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At least 199 records · Page 11Linked to original sources
PubMed1986

Refined models for computer calculations in protein engineering. Calibration and testing of atomic potential functions compatible with more efficient calculations.

A reappraisal has been made of interatomic potential functions for protein structure calculations using the all-atom approximation (except CH, CH2 and CH3, which are treated as "united atoms"). Some key problems are identified and treated. The potential functions are somewhat novel in form and consistent with more efficient and robust folding algorithms. In addition, the potentials are calibrated for for the rigid geometry approximation, since use of fixed standard bond lengths and valence angles (and fixed trans planar peptide groups) reduces the number of conformational variables and saves a great deal of computer time. Though these algorithms demand the use of potential functions of this special type, these functions can be readily implemented in more classical programs for the conformational analysis of proteins. They are calibrated or tested against a large body of experimental data, including extended basis set ab initio, quantum mechanical calculations, nuclear magnetic resonance spectroscopic data and dipole moment data for di- and oligopeptides, characteristic ratio data for random coil homopolypeptides, extensive data from peptide solubility studies, and experimental structures of polyalanine fibres and globular proteins. This paper will form the basis of a further report, which will include investigations of how water might be more realistically represented subject to the computing power available.

Amino Acid Sequence↗
PubMed1987

A simple quantitative analysis system for coronary cineangiograms using a personal computer.

We have developed a simple quantitative analysis system for coronary cineangiograms using a personal computer and a standard projector-video camera system. The selected frame of cinefilm was projected onto the target area of a CCD video camera. To decrease spatial fluctuations due to quantum noise, the digital data were smoothed spatially by applying a moving averaged filter and a median filter. Following the smoothing process, the digital data with gray level were transformed to binary data by quantifying the threshold property of their gray level. To minimize the geometric influence, mainly pincushion effect, a cinefilm of a 1 cm grid was placed against the input screen of the image intensifier to correct the distortion by using 3rd degree polynomials. The accuracy of the contour detection procedure was validated on the basis of phantom models filled with a contrast medium. Despite the potential influence of many radiographic variables on computerized diameter measurements, the overall accuracy was found to be 0.26-0.33 mm over a wide range of clinically relevant artery diameters and radiographic conditions. Using this system we demonstrated one method of examining the effects of acetylcholine and nitroglycerin on coronary artery diameter in adult humans.

Acetylcholine↗
PubMed1973

Spontaneous quantal transmitter release: a statistical analysis and some implications.

1. Miniature end-plate potentials (m.e.p.p.s) were intra- and extracellularly recorded from neuromuscular junctions in rat phrenic nerve-diaphragm preparations in vitro.2. Statistical analysis of the intervals between m.e.p.p.s showed that when the mean number of events in time t was plotted as a function of the variance of the events in time t there was a significant deviation from the straight line relationship expected for a Poisson process. Computer simulation showed that this deviation is explicable if release was generated by the random phasing of the activity of a number of releasing sites.3. There was no indication that release of one quantum influences the probability of release of remaining quanta (drag, clustering). It is suggested that m.e.p.p.s whose amplitude is larger than the mode result from the release of the contents of vesicles whose volume is also supramodal.4. The effects of depolarization of nerve terminals upon the variance-mean curve suggest an increase in the activity of sites rather than an increase in their number.5. Statistical analysis indicated at least 200 +/- 100 (mean +/- 1 S.E.) releasing sites. This number is of the same order as the number of sites of vesicle aggregation and presynaptic membrane density seen in electron micrographs of nerve terminals of this preparation.

Animals↗
PubMed1993

Binding of cyanide, cyanate, and thiocyanate to human carbonic anhydrase II.

