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At least 613 records · Page 34Linked to original sources

PubMedDate not supplied

3-D mapping of body surface potentials.

A new system has been developed in which the human body surface potentials are displayed in a 3-dimensional format using computer graphics. A wire-frame model of the human torso is constructed using geometrical data from several cross-sectional slices. The body surface potentials are measured and the isopotential lines drawn. By mapping the co-ordinates obtained with the isopotential line subroutine to the X, Y and Z torso arrays, a 3-dimensional representation of the depolarization wave travelling across the body surface can be displayed. The deviations from its normal path are clearly seen in the 2 clinical cardiac conditions presented (right bundle branch block and left ventricular premature beat). The increased realism and spatial resolution, as compared to ECG and the 2-dimensional contour map, lead to a clear understanding and interpretation of the underlying electrical phenomena of the heart while making a diagnosis or presenting experimental results.

Bundle-Branch Block↗

PubMed1990

L-alpha-glycerophosphate binding to bovine gamma-crystallin: a potential link between metabolism and supramolecular order.

The highly selective nature of protein-ligand interactions provides a sensitive mechanism for the modulation of cellular activity by proteins. In the eye lens the supramolecular order of the lens crystallins, which is expected to be susceptible to protein electrostatic charge, in part defines transparency. The binding of charged ligands to proteins is one way of achieving an alteration in protein electrostatic charge. Evidence is presented that L-alpha-glycerophosphate, a major phosphorus metabolite of eye lens metabolism, binds to the globular protein, gamma-crystallin with moderately high affinity and in a positive cooperative manner. The following binding parameters were obtained from equilibrium measurements: minimum number of binding sites, n = 2; Kassoc = 6.2 +/- 0.5 x 10(3) M-1; cooperativity parameter, alpha H = 1.9 +/- 0.1. Interactive computer graphics display techniques were used to locate putative ligand binding sites, and in turn, to identify the possible molecular interactions responsible for the binding of ligand to protein at one of the sites. One putative binding site was located in the cleft between the two domains of gamma II-crystallin. Arginyl residues 79 and 147 are involved in ligand binding as are the peptide carbonyl oxygens of residues Tyrosyl-50 and Aspartyl-156. Five hydrogen bonds between the ligand and the protein structure are predicted for the binding of L-alpha-glycerophosphate, whereas only 3 occur for the binding of the "unnatural" D-enantiomorph. Modulation of both lens protein supramolecular organization and lens metabolism is predicted to be a consequence of L-alpha-glycerophosphate binding to gamma-crystallin in the lens.

Animals↗

PubMed1996

Sub-pixel accuracy: psychophysical validation of an algorithm for fine positioning and movement of dots on visual displays.

Many visual experiments call for visual displays in which dots are plotted with very fine positional accuracy. Spatial hyperacuities and motion displacement thresholds can be as low as 5 sec arc. On computer graphics displays small angular displacements of a pixel can be obtained only with long viewing distances which impose a small field of view. To overcome this problem, we describe a method for positioning the centroid of a quadrel (a 2 x 2 block of pixels) with very high accuracy, equivalent to 0.4% of a pixel width. This enables dot displays to be plotted with high positional accuracy at short viewing distances with larger fields of view. We show psychophysically that hyperacuities can be measured with sub-pixel accuracy in quadrel displays. Motion displacement thresholds of 16 sec arc were measured in multiple-dot and single-dot displays even though the pixel spacing was 1.2 min arc. Quadrel displays may be especially useful in studies of optic flow and structure-from-motion which demand a fairly large field of view along with fine positional accuracy.

Algorithms↗

PubMed1988

A model for the spatial arrangement of the proteins in the large subunit of the Escherichia coli ribosome.

A three-dimensional model for the arrangement of 29 of the 33 proteins from the Escherichia coli large ribosomal subunit has been generated by interactive computer graphics. The topographical information that served as input in the model building process was obtained by combining the immunoelectron microscopically determined network of epitope-epitope distances on the surface of the large ribosomal subunit with in situ protein-protein cross-linking data. These two independent sets of data were shown to be compatible by geometric analysis, thus allowing the construction of an inherently consistent model. The model shows (i) that the lower third of the large subunit is protein-poor, (ii) that proteins known to be functionally involved in peptide bond formation and translocation are clustered in two separate regions, (iii) that proteins functionally interdependent during the self-assembly of the large subunit are close neighbours in the mature subunit and (iv) that proteins forming the early assembly nucleus are grouped together in a distinct region at the 'back' of the subunit.

