Gene/Protein Disease Symptom Drug Enzyme Compound
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 11,252 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server "netserv@embl-heidelberg.de." The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three-dimensional protein structures.
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PMID:Selection of representative protein data sets. 130 48

The electromagnet provides a favorable environment for certain applications of NMR microscopy. These include plant imaging experiments and measurements of slow molecular diffusion, where high magnetic field gradients for the pulsed gradient spin echo (PGSE) technique are required. In this paper, two probes designed specifically for these two applications are described. In the first case, the open space within the probe has been maximized in order to incorporate environmental support systems for the plant, while in the second the smallest possible PGSE gradient coil former has been used to maximize the gradient strength. Examples are given of Dynamic NMR Microscopy experiments on a castor bean stem and on poly(ethylene oxide)/water solutions under shear thinning conditions.
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PMID:Purpose-designed probes and their applications for dynamic NMR microscopy in an electromagnet. 140 91

Cardiac depression in the isolated rat heart perfused with 4% ethanol was correlated with intracellular phosphate energetics and tissue water distributions. Energy metabolites were assessed using 31P magnetic resonance spectroscopy (MRS) and correlated to the mitochondrial redox state using epicardial surface fluorometry. Changes in myocardial water compartmentation were measured by using 1H NMR spectroscopy with an extracellular chemical-shift reagent (DyTTHA) and correlated to results of 2D echocardiography (2DE). During alcohol perfusion there was a significant decrease in developed pressure and in coronary flow. No change was seen in ATP, PCr, pHi, Pi, or NADH. After withdrawal of alcohol from the perfusate cardiac function reverted to control values without a depletion of energy levels. During alcohol perfusion 1H MRS showed a marked redistribution of water from the intra- to the extracellular space, corresponding to a 35% left ventricular wall thinning confirmed by 2DE. The results indicate that acute alcohol cardiac depression is related to a dehydration of myocardial cells, but is not associated with intracellular acidosis or energy depletion.
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PMID:31P and 1H magnetic resonance spectroscopy of acute alcohol cardiac depression in rats. 317 69

Proton NMR imaging of myocardial ischemia without infarction requires the use of paramagnetic contrast agents. Even during the first few hours of infarction, imaging without contrast enhancement reveals only slight natural image contrast. Myocardial infarction, however, is much more readily detected during the first few days and weeks post coronary occlusion; this is due to a marked elevation in T2 during this time period. Chronic infarction, several months after the acute event, does not demonstrate altered signal intensity, but can be detected by visualizing myocardial wall thinning and aneurysm formation. Information regarding high energy phosphate metabolism can be acquired in vivo in ischemic animal preparations; preliminary data has demonstrated that it is possible to acquire similar information noninvasively in man. Development of this technique will eventually permit the study of pharmacological and mechanical interventions aimed at preserving myocardium in the ischemic heart. Exogenous labelling of myocardial tissue with carbon-13 permits the study of the effects of substrates on cellular metabolism. Ultimately, the technique of chemical shift imaging will provide a method of spatially resolving valuable metabolic information in the form of an NMR image. Eventually, with the gradual development of NMR technology, imaging and spectroscopy will become truly important clinical tools in the investigation of ischemic heart disease in man.
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PMID:Evaluation of myocardial ischemia and infarction by nuclear magnetic resonance techniques. 328 14

We have developed an ECG-gated NMR-CT, and used it with 16 patients. The saturation recovery images are not able to separate heart muscle from the blood pool, but in inversion recovery images, heart muscle can be differentiated from the ventricles. The region of myocardial infarction is revealed as wall thinning and/or wall motion abnormality. From the two-gated inversion recovery images (the end-diastole and end-systole images) we obtained, we evaluated a wall motion abnormality in the left ventricle, and calculated the ejection fraction of the left ventricle. This information was then compared with the findings of a nuclear medicine study carried out one week interval and which included 10 of the 16 patients tested with the ECG-gated NMR-CT. The wall motions in both methods are well correlated, with the exception of the inferior wall. The values of the ejection fraction in the NMR image were moderately low, but two modalities showed a satisfactory correlation (r = 0.85).
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PMID:ECG-gated NMR-CT for cardiovascular disease. 668 Feb 4

Polypeptides have been prepared by solid-phase peptide synthesis and labelled with 15N at single sites to be used for static or magic angle spinning solid-state NMR spectroscopy. After reconstitution into oriented membranes, the alignment of polypeptide alpha-helices with respect to the bilayer surface is accessible by proton-decoupled 15N solid-state NMR spectroscopy. In addition, limiting values of rotational diffusion coefficients are obtained. The effects of membrane inserted peptides on the bilayer phospholipids have been investigated by 2H and 31P solid-state NMR spectroscopy. Long hydrophobic peptides such as the channel-forming domains of Vpu of HIV-1 or M2 of influenza A adopt stable alignments approximately parallel to the bilayer normal in agreement with models suggesting transmembrane helical bundle formation. The 15N chemical shift data agree with tilt angles of approximately 20 degrees and 33 degrees, respectively. In contrast, multi-charged amphipathic alpha-helices adopt stable orientations parallel to the bilayer surface. In the presence of these peptides, decreased order parameters of the fatty acyl chains, membrane thinning, and the loss of long-range order are observed. Peptides that change topology in a pH dependent manner are more potent in antibiotic assays under experimental conditions where they show in-plane alignments. This result suggests that their detergent-like properties, rather than the formation of transmembrane helical bundles, are responsible for their cell-killing activities. Topological equilibria are also observed within proteins or for polypeptides that do not match the hydrophobic thickness of the bilayer.
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PMID:Biophysical investigations of membrane perturbations by polypeptides using solid-state NMR spectroscopy (review). 1112 72

