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PubMed1988

A receptor model for tumor promoters: rational superposition of teleocidins and phorbol esters.

Four 12-O-tetradecanoyl-13-O-acetylphorbol-type tumor promoters--teleocidin, phorbol ester, aplysiatoxin, and ingenol ester--are superposed in an attempt to understand their common biological activity on the assumption that they may bind to the same receptor site. A method using three-dimensional computer graphics was applied for superposing molecules and receptor mapping. The main feature of the method is that molecules are superposed in terms of spatial arrangement of physical and chemical properties but not in terms of the atomic positions as in conventional methods. This led to successful extraction of common structural features required for potent tumor-promoting activity: two hydrogen donors, a hydrogen acceptor, and a large lipophilic group. Their mutual spatial arrangements are most important for biological activity.

Caenorhabditis elegans Proteins↗

PubMed1996

Selectivity of the parietal visual neurones in 3D orientation of surface of stereoscopic stimuli.

We identified a group of neurones in the posterior parietal cortex of the monkey that responded preferentially to a flat stimulus in a particular orientation on a 3D computer graphics display. We designated these neurones surface-orientation selective (SOS) neurones since they showed tuning to the 3D orientation of the surface. Almost all of the SOS neurones were sensitive to binocular disparity and their responses increased with the width or length of the stimulus, but the responses of only some of them decreased with increasing thickness of the stimulus. These results suggest that SOS neurones extract surface orientation signals from the binocular disparity signals and play an important role in the perception of 3D shape and the visual guidance of hand movement.

Animals↗

PubMed1998

The object technology framework: an object-oriented interface to molecular data and its application to collagen.

We describe the Object Technology Framework (OTF) software system developed at the University of California, San Francisco Computer Graphics Laboratory for creating C+2 classes that facilitate rapid biomolecular application development and the application of the OTF to collagen modeling. C+2 class libraries for accessing and manipulating data from standard scientific data sources can be generated using the program genlib and its class library toolkit Molecule, thereby facilitating development of new applications. Use of the OTF for generating ideal collagen structural models (gencollagen) is described. The source code for the OTF is freely available at http:/(/)www.cgl.ucsf.edu/off/ to interested application developers.

Collagen↗

PubMed1990

Protein modeling of human prorenin using the molecular dynamics method.

To study the activation-inactivation mechanism of the renin zymogen, prorenin, a tertiary structural model of human prorenin was constructed using computer graphics and molecular dynamics calculations, based on the pepsinogen structure. This prorenin model shows that the folded prosegment polypeptide can fit into the substrate binding cleft of the renin moiety. The three positively charged residues, Arg10, Arg15, and Arg20, in the prosegment make salt bridges with Asp225, Glu331, and Asp60, respectively, in renin. Arg43, which is in the processing site, forms salt bridges with the catalytic residues of Asp81 and Asp269. These ionic interactions between the prosegment and the renin may contribute to keeping the prorenin structure as an inactive form.

Amino Acid Sequence↗

PubMed1987

Selective alteration of substrate specificity by replacement of aspartic acid-189 with lysine in the binding pocket of trypsin.

To test the role of Asp-189 which is located at the base of the substrate binding pocket in determining the specificity of trypsin toward basic substrates, this residue was replaced with a lysine residue by site-directed mutagenesis. Both rat trypsinogen and Lys-189 trypsinogen were expressed and secreted into the periplasmic space of Escherichia coli. The proteins were purified to homogeneity and activated by porcine enterokinase, and their catalytic activities were determined on natural and synthetic substrates. Lys-189 trypsin displayed no catalytic activity toward arginyl and lysyl substrates. Further, there was no compensatory change in specificity toward acidic substrates; no cleavage of aspartyl or glutamyl bonds was detected. Additional studies of substrate specificity involving gas-phase sequence analyses of digested natural substrates revealed an inherent but low chymotrypsin-like activity of trypsin. This activity was retained but modified by the Asp to Lys change at position 189. In addition to hydrolyzing phenylalanyl and tyrosyl peptide bonds, the mutant enzyme has the unique property of cleaving leucyl bonds. On the basis of computer graphic modeling studies of the Lys-189 side chain, it appears that the positively charged NH2 group is directed outside the substrate binding pocket. The resulting hydrophobic cavity may explain the altered substrate specificity of the mutant enzyme. The relatively low chymotrypsin-like activity of both recombinant enzymes may be due to distorted positioning of the scissile bond with respect to the catalytic triad rather than to the lack of sufficient interaction between the hydrophobic side chains and the substrate binding pocket of the enzyme.