Computer simulation techniques are used to address the question of how cyanide and related ions interact with human carbonic anhydrase II (HCAII). Spectroscopic results have suggested that cyanide is coordinated with the zinc ion, while recent X-ray results suggest that the cyanide ion is noncovalently associated with the zinc-water or zinc-hydroxide form of the enzyme. We have carried out simulations on three models in an attempt to shed light on why the spectroscopic and X-ray results differ. The first model we studied (Model I) has cyanide directly coordinated to the zinc ion, the second has it noncovalently interacting with the zinc-hydroxide (high pH) form of the enzyme (Model II), and the third has cyanide noncovalently interacting with the zinc-water (low pH) form of the enzyme (Model III). None of these models is satisfactory in explaining the available structural data obtained from X-ray crystallography. This leads us to propose an alternative model, in which HCAII hydrates HCN to form an OH-/HCN complex coordinated to the Zn ion. Ab initio calculations are consistent with this model. Based on these results we are able to explain the observed crystallographic behavior of cyanate and, by inference, thiocyanate.

Bicarbonates↗
PubMed1994

A theoretical framework for quantal analysis and its application to long-term potentiation.

1. We present a new mathematical description of the complete distribution of electrical responses to stochastic synaptic activity (quantal analysis) that is intended as a model of experiments on central neuronal synapses. Unlike previous treatments, this distribution is calculated for each instant after the release of transmitter into the cleft. 2. We follow the traditional description of probabilistic presynaptic vesicle release. On the postsynaptic side, however, we assume that channel fluctuations are important and we take them into account. The probability of finding a given channel open after a certain amount of transmitter is released is calculated from detailed receptor/channel and neurotransmitter clearance kinetics. This approach allows us to naturally include the nonlinear dependence of open probability on the amount of transmitter released, with saturation for large transmitter doses. The distribution of open channels is calculated from this probability. 3. We also allow the possibility that multiple synaptic inputs to a target neuron may be active in a typical experiment. We have not treated cable effects. We explore the implications of multiple synapses for the nonlinearities of the system. The most important of these is that vesicles in different synapses have independent responses, and therefore their effects add linearly. 4. The resulting distributions depend heavily on what region of the nonlinear dose-response curve the synapses are in. Far from saturation, peaks in the distribution are due to vesicles, and close to saturation they are due to active synapses. Peak widths are due to channel fluctuations and instrumental noise, which we introduce to make closer contact with experiments.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1984

[Digital radiography using a computed tomography instrument in comparison with conventional film-screen images].

Parameters of image quality, comprising spatial resolution and contrast, have been determined in the form of a contrast/detail diagram for a digital system (Topogram) and a film-screen system. The digital system was particularly examined concerning its contrast sensitivity in relation to quantum noise. The clinical implications of the comparison of the systems, where evaluated on chest x-rays of 250 patients. Despite lower image sharpness, the digital method is already able to produce equivalent or better diagnostic results in certain circumstances. The advantages and disadvantages of both systems are discussed in detail.

Breast Neoplasms↗
PubMed1995

High-resolution structure of the phosphorylated form of the histidine-containing phosphocarrier protein HPr from Escherichia coli determined by restrained molecular dynamics from NMR-NOE data.

The solution structure of the phosphorylated form of the histidine-containing phosphocarrier protein, HPr, from Escherichia coli has been determined by NMR in combination with restrained molecular dynamics simulations. The structure of phospho-HPr (P-HPr) results from a molecular dynamics simulation in water, using time-dependent distance restraints to attain agreement with the measured NOEs. Experimental restraints were identified from both three-dimensional 1H-1H-15N HSQC-NOESY and two-dimensional 1H-1HNOESY spectra, and compared with those of the unphosphorylated form. Structural changes upon phosphorylation of HPr are limited to the active site, as evidenced by changes in chemical shifts, in 3JNHH alpha-coupling constants and NOE patterns. Chemical shift changes were obtained mainly for protons that were positioned close to the phosphoryl group attached to the His15 imidazole ring. Differences could be detected in the intensity of the NOEs involving the side-chain protons of His15 and Pro18, resulting from a change in the relative position of the two rings. In addition, a small change could be detected in the three-bond J-coupling between the amide proton and the H alpha proton of Thr16 and Arg17 upon phosphorylation, in agreement with the changes of the phi torsion angle of these two residues obtained from time-averaged restrained molecular dynamics simulations in water. The proposed role of the torsion-angle strain at residue 16 in the mechanism of Streptococcus faecalis HPr is not supported by these results. In contrast, phosphorylation seems to introduce torsion angle strain at residue His15. This strain could facilitate the transfer of the phosphoryl group to the A-domain at enzyme II. The phospho-histidine is not stabilised by hydrogen bonds to the side-chain group of Arg17; instead stable hydrogen bonds are formed between the phosphate group and the backbone amide protons of Thr16 and Arg17, which show the largest changes in chemical shift upon phosphorylation, and a hydrogen bond involving the side-chain O gamma proton of Thr16. HPr accepts the phosphoryl group from enzyme I and donates it subsequently to the A domain of various enzyme II species. The binding site for EI on HPr resembles that of the A domain of the mannitol-specific enzyme II, as can be concluded from the changes on the amide proton and nitrogen chemical shifts observed via heteromolecular single-quantum coherence spectroscopy.

