Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data resolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed2000

3D map of the plant photosystem II supercomplex obtained by cryoelectron microscopy and single particle analysis.

Here we describe the first 3D structure of the photosystem II (PSII) supercomplex of higher plants, constructed by single particle analysis of images obtained by cryoelectron microscopy. This large multisubunit membrane protein complex functions to absorb light energy and catalyze the oxidation of water and reduction of plastoquinone. The resolution of the 3D structure is 24 A and emphasizes the dimeric nature of the supercomplex. The extrinsic proteins of the oxygen-evolving complex (OEC) are readily observed as a tetrameric cluster bound to the lumenal surface. By considering higher resolution data, obtained from electron crystallography, it has been possible to relate the binding sites of the OEC proteins with the underlying intrinsic membrane subunits of the photochemical reaction center core. The model suggests that the 33 kDa OEC protein is located towards the CP47/D2 side of the reaction center but is also positioned over the C-terminal helices of the D1 protein including its CD lumenal loop. In contrast, the model predicts that the 23/17 kDa OEC proteins are positioned at the N-terminus of the D1 protein incorporating the AB lumenal loop of this protein and two other unidentified transmembrane helices. Overall the 3D model represents a significant step forward in revealing the structure of the photosynthetic OEC whose activity is required to sustain the aerobic atmosphere on our planet.

Cryoelectron Microscopy↗
PubMed2006

Global distribution and conservation of rare and threatened vertebrates.

Global conservation strategies commonly assume that different taxonomic groups show congruent geographical patterns of diversity, and that the distribution of extinction-prone species in one group can therefore act as a surrogate for vulnerable species in other groups when conservation decisions are being made. The validity of these assumptions remains unclear, however, because previous tests have been limited in both geographical and taxonomic extent. Here we use a database on the global distribution of 19,349 living bird, mammal and amphibian species to show that, although the distribution of overall species richness is very similar among these groups, congruence in the distribution of rare and threatened species is markedly lower. Congruence is especially low among the very rarest species. Cross-taxon congruence is also highly scale dependent, being particularly low at the finer spatial resolutions relevant to real protected areas. 'Hotspots' of rarity and threat are therefore largely non-overlapping across groups, as are areas chosen to maximize species complementarity. Overall, our results indicate that 'silver-bullet' conservation strategies alone will not deliver efficient conservation solutions. Instead, priority areas for biodiversity conservation must be based on high-resolution data from multiple taxa.

Animals↗
PubMed2001

High-resolution IR studies of hydrogen bonded clusters: large amplitude dynamics in (HCl)n.

Structural and dynamical information on small hydrogen-bonded systems is revealed by high-resolution IR spectroscopy of HCl dimer, trimer and tetramer. In (HCl)2, four combination bands tentatively assigned to the Van der Waals stretch nu 4 and geared band nu 5 vibrations are observed. The study focuses on two unexpected results: (i) all of the observed bands are built only on the bound HCl stretch nu 2, and (ii) the bands predominantly originate from the 9-fold less populated upper tunneling level of the ground state. Model 3D quantum calculations are presented to show that both these surprising trends originate from the large amplitude tunneling dynamics in the dimer. The (HCl)3 spectra are assigned and analyzed for multiple isotopomeric contributions. The spectral fit reveals large homogeneous line broadening indicating the excited state lifetime of approximately 1.6 ns and tentatively associated with dynamics of intramolecular vibrational energy distribution (IVR) induced trimer ring opening. Finally, first high-resolution data on the HCl stretch fundamental spectrum of (HCl)4 are presented.

Journal Article↗
PubMed2005

Polyketide stereotetrads in natural products.

Natural products (or secondary metabolites) remain as the most important source for discovery of new and potential drug molecules. With high resolution data of their structures, and the advancement of synthesis possibilities, analysis of the natural products based on their specific structural features is valuable to those entering the field. In this tutorial review we attempt such an analysis indicating the salient features of the structural classes with examples of the synthesis of each one of them. As the particular class of natural products, we have chosen polyketides.

Fatty Acids, Unsaturated↗
PubMed2005

Simulation studies of the interactions between membrane proteins and detergents.

Interactions between membrane proteins and detergents are important in biophysical and structural studies and are also biologically relevant in the context of folding and transport. Despite a paucity of high-resolution data on protein-detergent interactions, novel methods and increased computational power enable simulations to provide a means of understanding such interactions in detail. Simulations have been used to compare the effect of lipid or detergent on the structure and dynamics of membrane proteins. Moreover, some of the longest and most complex simulations to date have been used to observe the spontaneous formation of membrane protein-detergent micelles. Common mechanistic steps in the micelle self-assembly process were identified for both alpha-helical and beta-barrel membrane proteins, and a simple kinetic mechanism was proposed. Recently, simplified (i.e. coarse-grained) models have been utilized to follow long timescale transitions in membrane protein-detergent assemblies.

Bacterial Outer Membrane Proteins↗
PubMed1998

Reduction of charging in protein electron cryomicroscopy.

Charging causes a loss of resolution in electron cryomicroscopy with biological specimens prepared without a continuous carbon support film. Thin conductive films were deposited onto catalase crystals prepared across holes using ion-beam sputtering and thermal evaporation and evaluated for the effectiveness of charge reduction. Deposits applied by ion-beam sputtering reduced charging but concurrently resulted in structural damage. Coatings applied by thermal evaporation also reduced charging, and preserved the specimen structure beyond 5 A resolution as judged from electron diffraction patterns and images of glucose-embedded catalase crystals tilted to 45 degrees in the microscope. This study demonstrates for the first time the feasibility of obtaining high-resolution data from unstained, unsupported protein crystals with a conductive surface coating.