Amino Acid Sequence↗

PubMed1989

Some observations on the replacement of the conserved amino acid residues of immunoglobulin domains.

1. Computer graphics have been used to model replacements of conserved residues in immunoglobulin domains. 2. Replacements, even those involving large changes in side chain volume, could be accommodated in the domain but rotation and repacking of surrounding side chains was generally necessary. 3. Repacking often resulted in increases in inter-atomic distances between side chains and loss of some van der Waals' contacts. This would be expected to make the domain slightly less stable. 4. Losses in domain stability might not have a serious affect on antigen binding but could result in circulating antibody becoming more susceptible to biological degradation with considerable reduction in biological half-life.

Alanine↗

PubMed1988

[New strategies in the search for drugs].

The development of selective, reliable and safe drugs turns out to be a very expensive and time consuming task. Supported by computer graphics, structural chemistry provides tools for the understanding of the drug-receptor interaction on a molecular level. As a prerequisite for these investigations, the structures of both the biochemical receptor and the drug must be experimentally determined or numerically simulated. Subsequently, the three dimensional geometry of the drug molecule can be modified to enable an optimal fit together with a high selectivity for the binding to the active site of the target receptor. Even without knowledge of the structure of the receptor, a particular class of compounds can be optimized by a systematic comparison of drug molecules which allows the elucidation of the pharmacophore pattern relevant to a certain action.

Chemical Phenomena↗

PubMed1999

Morphology and development of the human vocal tract: a study using magnetic resonance imaging.

Magnetic resonance imaging was used to quantify the vocal tract morphology of 129 normal humans, aged 2-25 years. Morphometric data, including midsagittal vocal tract length, shape, and proportions, were collected using computer graphic techniques. There was a significant positive correlation between vocal tract length and body size (either height or weight). The data also reveal clear differences in male and female vocal tract morphology, including changes in overall vocal tract length and the relative proportions of the oral and pharyngeal cavity. These sex differences are not evident in children, but arise at puberty, suggesting that they are part of the vocal remodeling process that occurs during puberty in males. These findings have implications for speech recognition, speech forensics, and the evolution of the human speech production system, and provide a normative standard for future studies of human vocal tract morphology and development.

Adolescent↗

PubMedDate not supplied

Direct measurement of dimensional accuracy with three denture-processing techniques.

The Michigan Computer-Graphics Coordinate Measurement System (MCGCMS) was used to determine the dimensional accuracy of dentures processed by three different techniques: conventional heat compression, microwave, and visible-light activation. Standardized dentures were fabricated from casts made in an RTV silicone mold. All casts were duplicated with hydrocolloid and 42 dentures were made (ie, 14 dentures for each technique). The MCGCMS measured 22 points on two frontal planes to compare master casts to dentures. The results showed no significant difference in overall dimensional accuracy. At specific sites, however, the visible-light-activated technique produced significantly more flange distortion than did either the conventional or microwave techniques.

Acrylic Resins↗

PubMed1989

A molecular modeling study on binding of drugs to calmodulin.

Computer-graphical methods have been used to study the interaction between a series of drugs and calmodulin. Based on the X-ray crystallographic coordinates of the alpha-C atoms of calmodulin, a molecular model of the helical sequences was built. The model has been used to derive two possible binding sites for phenothiazines and one binding site for penfluridol. The principal binding forces occur through contacts between acidic amino acids of calmodulin and the protonated side-chain nitrogen of the drugs as well as between a basic amino acid and the electronegative substituents of the aromatic rings. Calculated interaction energies show a good correlation with experimental inhibition data.

Amino Acid Sequence↗

PubMed1999

What object attributes determine canonical views?