Bacterial Proteins↗

PubMed1991

Three-dimensional structure and molecular dynamics of cis(Z)- and trans(E)-chlorprothixene.

cis(Z)-Chlorprothixene has antidopaminergic potency, while trans(E)-chlorprothixene is virtually inactive. In order to reveal the structural features causing the difference in activity, the three-dimensional molecular and electronic structures of cis(Z)- and trans(E)-chlorprothixene were examined by computer graphics and molecular mechanical and quantum mechanical calculations. The internal molecular motions of the isomers were studied by molecular dynamics simulations in vacuo and in aqueous solution. The cis(Z)-isomer had lower potential molecular energy than the trans(E)-isomer, mainly due to electrostatic interactions within the side-chain and between the dimethylamino group and the chlorine atom. During molecular dynamics simulations in aqueous solution, the side-chain of the trans(E)-isomer stayed closer to the central S-C axis of the ring system than did the side-chain of the cis(Z)-isomer. The molecular electrostatic potentials were significantly lower in the vicinity of the chlorine atom in the trans(E)- than in the cis(Z)-isomer. Differences in molecular electrostatic potentials and in three-dimensional structure are suggested to be the main reasons for the difference in pharmacological activities of cis(Z)- and trans(E)-chlorprothixene.

Chlorprothixene↗

PubMed1997

Development of the computerized dental cast form analyzing system--three dimensional diagnosis of dental arch form and the investigation of measuring condition.

To analyze the functional and morphological harmonies of the tooth and dental arch, a computerized system to measure a dental cast and to detect the apex of dental cusps and angle points of incisors was developed. Detailed morphology in the measured dental cast could be displayed distinctively by computer graphics (CG) with a surface model. Accuracy in determining the position of the apex of the dental cusp was examined by increasing the measuring pitch from 50 microns to 400 microns, the error increased gradually with increased measuring pitch. Taking the measuring error, the time for measurement and the memory size for analysis into account, a measuring pitch of 200 microns was determined to be reasonable. Three-dimensional data measurements from the apex of the dental cusp in molar, and the mesial and distal angles in canine and incisor were fitted to a polynomial formula. In the present measured model, the 4th order polynomial formula was used for the dental arch, and the 2nd order polynomial formula was used for the anteroposterior and lateral occlusal curves. These formulae could be simultaneously superimposed on the surface model of the dental cast, and displayed using CG.

Computer Graphics↗

PubMed1988

Comparative molecular model building of two serine proteinases from cytotoxic T lymphocytes.

Two genes that are expressed when precursor cytotoxic T lymphocytes are transformed to T killer cells have been cloned and sequenced. The derived amino acid sequences, coding for cytotoxic cell protease 1 (CCP1) and Hannuka factor (HF) are highly homologous to members of the serine proteinase family. Comparative molecular model building using the known three-dimensional structures and the derived amino acid sequences of the lymphocyte enzymes has provided useful structural information, especially in predicting the conformations of the substrate binding sites. In applying this modelling procedure, we used the X-ray structures of four serine proteinases to provide a structurally based sequence alignment: alpha-chymotrypsin (CHT), bovine trypsin (BT), Streptomyces griseus trypsin (SGT), and rat mast cell protease 2 (RMCP2). The root mean square differences in alpha-carbon atom positions among these four structures when compared in a pairwise fashion range from 0.79 to 0.97 A for structurally equivalent residues. The sequences of the two lymphocyte enzymes were then aligned to these proteinases using chemical criteria and the superimposed X-ray structures as guides. The alignment showed that the sequence of CCP1 was most similar to RMCP2, whereas HF has regions of homology with both RMCP2 and BT. With RMCP2 as a template for CCP1 and the two enzymes RMCP2 and BT as templates for HF, the molecular models were constructed. Intramolecular steric clashes that resulted from the replacement of amino acid side chains of the templates by the aligned residues of CCP1 and HF were relieved by adjustment of the side chain conformational angles in an interactive computer graphics device. This process was followed by energy minimization of the enzyme model to optimize the stereochemical geometry and to relieve any remaining unacceptably close nonbonded contacts. The resulting model of CCP1 has an arginine residue at position 226 in the specificity pocket, thereby predicting a substrate preference for P1 aspartate or glutamate residues. The model also predicts favorable binding for a small hydrophobic residue at the P2 position of the substrate. The primary specificity pocket of HF resembles that of BT and therefore predicts a lysine or arginine preference for the P1 residue. The arginine at position 99 in the model of HF suggests a preference for aspartate or glutamate side chains in the P2 position of the substrate. Both CCP1 and HF have a free cysteine in the segment of polypeptide 88 to 93.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed1988

Color vision defects in ocular hypertension and glaucoma. Quantification with a computer-driven color television system.