Mastoparan X (MPX: INWKGIAAMAKKLL-NH2) belongs to a family of ionophoric peptides found in wasp venom. Upon binding to the membrane, MPX increases the cell's permeability to cations leading to a disruption in the electrolyte balance and cell lysis. This process is thought to occur either through a membrane-thinning mechanism, where the peptide resides on the membrane surface thereby disrupting lipid packing, or through formation of an oligomeric pore. To address this issue, we have used both high-resolution and solid-state 2H NMR techniques to study the structure and orientation of MPX when associated with bicelles. NOESY and chemical shift analysis showed that in bicelles, MPX formed a well-structured amphipathic alpha-helix. In zwitterionic bicelles, the helical axis was found to rest generally perpendicular to the membrane normal, which could be consistent with the "carpet" mechanism for lytic activity. In anionic bicelles, on the other hand, the helical axis was generally parallel to the membrane normal, which is more consistent with the pore model for lytic activity. In addition, MPX caused significant disruption in lipid packing of the negatively charged phospholipids. Taken together, these results show that MPX associates differently with zwitterionic membranes, where it rests parallel to the surface, compared with negatively charged membranes, where it penetrates longitudinally.
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PMID:Orientation and effects of mastoparan X on phospholipid bicelles. 1115 1

The extracellular fungal polysaccharide, epiglucan, synthesised by Epicoccum nigrum is a side-chain/branched (1 --> 3;1 --> 6)-D-beta-glucan. Methylation analysis, 13C DEPT NMR and specific enzymic digestion data show slight variation in branching frequency among the epiglucans from the three strains examined. The (1 --> 3)-beta-linked backbone has (1 --> 6)-beta-linked branches at frequencies greater than the homologous glucans, scleroglucan and schizophyllan, from Sclerotium spp. and Schizophyllum commune, respectively. The structural analyses do not allow a distinction to be made between structures I and II. [structures: see text] Epiglucan displays non-Newtonian shear thinning rheological properties, typical of these glucans.
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PMID:Structure of epiglucan, a highly side-chain/branched (1 --> 3;1 --> 6)-beta-glucan from the micro fungus Epicoccum nigrum Ehrenb. ex Schlecht. 1132 30

The depth of insertion of an antimicrobial peptide, protegrin-1 (PG-1), in lipid bilayers is investigated using solid-state NMR. Paramagnetic Mn(2+) ions bind to the surface of lipid bilayers and induce distance-dependent dipolar relaxation of nuclear spins. By comparing the signal dephasing of the peptide with that of the lipids, whose segmental depths of insertion are known, we determined the depths of several residues of PG-1 in 1,2 dilauryl-sn-glycero-3-phosphotidylcholine (DLPC) bilayers. We found that residues G2 at the N-terminus and F12 at the beta-turn of the peptide reside near the membrane surface, whereas L5 and V16 are embedded in the acyl chain region. The depths increase in the order of G2 < F12 < L5 < V16. These intensity-dephasing results are confirmed by direct measurement of the paramagnetically enhanced (13)C transverse relaxation rates. The relative depths indicate that PG-1 is tilted from the bilayer normal, which is consistent with independent solid-state NMR measurements of PG-1 orientation in the same lipids (Yamaguchi et al., 2001). They also indicate that PG-1 is fully immersed in the lipid bilayer. However, a quantitative mismatch between the bilayer thickness and PG-1 length suggests a local thinning of the DLPC bilayer by 8-10 A. The depth sensitivity of this Mn(2+) dephasing technique is tunable with the Mn(2+) concentration to focus on different regions of the lipid bilayer.
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PMID:Solid-state NMR investigation of the depth of insertion of protegrin-1 in lipid bilayers using paramagnetic Mn2+. 1450

NMR velocimetry has been used to observe the steady-shear rheological behaviour of a concentrated suspension of hard-sphere like 370 nm diameter PMMA core-shell latex particles at the volume fraction phi = 0.46, the liquid core of the spheres rendering possible NMR observation of the particles themselves. Rheological measurements in a cone-and-plate geometry indicate that when aged (i.e. left at rest for two weeks), the material exhibits yield stress behaviour at very low shear rates. For shear rates greater than 1 s(-1) a transition to liquid-like behaviour was observed, leading to a rejuvenated fluid state which exhibits shear-thinning behaviour over a wide range of shear rates. A similar yield stress behaviour was reflected in NMR velocimetry measurements in a Couette geometry, where the solid-to liquid transition could be clearly observed. Under steady-state flow, the fluid state inside the radius at which yield stress was observed, exhibited shear-thinning behaviour with a power law exponent n slowly approaching unity with increasing shear rate. This behaviour has some similarities with a model of Derec et al. in which aging and rejuvenation effects compete. Substantial wall slip was observed both at the inner and at the outer wall, an effect which disappeared as the shear rate was increased. No radial particle migration from the high-shear region at the inner wall was observed.
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PMID:NMR velocimetry studies of the steady-shear rheology of a concentrated hard-sphere colloidal system. 1617 5


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