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At least 253 records · Page 14Linked to original sources
PubMed1997

Regiospecificity of peroxyl radical addition to (E)-retinoic acid.

The regiochemistry of peroxyl radical addition to (E)-retinoic acid (RA) was investigated. Peroxyl radicals, generated by reaction of 13-hydroperoxy-(9Z,11E)-octadecadienoic acid with hydroxo(porphyrinato)iron(III) in Tween 20 micelles, were reacted with RA. The major, and virtually exclusive, RA oxidation product was 5,6-epoxy-RA which was identified on the basis of cochromatography with the synthetic synthetic oxirane (in a reverse phase HPLC system), electronic absorption spectroscopy, high-field 1H-NMR, and EI mass spectrometry. These results suggest that peroxyl radicals react with RA by regioselective addition to either C5 or C6 yielding an endocyclic tertiary allylic or tertiary carbon-centered radical adduct, respectively. Subsequent beta-elimination of an alkoxyl radical yields the oxirane. Computational studies were carried out in order to gain mechanistic insights into the observed regiospecificity of the peroxyl radical-dependent epoxidation reaction; molecular mechanics and semiempirical quantum mechanical calculations were carried out using Tripos force field parameters and AM1, respectively. The results suggest that the regiospecific epoxidation may be influenced by the 5,6-olefinic function behaving as a partially-isolated double bond as well as inherent allylic A1,2 strain in the substituted cyclohexene ring as a consequence of substitutions at C1 and C6. In addition, calculated heats of formation indicated preferential peroxyl radical addition to C5 versus C6; this may reflect differences in the geometries of sp2-orbitals containing the radical densities rather than resonance contributions by the highly conjugated polyene system.

Chromatography, High Pressure Liquid↗
PubMed1984

[Observation of magnetic fields from three directions, and the moving image of the heart in a normal subject].

Three components of the magnetic field generated by the heart over the anterior aspect of the chest in a normal subject were detected using a Superconducting Quantum Interference Device (SQUID) magnetometer with a single detecting coil in a magnetically shielded room. Contour maps and color density maps of the field were prepared by computer. Movies of sequential magnetic fields of the vertical component on the anterior aspect of the chest were made from these maps. In the movies, the maximum moved from the upper central portion to right lower portion in the early stage of ventricular excitation. It moved to the central portion in the middle stage, then returned to the upper central portion in the late stage. Three-dimensional maps of instantaneous magnetic fields over the anterior portion of the chest were derived from maps of three components of the field, and from presumed heart vectors and were drawn as arrows, based on the Viot-Savart theorem. Heart vectors from these field maps corresponded well with septal forces in the early stage, left ventricular free wall force in the middle stage and the basal force in the late stage, respectively. However, large circulating vectors in the form of clockwise rotation in the central portion were also presumed. These circulating heart vectors did not correspond with the sequence of cardiac excitation as reported by Durrer et al. This discrepancy may have been caused by the fact that the vertical electric current could not be expressed from our display for presuming an electric force. Therefore, new displays and interpretations may be required for the expression of heart vectors.

Heart↗
PubMed1990

Solution structure studies of d(AC)4.d(GT)4 via restrained molecular dynamics simulations with NMR constraints derived from two-dimensional NOE and double-quantum-filtered COSY experiments.

The structure of d(AC)4.d(GT)4 is investigated by constrained molecular dynamics simulations. The constraints include proton pair distances derived from 2D NOE intensities by using the iterative relaxation matrix analysis algorithm MARDIGRAS and sugar pucker phases and amplitudes derived from double-quantum-filtered COSY spectra. Molecular dynamics runs on simulated intensity and distance sets as well as the experimental data were carried out to determine the effects of starting structure, distance constraint derivation, energy functions, and experimental errors on the end result. It was found that structural details could not be elucidated within about 1.5-A overall atomic deviation. This limitation is due in part to the accuracy of the experimental data but, more importantly, is attributable to the quantity of experimental constraints available and to imperfections in the force field utilized in the molecular dynamics calculations. Within the limits of the method, some structural characteristics of d(AC)4.d(GT)4 could be elucidated.

Computer Simulation↗
PubMed1982

Cooperative effects in water-biomolecule crystal systems.

