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At least 1,099 records · Page 61Linked to original sources

PubMed1988

The three-dimensional structure of P2 myelin protein.

The three-dimensional structure of P2 protein from peripheral nervous system myelin has been determined at 2.7 A resolution by X-ray crystallography. The single isomorphous replacement/anomalous map was interpreted using skeletonized electron density on a computer graphics system. An atomic model was built using fragment fitting. The structure forms a compact 10-stranded up-and-down beta-barrel which encapsulates residual electron density that we interpret as a fatty acid molecule. This beta-barrel shows some similarity to, but is different from, the retinol binding protein family of structures. The relationship of the P2 structure to a family of cytoplasmic, lipid binding proteins is described.

Amino Acid Sequence↗

PubMed1989

Molecular modeling in the design of phospholipase A2 inhibitors.

The X-ray structures of pancreatic bovine and porcine phospholipases A2 have been used along with interactive computer graphics to design conformationally rigid, novel compounds (1-meta-hydroxybenzyl-2-substituted acenaphthenes) directed at the active sites of these enzymes. In vitro testing confirmed that the designed compounds are potent inhibitors of the porcine pancreatic phospholipase A2 and exhibit both stereoselectivity and structure-activity relationships that are consistent with the proposed mode of binding. These compounds take advantage of a hydrophobic "slot" positioned between residues Leu-2 and Tyr-69 while positioning hydrogen-bonding functionality directed at the nd1-N of His-48. Experimental evidence shows a regioselective preference for this H-bond acceptor. A second part of the strategy used a tethered amine to displace the essential calcium providing a bisubstrate analog.

Acenaphthenes↗

PubMed2001

Visualization of flow patterns distal to aortic valve prostheses in humans using a fast approach for cine 3D velocity mapping.

The fluid dynamic performance of mechanical heart valves differs from normal valves and thus is considered related to late clinical complications in patients. Since flow patterns evolving around heart valves are complex in space and time, flow visualization based on time-resolved 3D velocity data might add important information regarding the performance of specific valve designs in vivo. However, previous cine 3D techniques for three-directional phase-contrast velocity mapping suffer from long scan duration and therefore might hamper assessment in patients. A hybrid 3D phase-contrast sequence combining segmented k-space acquisition with short EPI readout trains is presented with its validation in vitro. The technique was applied to study flow patterns downstream from a bileaflet aortic prosthesis in six patients. Navigator echoes were incorporated for respiratory motion compensation. Before flow visualization, spurious phase errors due to concomitant gradient fields and eddy currents were corrected. Flow visualization was based on particle paths and animated velocity vector plots. Dedicated algorithms for particle path integration were implemented to account for the considerable motion of the ascending aorta during the cardiac cycle. A distinct flow pattern reflecting the valve design was observed closest to the valve during early flow acceleration. Reverse flow occurred adjacent to high velocity jets and above the hinge housings. Later in systole, flow became confined to the central vessel area and reverse flow along the inner aortic curvature developed. Further downstream from the valve, flow patterns varied considerably among patients, indicating the impact of varying aortic anatomy in vivo. It is concluded that MR velocity mapping is a potential tool for studying 3D flow patterns evolving around heart valve prostheses in humans. J. Magn. Reson. Imaging 2001;13:690-698.

Aged↗

PubMed2001

Combined MR imaging and CFD simulation of flow in the human descending aorta.

A combined MR and computational fluid dynamics (CFD) study is made of flow in the upper descending thoracic aorta. The aim was to investigate further the potential of CFD simulations linked to in vivo MRI scans. The three-dimensional (3D) geometrical images of the aorta and the 3D time-resolved velocity images at the entry to the domain studied were used as boundary conditions for the CFD simulations of the flow. Despite some measurement uncertainties, comparisons between simulated and measured flow structures at the exit from the domain demonstrated encouraging levels of agreement. Moreover, the CFD simulation allowed the flow structure throughout the domain to be examined in more detail, in particular the flow separation region in the distal aortic arch and its influence on the downstream flow during late systole. Additional information such as relative pressure and wall shear stress, which could not be measured via MRI, were also extracted from the simulation. The results have encouraged further applications of the methods described. J. Magn. Reson. Imaging 2001;13:699-713.

Adult↗

PubMedDate not supplied

Quantification of in-plane motion of the coronary arteries during the cardiac cycle: implications for acquisition window duration for MR flow quantification.