In order to detect early defects of color vision caused by increased intraocular pressure, a computer graphics device and color monitor system were used to measure color contrast sensitivity. The system determines the threshold chrominance of a colored grating in which there is no change in luminance. The study included 13 control subjects aged 10 to 57 years and 19 patients with ocular hypertension or glaucoma aged 20 to 58 years. In the 13 eyes with visual field loss, color contrast sensitivity was profoundly reduced when the grating colors fell on a tritan color confusion line. In the eyes without visual field loss, tritan color contrast sensitivity was reduced to an average level considerably below the extreme limits of the control group. These results were compared with those of other color vision tests and diagnostic criteria for glaucoma. The findings suggest that among the tests used, color contrast sensitivity testing was able to discriminate most effectively between patients who had retinal damage and the normal population.

Color Perception Tests↗

PubMed1991

A model of the lac repressor-operator complex based on physical and genetic data.

Computer graphics were used to build a molecular model of the complex of Lac repressor and lac operator. The model is based (a) on the NMR data of the Kaptein group [Boelens, R., Lamerichs, R. M. J. N., Rullmann, J. A. C., van Boom, J. H. & Kaptein, R. (1988) Protein Sequence Data Anal. 1, 487-498] and (b) on our genetic and biochemical data including specificity changes [Lehming, N., Sartorius, J., Kisters-Woike, B., von Wilcken-Bergmann, B. & Müller-Hill, B. (1990) EMBO J. 9, 615-621]. Effects of amino acid exchanges in the recognition helix could be predicted by the model and were subsequently tested and confirmed by genetic experiments. Comparison of the modelled lac complex with the known crystallographic structures of several helix-turn-helix DNA complexes reveals striking similarities and suggests rules which govern the recognition between particular amino acid side chains and particular base pairs in these systems.

Amino Acid Sequence↗

PubMed1990

Visualization of molecular flexibility and its effects on electrostatic recognition.

To study the effect of protein flexibility on electrostatic recognition, we have devised two novel computer graphic representations of the changes in the electrostatic field of a protein resulting from its internal motions. The atomic structure of Cu, Zn superoxide dismutase was minimized, and the 200 lowest frequency normal modes of the enzyme were determined. Individual and combined normal-mode vibrations were visualized interactively with the program Flex. Normal-mode motions are fast enough (approximately 10(-11) s cycle-1) to evade solvent damping, thus allowing long-range electrostatic interactions to dominate. The changing electrostatic environment of the protein was examined by animating precalculated frames of electrostatic field vectors with GRAMPS. With Vu, changes in electrostatic potential were displayed as variations in the color-coding of dots lying on a consensus surface that maintains the protein's shape. The consensus surface was calculated with the program Sphinx, and was derived from spherical harmonic approximations of expanded molecular surfaces. The ability to view the effects of molecular motions interactively should be useful in understanding the relationships of protein structure to function.

Computer Graphics↗

PubMed1989

Corneal topography and fluctuating visual acuity after radial keratotomy.

A high-resolution photokeratoscope using computer graphics to model corneal topography was used on patients who had undergone radial keratotomy. After radial keratotomy, central optical zones are created that can be characterized as round, oval or band-like, or dumbbell-shaped or split. The dumbbell form of optical zone was associated with larger amounts of refractive and keratometric astigmatism than the round or band-like zones. The authors correlated the shape of the optical zone with the presence or absence of diurnal variation (fluctuation) in visual acuity. Of the 26 eyes studied, 11 experienced fluctuation and 15 did not. Of those 11 eyes with fluctuating visual acuity, 10 (91%) had dumbbell-shaped or split optical zones and 1 (9%) had a round optical zone. Of the 15 eyes without fluctuation, 12 (80%) had round optical zones and 3 (20%) had band-like zones. The presence of a split or dumbbell-shaped optical zone after radial keratotomy indicates that the patient is likely to experience diurnal fluctuation of visual acuity.

Astigmatism↗

PubMed1994

Application of a new morphometry system based on SEM stereo-pairs to the study of intestinal mucosa of rodents.