Bacterial Proteins↗
PubMed1992

Superresolved tomography by convex projections and detector motion.

If the spatial resolution of an image-acquisition system is limited by the size of its component detector elements, then scanning may be required for the signal to be fully sampled. In such cases interpolation methods are normally applied to reproduce a uniformly sampled signal from the set of observations. Alternatively, however, this step can be treated as a restoration problem, in which case the extra measurements made accessible by detector motion may contain sufficient information to superresolve the signal, i.e., to recover information beyond the limit normally associated with finite detector size. We describe the application of this concept to the problem of constructing the projection matrix from a set of noise-corrupted tomographic measurements made by a moving detector array. In particular we focus on the case encountered in many tomographic applications in which the spatial response functions are approximately stationary with object depth. The method of projections onto convex sets is used in conjunction with an underrelaxation scheme to recover the projection matrix, from which the image is reconstructed by the standard filtered backprojection algorithm. Simulation results demonstrate that this approach applied to data acquired by a wobbling positron emission tomography system can substantially enhance the quality of the reconstructed image, even in the presence of high levels of quantum noise. The projection-matrix recovery step can be performed in a matter of seconds; thus the benefits of signal recovery are gained without a significant sacrifice in computation time.

Image Processing, Computer-Assisted↗
PubMed1978

Proem to a quantum leap in audiometric data collection and management.

A revolution began in 1961 when Weiss first mated a minicomputer to an audiometer. Today's technology offers a number of aids to the audiometrist in standardizing stimulus presentation patterns, objectifying and validating responses, computing HTL from a response pattern, computing significant threshold shifts from baseline audiograms, computing percentage binaural hearing impairment for a person, etc. Audiometers can be made which self-calibrate and are fail-safe. Furthermore, a revolution has occurred in replacing an audiogram written record, for example a card, with a system in which the audiometer transfers HTL data directly into computer storage without the possibility of transcription error. A group of turnkey and interlocking terminals allows the audiometric data of any individual serviced to be retrieved and/or updated from any terminal in the system. This paper lists commercial models simulating standard manual audiometry, models computerizing Bekesy audiometry, and some experimental models on yet other principles. Psychometric methods and methods for response validation suitable for audiometry are discussed, and out of many possible suggestions a few are offered for audiometric paradigms which may go beyond simulation of ASHA guidelines and ANSI specifications for manual threshold audiometry in order to take advantage of the power available from the computer as a tool in audiometry. For example, a computer can scan the responses of as many as 32 subjects simultaneously, offer each an adaptive program based on his response, and printout HTL's in conventional audiometric format.

Adolescent↗
PubMed1983

Computer methods for the assessment of toxicity.

The prediction of the biological activity of chemical compounds by means of mathematical models is discussed. Biological activity of chemicals, including their toxicity on man and other biological organisms and systems, involves too complex phenomena to presently be predictable by fundamental models such as ab initio quantum mechanical models or statistical mechanical models. Hence one takes recourse to semi-empirical and empirical models which relate the variation in chemical structure of chemical compounds to the variation in their measured biological activity, e.g. toxicity in one or several test systems. These models are "calibrated" on series of similar compounds with "known" toxicity, the training set. Thereafter the models can--in fortunate cases--be used to predict the toxicity of compounds which are structurally similar to the training set compounds. The formulation and applicability of semi-empirical and empirical models relating chemical structure to biological activity is discussed. Causes and remedies for commonly encountered fallacies are presented.