Motion of the coronary arteries during the heart cycle can result in image blurring and inaccurate flow quantification by MR. This condition applies particularly for longer acquisition windows that are typical of breath-hold coronary flow measurements. To determine the sensitivity of the technique to in-plane motion of different coronary arteries, the temporal variation in coronary position was measured in a plane perpendicular to the proximal portion of the vessel. The results indicated the presence of substantial displacement of the coronary arteries within the cardiac cycle, with a magnitude of motion approximately twice as large for the right as for the left coronary arteries. An estimation of the resulting vessel blurring was calculated, showing that the duration of the acquisition window for high spatial resolution coronary flow acquisitions should be less than 25 to 120 msec, depending on the specific coronary artery studied. In addition, these data specify optimal acquisition window placement for high resolution coronary angiography.

Adult↗

PubMedDate not supplied

Quantification of mitral regurgitation with MR phase-velocity mapping using a control volume method.

Reliable diagnosis and quantification of mitral regurgitation are important for patient management and for optimizing the time for surgery. Previous methods have often provided suboptimal results. The aim of this in vitro study was to evaluate MR phase-velocity mapping in quantifying the mitral regurgitant volume (MRV) using a control volume (CV) method. A number of contiguous slices were acquired with all three velocity components measured. A CV was then selected, encompassing the regurgitant orifice. Mass conservation dictates that the net inflow into the CV should be equal to the regurgitant flow. Results showed that a CV, the boundary voxels of which excluded the region of flow acceleration and aliasing at the orifice, provided accurate measurements of the regurgitant flow. A smaller CV provided erroneous results because of flow acceleration and velocity aliasing close to the orifice. A large CV generally provided inaccurate results because of reduced velocity sensitivity far from the orifice. Aortic outflow, orifice shape, and valve geometry did not affect the accuracy of the CV measurements. The CV method is a promising approach to the problem of quantification of the MRV.

Blood Flow Velocity↗

PubMedDate not supplied

Slice-selective fat saturation in MR angiography using spatial-spectral selective prepulses.

Presaturation of fat signals by frequency-selective radiofrequency (RF) pulses is often applied in MR angiography to improve the visualization of the blood vessels. Unfortunately, standard fat saturation methods might cause a considerable reduction of the blood signal in the measured slices. This effect is caused by an attenuation of blood magnetization in remote tissue regions with water protons showing a similar Larmor frequency as the fat protons in the recorded slice. The affected blood water protons subsequently flow into the recorded slice and provide low signal intensity. Suitable spatial-spectral selective methods for slice-selective fat saturation were developed to avoid this unwanted effect. A spatial-spectral fat saturation technique was compared with a corresponding only spectrally selective approach. Both saturation techniques were included in a standard two-dimensional (2D) cine sequence and applied in angiographic examinations of the thighs. The results indicate that spatial-spectral saturation (acting slice selectively) leads to a clearly higher blood signal intensity in fat-suppressed MR angiography compared with standard techniques, especially in measurements performed during the systolic phase of the cardiac cycle.

Adipose Tissue↗

PubMed1987

Evidence for solid- and liquid-state interactions in a furosemide-polyvinylpyrrolidone solid dispersion.

The solid-state interactions between furosemide (FUR) and polyvinylpyrrolidone (PVP) in a solid dispersion system have been investigated by dispersive and Fourier Transform IR. Using spectral subtraction procedures, shifts to lower frequencies are seen in FUR-NH stretching vibrations in amorphous FUR-PVP systems in comparison with the crystalline FUR spectrum. The magnitude of shifts are similar to those seen when FUR is dissolved in the hydrogen-bonding solvent 1,4 dioxan (0.015-0.155 M, 20 degrees C). Spectral assignment indicates the FUR sulfonamide group binds to PVP in preference to the FUR secondary amine which is shown to possess an intramolecular hydrogen bond by analysis of published X-ray crystal data. With a molecular graphics computer program, the FUR crystal unit cell was compiled, and analyses of nonbonded intermolecular distances are useful in interpreting IR shift data in amorphous solid dispersions. A study of FUR-PVP interactions in solution, examined by proton NMR, reveals a downfield shift of the FUR sulfonamide proton resonance. This shift exhibits dilution and temperature (298-338 K) dependence consistent with an intermolecular hydrogen bond. The secondary amine proton resonance exhibits temperature but not dilution or solvent bonding potential dependence, characteristics of an intramolecular hydrogen bond. The proposed hydrogen bond FUR-PVP interaction may account for the formation and stabilization of the amorphous solid dispersion.

Furosemide↗

PubMed1995

1H-NMR microscopy of tablets.