We investigated preferred or canonical views for familiar and three-dimensional nonsense objects using computer-graphics psychophysics. We assessed the canonical views for objects by allowing participants to actively rotate realistically shaded three-dimensional models in real-time. Objects were viewed on a Silicon Graphics workstation and manipulated in virtual space with a three-degree-of-freedom input device. In the first experiment, participants adjusted each object to the viewpoint from which they would take a photograph if they planned to use the object to illustrate a brochure. In the second experiment, participants mentally imaged each object on the basis of the name and then adjusted the object to the viewpoint from which they imagined it. In both experiments, there was a large degree of consistency across participants in terms of the preferred view for a given object. Our results provide new insights on the geometrical, experiential, and functional attributes that determine canonical views under ecological conditions.

Adolescent↗

PubMed1995

A mathematically based classification of root canal curvatures on natural human teeth.

Testing of root canal-shaping instruments on natural human teeth has many difficulties, because of the different anatomical forms of root canals. There is a lack of an internationally accepted and mathematically based classification of root canal morphology. The aim of this study was to give a mathematical description of root canal forms with the help of differentiated geometrical pattern analysis and computer graphics. The measurements of 433 roots were conducted on isometric radiographs taken from the clinical view. Measured points of the same radiographs were approximated using fourth degree polynomial functions describing the imaginary axis of canals. The classification of root canal morphology on the basis of Schneider's angle differs from the classification of geometrical pattern analysis. Fourth-degree function approximation as a new method for the description of the shape of root canal curvatures seems to be exact and reliably repeatable. This type of classification of root canals is suitable for standardizing test specimens, including natural human teeth used for testing root forms: I (straight), J (apical curve), C (entirely curved), or S (multicurved).

Chi-Square Distribution↗

PubMed1996

The three-dimensional bone interface of an osseointegrated implant. I: A morphometric evaluation in initial healing.

Direct bone-implant interface as an indicator of endosseous implant success appears to have been overinterpreted because 100% bone apposition is not necessarily obtained at the surface of the endosseous dental implant. The purpose of this study was to obtain quantitative information about the three-dimensional bone structure around three hydroxyapatite-coated titanium alloy dental implants. Implants were placed in the mandible in three monkeys, and the surface bone contact ratio in the buccal, lingual, mesial, and distal directions was computed. Computer graphics were generated by the integration of data for serial ground surfaces obtained at 75 microm intervals of the tissue block involved with the implant. The bone contact ratio of the whole surface of each of the three implants was 80.8%, 68.1%, and 68.8%, and the bone contact ratio for each direction and portion varied with the conditions of implant placement. The bone volume ratios around the implant at the 0 to 300 microm zone were also calculated, and total ratios ranged from 58% to 81%. These results may provide useful quantitative information about the bone structure around the hydroxyapatite-coated implants and contribute to the development of realistic finite element analysis models based on the biologic bone structure around the implants.

Animals↗

PubMed1990

Comparative study on specificities of rat cathepsin L and papain: amino acid differences at substrate-binding sites are involved in their specificities.

Sixty-nine rat cathepsin L-susceptible peptide bonds were analyzed employing various peptide substrates. The proteolytic specificities of rat cathepsin L and papain were compared and the results are discussed in relation to differences in amino acid residues around their binding sites. The specificity of cathepsin L, which is characterized by a remarkable preference for hydrophobic amino acids at the P2 site of the scissile peptide bonds, was analogous to that of papain as a whole. This analogous specificity suggests that the binding sites of the two proteases are analogous, as expected from their homologous amino acid sequences. However, there is a slight difference in the preference for S3 site between them. That is, cathepsin L showed a greater preference for bulky and hydrophobic amino acids at the S3 site than did papain. Based on the computer-graphically deduced structure of the binding sites of cathepsin L, the preferences for hydrophobic amino acids at the S2 site and for bulky and hydrophobic amino acids at the S3 site of the protease are supposed to be related to the compensating amino acid substitutions at the S2 site (V133A and V157L) and the reduction in size at the S3 site (Y61Q and Y67L), respectively. The discussion of the effect of the amino acid substitutions on the proteolytic activities of cathepsin L and papain in this paper provides a basis for more advanced studies of the relationship between structure and function of proteases belonging to the papain superfamily by means of protein engineering.

Amino Acid Sequence↗

PubMed2002

Partnership status and the temporal context of relationships influence human female preferences for sexual dimorphism in male face shape.

