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At least 217 records · Page 12Linked to original sources
PubMed1996

Glycine and GABA receptors: molecular mechanisms controlling chloride ion flux.

We have been able to show that the three clearly identified atoms common to the inhibitory neurotransmitters glycine and GABA, that we previously hypothesized to serve as attachment points at the glycinergic and gabanergic receptor, can indeed interact through both electrostatic and hydrogen bonding to several amino acids, which have been identified in molecular biological investigations as both present and critical in the physiological functioning of key polypeptides common to these inhibitory receptors. In addition, amino acids also involved in stabilizing the interaction between the antagonists strychnine and R5135 at the glycinergic and gabanergic receptors, respectively, have been shown to fit our complex model. We identify in detail molecular mechanisms to explain how glycine and GABA initiate chloride ion movement from extraneuronal fluid in the synaptic cleft to intraneuronal volume. In addition, we also identify the molecular mechanisms involved in the blocking of chloride ion movement by strychnine at the glycinergic receptor and by R5135 at the gabanergic receptor. We also present two computer-generated color prints, one for the glycine receptor and one for the GABA receptor, which show the quantum mechanically geometry optimized complex formed between receptor side chains, i.e., the part of the amino acids in the polypeptide that interacts with the zwitterionic inhibitory neurotransmitters. These computer-generated color figures also show a) the important electrostatic and hydrogen bonding in these interactions, b) a van der Waals model of this complex to illustrate that no steric repulsions exist, and c) the molecular electrostatic potential energy map showing the electrostatic potentials of neurotransmitter bound to the receptor model. Finally, we show with computer calculations that the pseudo-rings, formed between the positive quanidinium group in arginine and one of the oxygen atoms in the carboxyl group in both glycine or GABA, result in a positive planar region which appears to be involved in a charge-transfer complex with aromatic benzene groups in amino acids such as phenylalanine and tryosine.

Androstanes↗
PubMed1998

Steady-state and time-resolved fluorescence of Esperase: comparison with the X-ray structure in the region of the two tryptophans.

Fluorescence emission properties of the alkaline protease Esperase have been investigated using steady-state and time-resolved fluorescence spectroscopy. The local polarity and solvent accessibility of the tryptophyl chromophores is characterized. Quenching studies demonstrated that Trp 6 and Trp 113 are 'buried' to acrylamide, iodide ions and caesium ions. An abnormally low tryptophan quantum yield was calculated showing that the emission of the two indole rings is significantly quenched by nearby side chains or peptide bonds. The fluorescence decay of PMS-Esperase was well fitted by two exponentials with lifetimes of 2.7 and 0.35 ns. X-ray data for Esperase (S. Klupsch, Ph.D. Thesis, University of Hamburg, Hamburg, Germany) in the region of the two tryptophans were used to explain the observed emission properties. Gln 182 and Asn 204 as well as Asn 117 and Met 119 are the most likely quenchers, respectively, of the Trp 6 and Trp 113 fluorescence. The two tryptophans in Esperase are 'buried' in hydrophobic regions and are excellent intrinsic probes to study folding-unfolding reactions. Experiments in the presence and absence of added calcium ions demonstrated the stabilizing role of the Ca(2+)-binding sites.

Computer Graphics↗
PubMed1993

Reproduction of correct electrostatic field by charges and dipoles on a closed surface.

A general algorithm based on the Green function theorem has been developed to correctly reproduce electrostatic fields inside a closed space by point charges and point dipoles on the surface surrounding the space. For actual computations, limited numbers of point charges, including charge pairs replacing point dipoles, are enough to approximate the inner fields. As examples, reaction fields were reproduced by the current surface charges and dipoles for the dielectric models, where a monopole, dipole, or quadrupole was individually set at the center in a vacuum sphere surrounded by high dielectric continuum. The potentials due to those reaction fields agree well with the analytical ones. As an application of this method to the analysis of the electronic structure of the active site of a protein, a combination of the continuum dielectric model and ab initio molecular orbital calculation was carried out. Other applications to molecular dynamics and quantum mechanical calculations are also discussed.

Algorithms↗
PubMed1994

Integration of graph theory and quantum chemistry for structure-activity relationships.

The objective of this article is to outline both graph-theoretically based and quantum chemically based structural indices of potential use in quantitative structure activity correlations. We consider graph-theoretical indices such as the connectivity index, topological index, Wiener index and molecular ID indices. Several structural and geometry-dependent indices can be derived from semiempirical and ab initio quantum calculations based on the charge densities, overlap matrices, frontier orbitals, molecular hardness, free valence, density matrices, quantum spectral difference indices, quantum spectral indices and bond matrices. Finally, the use of electrostatic potentials and charge densities for the prediction of reactive sites will be discussed.

Butadienes↗
PubMed1998

X-ray quantum limited portal imaging using amorphous silicon flat-panel arrays.