A new morphometry system for submicroscopic three-dimensional structures was developed on the same principles as for the aerial survey using SEM stereo-pairs. This computer graphic system was applied to the analysis of the surface features of the intestinal mucosa. After removing the epithelial layer by prolonged osmication, core structures of the intestinal villi were exposed and 100 villi each from rat and mouse were measured. Average height, basal area and surface area of a single core of the rat were 188 microns, 20,200 microns2 and 93,500 microns2, respectively. Those of the mouse were 148 microns, 7,530 microns2 and 37,100 microns2, respectively. Surface amplifications by the rat and the mouse villi, after compensating for epithelial thickness, were calculated as 3.5 and 4.3, respectively; though amplifications based on the villous core were 4.6 and 4.9, respectively. These three-dimensional features of the intestinal mucosa were illustrated as submicroscopic maps by drawing their contour lines. It was demonstrated that the present morphometry system makes it possible to know not only the average features of a large sample, but also a variety of features of individual structures which were directly observed under SEM.

Animals↗

PubMed1988

Secretion in yeast of human lysozymes with different specific activities created by replacing valine-110 with proline by site-directed mutagenesis.

Computer graphics indicate that a steric hindrance exists between valine-110 side chain of human lysozyme (EC 3.2.1.17) and an acetyl group of a modified substrate that contains N6,O-diacetylmuramic acid. To alter the substrate specificity of human lysozyme to be effective on the modified substrate, we replaced the valine-110 residue with various amino acids by site-directed mutagenesis. One of the mutant proteins (valine residue replaced with proline:P110) was secreted in Saccharomyces cerevisiae as at least four components (P110-A, P110-B, P110-C, and P110-D) with different specific activities. Two components, P110-B and P110-D, were isolated in a pure form and structurally characterized. The results suggest that this mutation lowered the lytic activity against Micrococcus lysodeikticus by changing a local conformation of the catalytic site while keeping almost the same substrate binding sites. Our results also indicate that cis/trans isomerization of prolyl peptide bonds probably occurs in vivo and that the conformational change of protein as well as point mutations in genes might influence the molecular evolution of the protein.

Amino Acid Sequence↗

PubMed1991

Molecular recognition at the active site of subtilisin BPN': crystallographic studies using genetically engineered proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor).

Unlike trypsin-like serine proteases having only one conspicuous binding pocket in the active site, subtilisin BPN' has two such pockets, the S1 and S4 pockets, which accommodate the P1 and P4 residues of ligands (after Schechter and Berger notation) respectively. Using computer graphics, the geometrical nature of the two pockets was carefully examined and strategies for site-directed mutagenesis studies were set up against a protein SSI (Streptomyces subtilisin inhibitor), which is a strong proteinaceous inhibitor (or a substrate analogue) of subtilisin BPN'. It was decided to convert the P1 residue, methionine 73, into lysine (M73K) with or without additional conversion of the P4 residue, methionine 70, into glycine (M70G). The crystal structures of the two complexes of subtilisin BPN', one with the single mutant SSI (M73K) and the other with the double mutant SSI (M73K, M70G) were solved showing that (i) small 'electrostatic induced-fit movement' occurs in the S1 pocket upon introducing the terminal plus charge of the lysine side chain, and (ii) large 'mechanical induced-fit movement' occurs in the S4 pocket upon reducing the size of the P4 side chain from methionine to glycine. In both (i) and (ii), the induced-fit movement occurred in a concerted fashion involving both the enzyme and 'substrate' amino acid residues. The term 'substrate-assisted stabilization' was coined to stress the cooperative nature of the induced-fit movements.

Bacterial Proteins↗

PubMed1991

Three-dimensional model for stellacyanin, a "blue" copper-protein.

A three-dimensional model of the "blue" copper-glycoprotein stellacyanin from Rhus vernicifera has been derived by computer graphics, energy minimization and molecular dynamics techniques. The initial atomic co-ordinates were obtained by making substitutions and insertions in the known structure of another blue copper-protein, cucumber basic protein (CBP), which is 46% homologous with stellacyanin and has similar spectroscopic properties. An important difference between CBP and stellacyanin is that the latter lacks methionine, a residue that forms an exceptionally long bond to the copper atom in all blue copper-proteins of known structure. In the aligned amino acid sequences, stellacyanin has glutamine 97 at the position that corresponds to the copper-binding methionine 89 in CBP. The hypothesis that the copper atom in stellacyanin is co-ordinated by the side-chain functional groups of histidine 46, cysteine 87, histidine 92 and glutamine 97 leads to a model that enables the spectroscopic properties, redox potential and electron-transfer kinetics of the protein to be rationalized. The present model for stellacyanin is more plausible than an antecedent model derived from the structure of plastocyanin. This demonstrates that the output from molecular modeling calculations is strongly dependent on the input, and that sequence homology with the target molecule is an important criterion for the selection of a starting model.