Secondary sexual characteristics may indicate quality of the immune system and therefore a preference for masculinity may confer genetic benefits to offspring; however, high masculinity may be associated with costs of decreased paternal investment. The current study examined women's preferences for masculinity in male faces by using computer graphics to allow transformation between feminine and masculine versions of individual male faces. We found that preferences for masculinity are increased when women either have a partner or are considering a short-term relationship. Such preferences are potentially adaptive, serving to: (i) maximize parental investment and cooperation in long-term relationships by biasing choices towards feminine faced males, and (ii) maximize possible good-gene benefits of short-term or extra-pair partners by biasing choices towards masculine faced males. We also found that individuals using oral contraception do not show the above effects, indicating that such hormonal intervention potentially disrupts women's choices for evolutionarily relevant benefits from males.

Adolescent↗

PubMed1999

Structure based development of novel specific inhibitors for cathepsin L and cathepsin S in vitro and in vivo.

Specific inhibitors for cathepsin L and cathepsin S have been developed with the help of computer-graphic modeling based on the stereo-structure. The common fragment, N-(L-trans-carbamoyloxyrane-2-carbonyl)-phenylalanine-dimethyla mide, is required for specific inhibition of cathepsin L. Seven novel inhibitors of the cathepsin L inhibitor Katunuma (CLIK) specifically inhibited cathepsin L at a concentration of 10(-7) M in vitro, while almost no inhibition of cathepsins B, C, S and K was observed. Four of the CLIKs are stable, and showed highly selective inhibition for hepatic cathepsin L in vivo. One of the CLIK inhibitors contains an aldehyde group, and specifically inhibits cathepsin S at 10(-7) M in vitro.

Animals↗

PubMed2000

[Effects of different types of disparity cues on the response of axis-orientation selective cells in the monkey parietal cortex].

PURPOSE: To specify the cues for the discrimination of orientation in depth in axis orientation selective (AOS) neurons. METHODS: We analyzed the responses of AOS neurons in the monkey caudal intraparietal sulcus (cIPS) region using binocular disparity stimuli generated by stereoscopic 3 D computer graphics. RESULTS: Most AOS neurons (20/27) were sensitive to binocular disparity and showed tuning to the orientation of a slit in the sagittal plane with orientation disparity cues. For 12 neurons we also used an array of discs or dots instead of slits to eliminate orientation disparity. Half of the neurons (6/12) responded better to the slits than to the discs or dots, suggesting that they were sensitive to orientation disparity. Five neurons (5/12) responded equally well to the discs or dots suggesting that they were more sensitive to the gradient of horizontal disparity than to the orientation disparity. CONCLUSION: Both orientation disparity and disparity gradient were likely to be integrated in the cIPS area to represent axis orientation of an object in space.

Animals↗

PubMed2000

A tactile display for international space station (ISS) extravehicular activity (EVA).

BACKGROUND: A tactile display to increase an astronaut's situational awareness during an extravehicular activity (EVA) has been developed and ground tested. The Tactor Locator System (TLS) is a non-intrusive, intuitive display capable of conveying position and velocity information via a vibrotactile stimulus applied to the subject's neck and torso. In the Earth's 1 G environment, perception of position and velocity is determined by the body's individual sensory systems. Under normal sensory conditions, redundant information from these sensory systems provides humans with an accurate sense of their position and motion. However, altered environments, including exposure to weightlessness, can lead to conflicting visual and vestibular cues, resulting in decreased situational awareness. The TLS was designed to provide somatosensory cues to complement the visual system during EVA operations. METHODS: An EVA task was simulated on a computer graphics workstation with a display of the International Space Station (ISS) and a target astronaut at an unknown location. Subjects were required to move about the ISS and acquire the target astronaut using either an auditory cue at the outset, or the TLS. Subjects used a 6 degree of freedom input device to command translational and rotational motion. The TLS was configured to act as a position aid, providing target direction information to the subject through a localized stimulus. RESULTS: Results show that the TLS decreases reaction time (p = 0.001) and movement time (p = 0.001) for simulated subject (astronaut) motion around the ISS. CONCLUSION: The TLS is a useful aid in increasing an astronaut's situational awareness, and warrants further testing to explore other uses, tasks and configurations.

Aerospace Medicine↗