We have measured the linearity, spatial resolution (MTF), noise (NPS), and signal-to-noise characteristics (DQE) of an electronic portal imaging device (EPID) based on an amorphous silicon flat-panel array. The array has a 128 x 128-pixel matrix and each pixel is 0.75 x 0.75 mm2 in dimension so the array covers an area of 96 x 96 mm2. The array acts like a large area light sensor and records the optical signals generated in a metal plate/phosphor screen x-ray detector when the detector is irradiated by a megavoltage x-ray beam. In addition, approximately 0.5% of the total signal is generated by nonoptical processes. The noise measurements show that the device is quantum noise limited with the noise power generated by the x-ray quanta being up to 100 times greater than the noise added by the external readout electronics and flat-panel light sensor itself. However, the flat-panel light sensor does reduce the spatial resolution (compared to a perfect optical sensor with infinitesimal pixel size) because of its moderate pixel size and because optical spread can occur in the transparent glues used to attach the phosphor screen to the flat-panel light sensor. The response of the sensor is very linear and does not suffer from the glare phenomenon associated with TV camera-based EPIDs--characteristics which suggest that the amorphous silicon EPID will be well suited to transit dosimetry. Nevertheless, some limitations need to be overcome before these devices can be used clinically. These include developing larger flat-panel light sensors, the elimination of "noisy" pixels with high dark signal, and improvements in the uniform sensitivity of the sensors. This last requirement is only needed for transit dosimetry applications where it would greatly simplify calibration of the device. In addition, an image acquisition scheme must be developed to eliminate artifacts created by the pulsed x-ray beam generated by linear accelerators. Despite these limitations, our studies suggest that the amorphous silicon EPIDs are very well suited to portal imaging.

Artifacts↗
PubMedDate not supplied

Fast Fourier digital quantum mottle analysis with application to rare earth intensifying screen systems.

The advent of fast Fourier techniques has greatly facilitated the digital analysis of noise power spectra (Wiener spectra) by circumventing the need for the autocorrelation function. We are now able to Fourier analyze film data at about the same rate the microdensitometer-computer system can collect it (1000 points/sec). The new technique has been applied to the analysis of the quantum mottle of several rare earth intensifying screen systems confirming earlier estimates from our pilot studies that such screens are capable of reducing exposure by a factor of about 2 with imaging parameters comparable to those of conventional calcium tungstate systems.

Calcium↗
PubMed1998

An ab initio approach to the understanding of cytochrome P450-ligand interactions.

1. We describe the application of novel ab initio quantum mechanical methods to the study of ligand interactions with cytochrome P450cam (CYP101). 2. We find that our techniques accurately describe the transition from a low-spin state to a high-spin state of the haem Fe3+ on binding of a substrate. Furthermore, our methods correctly predict that a large fraction of low-spin character is retained on binding of an inhibitor. 3. We demonstrate the use of 'computational experiments' to elucidate key features of the mechanism of interaction. This leads us to identify a new mechanism for the suppression of the low- to high-spin transition on binding of an inhibitor, namely the shortening of the bond between the Fe atom and the coordinated S atom of the cysteine axial ligand.

Camphor 5-Monooxygenase↗
PubMed1998

Adaptive streak artifact reduction in computed tomography resulting from excessive x-ray photon noise.

The quality of a computed tomography (CT) image is often degraded by streaking artifacts resulting from excessive x-ray quantum noise. Often, a patient has to be rescanned at a higher technique or at a larger slice thickness in order to obtain an acceptable image for diagnosis. This results in a higher dose to the patient, a degraded cross plane resolution, or a reduced patient throughput. In this paper, we propose an adaptive filtering approach in Radon space based on the local statistical properties of the CT projections. We first model the noise characteristics of a projection sample undergoing important preprocessing steps. A filter is then designed such that its parameters are dynamically adjusted to adapt to the local noise characteristics. Because of the adaptive nature of the filter, a proper balance between streak artifact suppression and spatial resolution preservation is achieved. Phantom and clinical studies have been conducted to evaluate the robustness of our approach. Results demonstrate that the adaptive filtering approach is effective in reducing or eliminating quantum noise induced artifacts in CT. At the same time, the impact on the spatial resolution is kept at a low level.

Artifacts↗
PubMed1993

Modeling the anticancer action of some retinoid compounds by making use of the OASIS method.

The powerful OASIS (optimized approach based on structural indices set) approach is applied to the anticancer activity of a series of vitamin A analogs. The best three- and four-variable models obtained via the OASIS technique have correlation coefficients of 0.973 vs. 0.990 and standard deviations s2 = 0.11 and 0.05, respectively. The models incorporate the hydrophobicity factor log P, two geometric parameters (topological indices and/or 3-D steric ones), and the molecular dipole moment. For a set of 15 compounds studied here, the activity measured by ED50 was well correlated by models with approximately equal contribution of the through cell membrane transport and the geometric drug-receptor correspondence while weak nonspecific electronic interaction was also found to play some role. Comparison to previous treatments of this data is given and extension to larger sets is discussed.

Antineoplastic Agents↗
PubMed1999

Stereoselective characterization of the 1,4-dihydropyridine binding site at L-type calcium channels in the resting state and the opened/inactivated state.