Amino Acid Sequence↗

PubMedDate not supplied

Computer-aided three-dimensional reconstruction and morphometry of the outer hair cells of the guinea pig cochlea.

The outer hair cells and their nerve endings in the basal and third turns of the guinea pig cochlea were reconstructed three-dimensionally from serial thin sections by means of computer graphics, and morphometric data were obtained. The number of nerve endings in the third turn was two to three times greater than that in the basal turn. Many afferent and efferent terminals in the third turn did not demonstrate synaptic specialization. Presynaptic dense bodies were missing in the majority of outer hair cells in both basal and third turns. The morphologic arrangement of the subsurface cisternae and efferent fiber synapses on the side and base of the outer hair cells suggests a close functional relationship. The nerve fibers and cisternae may be involved in the contractile process of the cells. The volume of the outer hair cells in the first row of the basal turn was about 656 micron 3, and third turn, 1358 micron 3. The total count of mitochondria in the outer hair cells of the first row in the basal turn was 1425, and 1963 in the third turn. The density of mitochondria in the sensory cell in the basal turn was higher. The highest density was seen in the infranuclear region. The mitochondrial distribution patterns suggest that metabolic activity of the outer hair cells is higher in the basal turn than in the third turn and the energy requirement is greatest in the region close to nerve endings.

Animals↗

PubMed1997

New evaluation method for postoperative scar redness.

Even after successful operations, ugly postoperative skin scars are often distressing to patients and their parents. To judge the success of surgical methods and postoperative treatment, postoperative scars should be evaluated using a quantitative system. Height and width are easily measured, but scar redness is not. We have developed a simple and effective method for evaluating scar redness. According to the color definitions employed in computer graphics, each color can be expressed as RGB (red, green or blue) coordinates (r, g, b): 0 < or = r, g, b < or = 10. The degree of scar redness is defined by the following formula: redness score (RS) = (r1 - r0)2 + (g1 - g0)2 + (b1 - b0)2. Here, (r1, g1, b1) = coordinates of the scar color and (r0, g0, b0) = coordinates of the surrounding skin color. RS was evaluated in 59 children (35 males, 24 females; ages 1 month to 12 years old) who had scar redness after congenital cardiac surgery. For each patient, scar color and surrounding skin color was identified on the color sample table. Scar redness was also evaluated by the conventional grading method: 1 = mild, 2 = moderate and 3 = severe. The RS of the colored scars ranged from 4 to 100 (38 +/- 27). By the conventional grading method, 44 scars were grade 1, 15 grade 2 and none grade 3. RS was significantly higher among grade 2 than grade 1 patients, 52 +/- 25 and 33 +/- 27, respectively (P < 0.05). Given its subjectivity, the conventional grading method yields variable data surrounding skin color, moreover, is not considered. Our new evaluation method using RS effectively and accurately defines scar and skin colors, and allows quantitative studies of these factors.

Child↗

PubMed1987

Prothoracicotrophic hormone has an insulin-like tertiary structure.

A three-dimensional model of PTTH-II has been constructed using interactive computer graphics and energy, minimisation techniques, assuming homology with porcine insulin, the structure of which has been determined by X-ray analysis. The model shows that PTTH-II can assume an insulin-like tertiary structure, which is compact with the exception of the sequence variable NH2-terminal amino acids of the B chain. Most of the hydrophobic core residues including A2 Ile, A6 Cys, A11 Cys, A16 Leu, A20 Cys, B11 Leu, B15 Leu and B19 Cys are identical in PTTH-II and insulins. The glycines at A1, B8 and B23 allow the chain to assume the characteristic tertiary interactions of the insulin fold and although polypeptide chains are shorter at the COOH-termini of the A and B chains and extended at the NH2-terminus of the B chain, the insulin-like tertiary structure can still be assumed. It is unlikely that PTTH-II forms either dimers or hexamers, characteristic of porcine and human insulin, and the model is consistent with the inability of PTTH-II to bind anti-insulin antibodies or insulin receptors. A hydrophobic surface region of PTTH-II may be involved in intermolecular actions of physiological relevance. We discuss the implications of our model for evolution of this family of hormones and growth factors.

Animals↗