A 1H-nuclear magnetic resonance (NMR) microscopy method was utilized for the first time to determine the porosity distribution of physically intact tablets. The main advantage of this newly developed method was that porosity cross sections through whole tablets or specific locations could be obtained without mechanically destroying the tested tablet. This was achieved by filling tablet cavities with silicone oil under vacuum. The amount of silicone oil locally within the tablet was then determined by 1H-NMR microscopy, revealing the inverse inner structure. To reduce the measuring time, a paramagnetic gadolinium complex was added to the silicone oil. The cross sectional signals produced by 1H-NMR microscopy through the tablet were transformed into a color image by a specially designed computer graphic program. To improve the signal-noise ratio an algorithm of 3D-filtering was introduced. The maximal spatial resolution achieved with this method was about 95 microns for a cube's edge length corresponding to some 380,000 positions in a 9-mm-diameter compression-coated tablet. Uneven porosity distributions within tablets, cracks, or cavities could be visualized with this newly developed method. Different compaction mechanisms were observed with plastic- or brittle-type tablets. The different states of densification during compaction of powders could be detected. The integrity of compression coatings was determined to be dependent on the pressure load and the location of the core within the coat.

Magnetic Resonance Imaging↗

PubMed2005

Application of partial differential equation-based inpainting on sensitivity maps.

Inpainting is an image interpolation method. Partial differential equation (PDE)-based digital inpainting techniques are finding broad applications. In this paper, PDE-based inpainting techniques are applied to the field of MR parallel imaging. A novel model and its corresponding numerical method are introduced. This model is then applied to sensitivity maps. Coil sensitivity maps are important for parallel imaging, and they often require extrapolation and hole filling (holes being dark regions of low signal in MR images). These problems can be solved simultaneously by the application of inpainting techniques. Experiments for determining coil sensitivity maps for phantoms and cardiac MR images demonstrate the accuracy of the proposed model. Images generated using sensitivity encoding (SENSE) that utilizes inpainted sensitivity maps, thin-plate spline (TPS) estimated sensitivity maps, and Gaussian kernel smoothed (GKS) sensitivity maps are compared. From the experimental results, it can be seen that inpainted sensitivity maps produce better results than GKS sensitivity maps. The TPS method generates results similar to those of the inpainting technique but is much more time-consuming.

Algorithms↗

PubMed2004

New fetal cardiac imaging techniques.

Rapid advances in graphics computing and micro-engineering have offered new techniques for prenatal cardiac imaging. Some of them can be non-invasively applied to both clinical and laboratory settings, including dynamic three-dimensional echocardiography, myocardial Doppler imaging, harmonic ultrasound imaging, and B-flow sonography. With clinical constraints, a few others have been mainly used in laboratories, such as endoscopic ultrasound, magnetic resonance imaging and biomicroscopy. Appropriate use and co-use of these new tools will not only provide unique information for better clinical assessment of fetal cardiac disease but also offer new ways to improved understanding of cardiovascular development and pathogenesis.

Echocardiography↗

PubMed1988

Computer-assisted analysis of fetal behavioural states.

A computerized system which simultaneously acquires and quantifies several ultrasonically detected fetal activities, including gross body movements, breathing movements, and eye movements, was developed in order to obtain additional quantitative data on fetal behaviour. Movements were automatically related to fetal heart rate allowing computation of their mean incidence, duration, lag time and percentage time spent moving during different heart rate patterns. The incidence of various behavioural states was also calculated. The study of 15 healthy fetuses near term revealed the existence of statistically significant differences in these parameters between low and high variability patterns of fetal heart rate suggesting a quantitative modulation of fetal movements by behavioural states.

Computer Graphics↗

PubMed1992

Internal water molecules and H-bonding in biological macromolecules: a review of structural features with functional implications.

Conserved structural patterns of internal water molecules and/or H-bond chains were observed and are here correlated in this review, which then describes two functional properties: equilibration of hydrostatic pressure and proton transport. Available evidence in support of these hypotheses is presented, together with suggested experiments to test them. High-resolution crystal structures of a variety of proteins were studied with interactive computer graphics. Conserved H-bonding linkages may be used as a paradigm for a rationalization of proton transport in membranes. The concept of the "proton wire," which links buried active-site amino acids with the surface of the protein raises the more general question of the functional role of the various molecular components.

Amino Acid Sequence↗

PubMed1995

Monte Carlo docking with ubiquitin.