Via a 3D-QSAR pseudoreceptor modeling approach, atomistic binding site models for pharmacologically active 1,4-dihydropyridines (DHPs) were developed. Applying a training set of pure DHP enantiomers a pseudoreceptor model representing the resting state of voltage-gated calcium channels (VGCCs) was generated by correlating experimental versus predicted free energies of binding (DeltaG degrees). For validation further test set derivatives-not used for receptor generation-were predicted yielding root-mean-square (rms) deviation of 0.532 kcal/mol. Selectivity of the resting state model was checked by using the same DHP training set compounds but experimental data for the inactivated channel mode. Although there was found an almost perfect correlation for the training set, the following free relaxation of the corresponding test set applying a Monte Carlo protocol showed rms of 2.033 kcal/mol, clearly demonstrating the lack of any predicting character of the hybrid model. Taking into consideration 19 additional nifedipine analogues, a further verification of the model was performed. This yielded a good correlation for the 12 training set compounds and a satisfactory prediction for the test set molecules with rms of 0.409 kcal/mol. The generation of a pseudoreceptor model depicting the opened/inactivated state of VGCCs required one single additional residue to achieve a rms of 0.848 kcal/mol for the prediction of the test set derivatives. Since all pseudoreceptor models are composed of the same six amino acid residues-Thr, Phe, Gly, Met, Tyr, Tyr-transition from resting to open/inactivated state may be described by one additional hydrogen bond donor interaction (Thr) at the left-hand side of DHPs. Furthermore, a potential charge-transfer interaction for all electron-deficient 4-phenyl DHPs is postulated, because significant correlation between quantum chemically AM1 (R = 0.91) and RHF 6-31G (R = 0.84) computed LUMO energies and experimentally detected DeltaG degrees exp values was found.

Binding Sites↗
PubMed1997

Digital radiology using active matrix readout of amorphous selenium: theoretical analysis of detective quantum efficiency.

A flat-panel x-ray imaging detector using a layer of amorphous selenium (a-Se) for direct conversion of x rays (to charge) and an active matrix for self-scanned readout is being investigated for digital radiology. A theoretical analysis of the spatial frequency dependent detective quantum efficiency (DQE(f)) of the self-scanned a-Se detector is performed based on a model of signal and noise propagation in a cascaded imaging system. Because of the high intrinsic resolution of a-Se and the pixelated active matrix readout method, such detectors are inherently undersampled and aliasing is present. The presampling modulation transfer function (MTF) and aliased noise power spectrum (NPS) of the detector were used in the analysis of DQE(f). It is proven that the aliased NPS for the self-scanned a-Se detectors is white. Since the shape of DQE(f) is determined by the ratio of MTF squared and the NPS, the shape of DQE(f) follows the square of the presampling MTF of the detector as a result of the white NPS. The analysis also shows that DQE(0) is proportional to the pixel fill factor, i.e., the fraction of each pixel area used for image charge collection. The DQE analysis is applied to detector parameters for three x-ray imaging applications: mammography, chest radiography, and fluoroscopy. The effects of pixel fill factor, imaging geometry (i.e., incident angle of x rays), and various sources of electronic noise on the detector DQE(f) are discussed. Strategies for maximizing detector DQE for each x-ray imaging application are proposed.

Models, Theoretical↗
PubMed1997

Computational enzymology.

Numerical simulations of enzyme reaction mechanisms are beginning to provide quantitative as well as qualitative insights. Methods based on hybrid quantum mechanical/molecular mechanical technique permit the natural inclusion of protein solvation effects. Coupled with modern experimental techniques, the numerical simulations are providing details at the atomic level about how enzyme structure influences its function.

Computer Simulation↗
PubMed1986

Hydrophobic and ionic hydration phenomena.

Computer simulation offers an increasing opportunity to examine the details of solvation structure for well-defined solution models. One can characterize idealized models that exemplify specific aspects of solution behavior or those that realistically model systems experimentally difficult to access. As an example from the first category, results are presented for the aqueous solvation structure and solvent hydrogen bonding in the presence of a small apolar solute, and these are contrasted with the quite different behavior observed for a large apolar surface. As an example from the second category, structural results are presented for hydration of an excess electron in bulk water. These latter results, obtained via recent path integral simulation methods, manifest significant solvent structural disruption compared to the case of a simple ion, due to the irregular and fluctuating shape of the quantum solute.

Chemical Phenomena↗
PubMed1980

[Determination of effective atomic number and electronic density by computed tomography with dual energies. Application to the thalamus (author's transl)].

The authors have studied seven thalamic hyperdense lesions of five patients in managing, at the same level, successively two scans with a computer tomograph at two different energies. After they recall their methodology of testing their C.T. and computations, they have found the effective atomic number and the electron density of these lesions. All (one Fahr disease and six old hemorrhages) have both high effective atomic number and electron density. They discuss the limits of this technic but they emphasize the great interest to see the chemical aspects of the structures observed in C.T.

Brain Diseases↗