Monte Carlo computer simulation techniques have been used to model non-pair-additive (cooperative) effects in the water organization around several biomolecules. Although most models for water assume pair-additive potentials, both quantum mechanical calculations and experimental data indicate that cooperative effects are not negligible in hydrogen-bounded systems such as water. The many-body polarizable electropole (PE) model for water is used to examine the extent and the consequences of this cooperative behavior in several biomolecule hydrate crystals. Increases in the dipole moments of water molecules are predicted in all systems studied so far and can be as much as 50% more than the monomer value of 1.855 debyes. The average value of the individual dipole moments for any one system differs from that of another system and, therefore, should be considered a property of the system and not of the water molecule itself. When this previously calculated average value of the dipole moment for water molecules in a given system is used as a fixed parameter in the simulation, we find differences between this fixed calculation and the original unfixed simulation. An alternative procedure, which allows for a spread in dipole moments and is not dependent on a predetermined average value, has been developed to make simulations of large water-protein systems, including cooperative effects, computationally feasible.

Arginine↗
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↗
PubMed1995

Predicting tropospheric degradation of chemicals: from estimation to computation.

For the majority of commercial chemicals present in the troposphere, the reaction with OH radicals during the day and with NO3 radicals at night are the most important abiotic pathways for their degradation and removal from the troposphere. Today, there are only a couple of methods available for estimating the reactivity of commercial chemicals with tropospheric radicals, which are not class specific, he Atkinson fragment contribution method and QSAR models, based on a linear correlation of OH (NO3) radical reactivity with the corresponding ionization energies, allow a rapid estimation of the rate constants of OH or NO3 radicals for various classes of organic compounds. Both methods are described and their limitations are discussed. A lot of work has been done to develop QSAR models for tropospheric degradation of commercial chemicals that will be based on calculated quantum chemical descriptors. This fast expanding area of QSAR research is presented and evaluated. Particular emphasis is given to the precision of various methods as well as to the latest results from our laboratory. The recent dramatic development in computing technology enables to precisely calculate energy profiles of tropospheric reactions with OH radicals. The semiempirical and ab initio molecular orbital calculations have been performed for hydrogen abstraction reactions for several classes of tropospheric pollutants. The best results of the high-level ab initio molecular orbital calculations are presented and discussed.

Atmosphere↗
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↗
PubMed1993

Two-dimensional 1H-NMR study of the spatial structure of neurotoxin II from Naja naja oxiana.

The spatial structure of neurotoxin II from the venom of the central Asian cobra Naja naja oxiana was determined by two-dimensional 1H-NMR techniques and computational analysis. Nearly complete proton resonance assignments for 61 amino acid residues have been made using two-dimensional (2D) homonuclear total correlated spectroscopy, 2D homonuclear double-quantum-filtered correlated spectroscopy and 2D homonuclear NOE spectroscopy (NOESY) experiments. The cross-peak volumes in NOESY spectra spin-spin coupling constants of vicinal protons NH-C alpha H and C alpha H-C beta H and the observation of slow deuterium exchange of amide protons were used to define local structure and a set of constraints for distance geometry program DIANA. The average root-mean-square deviations are 53 pm for backbone heavy atoms and 118 pm for all heavy atoms of 19 final neurotoxin II conformations. The spatial structure is characterized by a short double-stranded (residues 1-5 and 13-17) and a triple-stranded (residues 22-30, 33-41 and 50-54) antiparallel beta-sheets.

Amino Acid Sequence↗
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↗
PubMed1996

Long-time quantum simulation of the primary charge separation in bacterial photosynthesis.

Accurate quantum mechanical simulations of the primary charge transfer in photosynthetic reaction centers are reported. The process is modeled by three coupled electronic states corresponding to the photoexcited chlorophyll special pair (donor), the reduced bacteriopheophytin (acceptor), and the reduced accessory chlorophyll (bridge) that interact with a dissipative medium of protein and solvent degrees of freedom. The time evolution of the excited special pair is followed over 17 ps by using a fully quantum mechanical path integral scheme. We find that a free energy of the reduced accessory chlorophyll state approximately equal to 400 cm(-1) lower than that of the excited special pair state yields state populations in agreement with experimental results on wild-type and modified reaction centers. For this energetic configuration electron transfer is a two-step process.

Bacteriochlorophylls↗
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↗