convex array probe of an ultrasonic scanner was mounted on a position sensor arm of a manual compound scanner in order to detect the position of the probe. A microcomputer was used to convert the position information to what could be recorded on a video tape as an image. This image was superimposed on the ultrasonic tomographic image simultaneously with a superimposer and recorded on a video tape. Fetuses in utero were scanned in seven cases. More than forty ultrasonic section image on the video tape were fed into a minicomputer. The shape of the fetus was displayed three-dimensionally by means of computer graphics. The computer-generated display produced a 3-D image of the fetus and showed the usefulness and accuracy of this system. Since it took only a few seconds for data collection by ultrasonic inspection, fetal movement did not adversely affect the results. Data input took about ten minutes for 40 slices, and 3-D reconstruction and display took about two minutes. The system made it possible to observe and record the 3-D image of the fetus in utero non-invasively and therefore is expected to make it much easier to obtain a 3-D picture of the fetus in utero.

Computer Systems↗
PubMed1985

Electrostatic interactions during electron transfer reactions between c-type cytochromes and flavodoxin.

The interaction of three different c-type cytochromes with flavodoxin has been studied by computer graphics modelling and computational methods. Flavodoxin and each cytochrome can make similar hypothetical electron transfer complexes that are characterized by nearly coplanar arrangement of the prosthetic groups, close intermolecular contacts at the protein-protein interface, and complementary intermolecular salt linkages. Computation of the electrostatic free energy of each complex showed that all were electrostatically stable. However, both the magnitude and behavior of the electrostatic stabilization as a function of solution ionic strength differed for the three cytochrome c-flavodoxin complexes. Variation in the computed electrostatic stabilization appears to reflect differences in the surface distribution of all charged groups in the complex, rather than differences localized at the site of intermolecular contact. The computed electrostatic association constants for the complexes and the measured kinetic rates of electron transfer in solution show a remarkable similarity in their ionic strength dependence. This correlation suggests electrostatic interactions influence electron transfer rates between protein molecules at the intermolecular association step. Comparative calculations for the three cytochrome c-flavodoxin complexes show that these ionic strength effects also involve all charged groups in both redox partners.

Clostridium↗
PubMed1988

Photographic assessment of the antiplaque properties of sanguinarine and chlorhexidine.

The purpose of this study was to assess the effect of rinsing and topical application of sanguinarine on labial surface plaque accumulation, compared with topically applied water, and compared with rinsing with chlorhexidine, while refraining from all oral hygiene measures for 5 days. Color photographs of the disclosed plaque were taken at the end of each phase of treatment and blindly traced using an Apple II micro-computer graphic tablet digitizer. The plaque score for each tooth was calculated by dividing the computer reading of the labial plaque surface area by the total labial surface area of the tooth. Topically applied sanguinarine showed better plaque reduction than mouthrinsing with sanguinarine. There was a significant reduction in plaque accumulation after rinsing with chlorhexidine compared with topically applied sanguinarine, water, and mouthrinsing with sanguinarine. The results of this study indicate that chlorhexidine is a more superior antiplaque agent than sanguinarine. The use of an Apple II micro-computer graphic tablet digitizer provided a valuable method for accurate plaque assessments.

Administration, Topical↗
PubMed1989

Painting with pixels.

Two decades ago the subject of computer graphics was regarded as pure science fiction, more within the realms of Star Trek fantasy than of everyday use, but today it is difficult to avoid its influence. Television programmes abound with slick moving, twisting, distorting images, the printing media throws colourful shapes and forms off the page at you, and computer games explode noisily into our living rooms. In a very short space of time computer graphics have risen from being a toy of the affluent minority to a working tool of the cost-conscious majority. Even the most purist of artists have realized that in order to survive in an increasingly competitive world they must inevitably take the plunge into the world of electronic imagery.

Computer Graphics↗
PubMed1988

Solid perception mechanism by a shading pattern: spatial frequency components in a corrugated wave pattern.

Illumination allows solid object perception to be obtained and depicted by a shading pattern produced by lighting. The shading cue, as one of solid perception cues (Gibson 1979), was investigated in regard to a white corrugated wave shape, using computer graphic device: Tospix-2. The reason the corrugated wave was chosen, is that an alternately bright and dark pattern, produced by shading, can be conveniently analyzed into contained spatial frequencies. This paper reports spatial frequency properties contained in the shading pattern. The shading patterns, input into the computer graphic device, are analyzed by Fourier Transformation by the same device. After the filtration by various spatial frequency low and high pass filters, Inverse Fourier Transformation is carried out for the residual components. The result of the analysis indicates that the third through higher harmonics components are important in regard to presenting a solid reality feeling in solid perception. Sakata (1983) also reported that an edged pattern, superimposed onto a lower sinusoidal pattern, was important in solid perception. The third through higher harmonics components express the changing position of luminance on the pattern, and a slanted plane relating to the light direction. Detection of a solid shape, constructed with flat planes, is assumed to be on the bottom of the perfect curved solid perception mechanism. Apparent evidence for this assumption, in difficult visual conditions, is that a flat paneled solid is seen before the curved solid. This mechanism is explained by two spatial frequency neural network systems, assumed as having correspondence with higher spatial frequency detection and lower spatial frequency detection.

Computer Graphics↗