The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple-start Monte Carlo docking method, we have reconstructed the known structure of diubiquitin from its two halves as well as from two copies of the uncomplexed monomer. For both of these cases, our relatively simple potential function ranked the correct solution among the lowest energy configurations. In the experiments involving the ubiquitin monomer, various structural modifications were made to compensate for the lack of flexibility and for the lack of a covalent bond in the modeled interaction. Potentially flexible regions could be identified using available biochemical and structural information. A systematic conformational search ruled out the possibility that the required covalent bond could be formed in one family of low-energy configurations, which was distant from the observed dimer configuration. A variety of analyses was performed on the low-energy dockings obtained in the experiment involving structurally modified ubiquitin. Characterization of the size and chemical nature of the interface surfaces was a powerful adjunct to our potential function, enabling us to distinguish more accurately between correct and incorrect dockings. Calculations with the structure of tetraubiquitin indicated that the dimer configuration in this molecule is much less favorable than that observed in the diubiquitin structure, for a simple monomer-monomer pair. Based on the analysis of our results, we draw conclusions regarding some of the approximations involved in our simulations, the use of diverse chemical and biochemical information in experimental design and the analysis of docking results, as well as possible modifications to our docking protocol.

Algorithms↗

PubMed1996

Simulated annealing with restrained molecular dynamics using CONGEN: energy refinement of the NMR solution structures of epidermal and type-alpha transforming growth factors.

The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF and 424 NMR-derived constraints for hTGF alpha were used in these energy-refinement calculations. Different weighting schemes and starting conformations were studied to check and/or improve the sampling of the low-energy conformational space that is consistent with all constraints. The results demonstrate that loosened (i.e., "relaxed") sets of the EGF and hTGF alpha internuclear distance constraints allow molecules to overcome local minima in the search for a global minimum with respect to both distance restraints and conformational energy. The resulting energy-refined structures of mEGF and hTGF alpha are compared with structures determined previously and with structures of homologous proteins determined by NMR and X-ray crystallography.

Animals↗

PubMed2006

The role of backbone stability near Ala44 in the high reduction potential class of rubredoxins.

Rubredoxins may be separated into high and low reduction potential classes, with reduction potentials differing by approximately 50 mV. Our previous work showed that a local shift in the polar backbone due to an A(44) versus V(44) side-chain size causes this reduction potential difference. However, this work also indicated that in the low potential Clostridium pasteurianum (Cp) rubredoxin, a V(44) --> A(44) mutation causes larger local backbone flexibility, because the V(44) side-chain present in the wild-type (wt) is no longer present to interlock with neighboring residues to stabilize the subsequent G(45). Since Pyrococcus furiosus (Pf) and other high potential rubredoxins generally have a P(45), it was presumed that a G(45) --> P(45) mutation might stabilize a V(44) --> A(44) mutation in Cp rubredoxin. Here crystal structure analysis, energy minimization, and molecular dynamics (MD) were performed for wt V(44)G(45), single mutant A(44)G(45) and double mutant A(44)P(45) Cp, and for wt A(44)P(45) Pf rubredoxins. The local structural, dynamical, and electrostatic properties of Cp gradually approach wt Pf in the order wt Cp to single to double mutant because of greater sequence similarity, as expected. The double mutant A(44)P(45) Cp exhibits increased backbone stability near residue 44 and thus enhances the probability that the backbone dipoles point toward the redox site, which favors an increase in the electrostatic contribution to the reduction potential. It appears that the electrostatic potential of residue 44 and the solvent accessibility to the redox are both determinants for the reduction potentials of homologous rubredoxins. Overall, these results indicate that an A(44) in a rubredoxin may require a P(45) for backbone stability whereas a V(44) can accommodate a G(45), since the valine side-chain can interlock with its neighbors.

Alanine↗

PubMed1987

Modeling the biochemical differences between rabbit muscle and human liver phosphorylase.

Glycogen phosphorylases catalyze the regulated breakdown of glycogen to glucose-1-phosphate. In mammals, glycogen phosphorylase occurs in three different isozymes called liver, muscle, and brain after the tissues in which they are preferentially expressed. The muscle isozyme binds and is activated cooperatively by AMP. In contrast, the liver enzyme binds AMP noncooperatively and is poorly activated. The amino acid sequence of human liver phosphorylase is 80% identical with rabbit muscle phosphorylase, and those residues which contact AMP are conserved. Using computer graphics software, we replaced side chains of the known rabbit muscle structure with those of human liver phosphorylase and interpreted the effects of these changes in order to account for the biochemical differences between them. We have identified two substitutions in liver phosphorylase potentially important in altering the cooperative binding and activation of this isozyme by AMP.

Adenosine Monophosphate↗

PubMed1990

Design of biologically active, conformationally constrained GnRH antagonists.

The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[delta 3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-bet a Ala] led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: Ac-delta 3,4Pro-D4FPhe-DTrp-Dap-Tyr-DTrp-Leu-Arg-Asp-Gly- NH2 and Ac-delta 3,4Pro-D4FPhe-DTrp-Dap-Tyr-D2Nal-Leu-Arg-Pro-Asp -NH2. These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.

Amino Acid Sequence↗