Animals↗
PubMed1995

Class IV charge models: a new semiempirical approach in quantum chemistry.

We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.

Alcohols↗
PubMed1991

Development of a conformational search strategy for flexible ligands: a study of the potent mu-selective opioid analgesic fentanyl.

An extensive conformational search of the potent opioid analgesic, fentanyl, was performed using the semiempirical quantum mechanical method AM1 and the CHARMm potential energy function. A combination of two procedures was used to search the conformational space for fentanyl, which included nested dihedral scans, geometry optimization and molecular dynamics simulation at different temperatures. In addition, the effect of a continuum solvent environment was taken into account by use of appropriate values for the dielectric constant in the CHARMm computations. The results of the conformational search allowed the determination of the probable conformation of fentanyl in polar and nonpolar solvents and of three candidate conformers for its bioactive form.

Fentanyl↗
PubMed1992

Theoretical framework for the interpretation of STM images of adsorbates.

A theoretical formalism for the interpretation of STM images of adsorbates is developed by approaching the calculation of the observed current as a transport problem in quantum statistical mechanics. The STM configuration is treated as a system of three groups of states--the substrate, the adsorbate and the tip--in contact with a thermal reservoir, with which it exchanges energy. A new definition of current is introduced, and shown to be related to that given in the traditional transfer Hamiltonian approach. The transport instrument used for the description is the stochastic Liouville equation, known to have the advantage of allowing the incorporation of thermal effects as well as arbitrary degree of coherence in the quantum transport. Some preliminary calculations of STM images of simple adsorbate models are presented.

Computer Simulation↗
PubMed1979

[Image properties of computer tomography. III. Measurements on homogenous materials. Relationship of attenuation and scatter to various parameters (author's transl)].

The present paper investigates the variations due to various parameters on the image of homogeneous materials as obtained with the Somatom CT scanner. Sugar solutions were used with concentrations equivalent to the absorption values of soft tissues. Because of quantum noise, attentuation at various points is not uniform, but is distributed in a Gaussian manner round a mean value. Using the Evaluskop it was possible to determine the degree of scatter. It was shown that, with increasing density of the material, the scatter increased and that this can be reduced by subjecting the tomogram to a smoothing process. It was further shown how the scatter depends on various parameters, such as thickness and dose. The amount of scatter in a tomogram is important in determining the density gradation which can be a achieved.

Absorptiometry, Photon↗
PubMed1982

Statistical contrast enhancement of subtraction images for radiographic caries diagnosis.

The effects of the nonlinear contrast-enhancement technique are examined in terms of diagnostic performance obtainable from subtracted dental radiographs for a variety of simulated exposures. Conventional bitewing radiographs of patients known to be free of caries were digitized by means of a computer interfaced with a conventional television camera. The resulting images were duplicated and stored in the computer. Radiolucencies similar in appearance to interproximal caries were simulated analytically in one set of the images. Reference images were superimposed spatially and subtracted from their counterparts containing the induced interproximal lesions after simulating the effects of quantum limited exposure on both sets. This was done for each separate image element independently by replacing original gray levels in each image with levels determined by a Poisson random deviate. The resulting difference images were contrast enhanced by a method which first smooths out local variations in gray level and then reassigns gray-level values in a way determined by the observed second-order spatial statistics. To aid in localization, these images were then again subtracted from the original noise-degraded pictures without lesions, rendering images similar to conventional radiographs but contrast enhanced. Observer performance by means of these enhanced images was compared with that produced from unenhanced-lesion-containing controls. The results suggest that enhancement increases the certainty with which diagnosis can be made and, further, that diagnostic accuracy can be improved in severely degraded images which simulate the effects of reduced levels of exposure.

Computers↗