Catalase↗
PubMed2006

High-resolution inner-shell excitation spectroscopy of H2-phthalocyanine.

We report on a combined experimental and theoretical carbon and nitrogen K-edge near-edge x-ray absorption fine structure investigation on condensed metal-free phthalocyanine (H2Pc). Based on the results from improved virtual orbital calculations, all resonances in the experimental high-resolution data can be assigned to various electronic transitions. The comparison between experiments and calculations further shows that a significant influence of the core hole, which affects both the transition energies and the cross sections, is present and must be considered in theoretical approaches. Moreover, additional fine structure is clearly resolved for the first N 1s-->pi* transition, which can be interpreted as vibronic coupling to the electronic core excitation.

Journal Article↗
PubMed2000

Coping skills training for youth with diabetes mellitus has long-lasting effects on metabolic control and quality of life.

OBJECTIVE: To determine whether initial effects on metabolic control and quality of life associated with a behavioral intervention combined with intensive diabetes management (IDM) can be sustained over 1 year in youth implementing intensive therapy regimens. STUDY DESIGN: Seventy-seven patients (43 females, 95% white) 12 to 20 years (mean = 14.2 +/- 1.9; duration, 8.7 +/- 3.9) electing to initiate IDM were randomly assigned to one of two groups: with or without coping skills training (CST), which consists of 6 small group sessions and monthly follow-up to help youth cope with their lives in the context of diabetes management; skills included social problem solving, cognitive behavior modification, and conflict resolution. Data were collected before the intervention and at 3, 6, and 12 months after the intervention by using the Self-Efficacy for Diabetes Scale, Children's Depression Inventory, Issues in Coping with IDDM, and the Diabetes Quality of Life: Youth scales. Clinical data (glycosylated hemoglobin level, height, weight, adverse effects) were collected monthly. RESULTS: The CST and IDM groups were comparable at baseline. CST subjects had lower glycosylated hemoglobin (P =.001) and better diabetes (P =.002) and medical (P =. 04) self-efficacy, and less impact of diabetes on their quality of life (P =.005) than youth receiving IDM alone after 1 year. In males, CST did not affect adverse outcomes of IDM hypoglycemia, diabetic ketoacidosis, and weight gain, but CST decreased the incidence of weight gain (P =.05) and hypoglycemia in females (P =.03). CONCLUSIONS: The addition of behavioral intervention to IDM in adolescence results in improved metabolic control and quality of life over 1 year.

Adaptation, Psychological↗
PubMed2005

Characterizing wildfire regimes in the United States.

Wildfires statistics for the conterminous United States (U.S.) are examined in a spatially and temporally explicit manner. We use a high-resolution data set consisting of 88,916 U.S. Department of Agriculture Forest Service wildfires over the time period 1970-2000 and consider wildfire occurrence as a function of ecoregion (land units classified by climate, vegetation, and topography), ignition source (anthropogenic vs. lightning), and decade. For the conterminous U.S., we (i) find that wildfires exhibit robust frequency-area power-law behavior in 18 different ecoregions; (ii) use normalized power-law exponents to compare the scaling of wildfire-burned areas between ecoregions, finding a systematic change from east to west; (iii) find that wildfires in the eastern third of the U.S. have higher power-law exponents for anthropogenic vs. lightning ignition sources; and (iv) calculate recurrence intervals for wildfires of a given burned area or larger for each ecoregion, allowing for the classification of wildfire regimes for probabilistic hazard estimation in the same vein as is now used for earthquakes.

Journal Article↗
PubMed1984

Structural stability in the 4-zinc human insulin hexamer.

X-ray studies on human insulins prepared by semisynthetic and biosynthetic methods have recently been undertaken. Human insulin differs from porcine insulin only at the COOH terminus of the B-chain. The present study reports the crystal structure of 4-zinc human insulin, which is used clinically as a slow-acting preparation. The structure has been refined, using 1.85-A resolution data, to a residual of 0.173. The unit cell is rhombohedral, space group R3, with hexagonal cell constants a = 80.953 and c = 37.636 A, and it is nearly isomorphous with that of 4-zinc porcine insulin. As a result of a conformational change of the first eight residues of the B-chain of molecule 1 from an extended conformation observed in the 2-zinc structure to an alpha-helical one, the coordination around one of the zinc ions on the 3-fold axis has changed, an additional zinc ion in a general position is bound by the hexamer, and additional hydrogen-bonded interactions help stabilize dimer and hexamer formation. Unlike the surface of the 2-zinc insulin hexamer, which possesses a shallow depression containing a zinc ion and its coordinating water molecules, the 4-zinc human insulin hexamer contains a zinc and chloride ion at the bottom of an 8-A tunnel produced by three parallel alpha-helices. These alpha-helices shield the zinc ion from the environment, decreasing the rate of dissociation of the hexamer, and provide an explanation for the slow-acting aspect of the 4-zinc crystalline form.

Amino Acid Sequence↗
PubMed1993

The first step in vision occurs in femtoseconds: complete blue and red spectral studies.

Femtosecond transient absorption measurements of the cis-trans isomerization of the visual pigment rhodopsin clarify the interpretation of the dynamics of the first step in vision. We present femtosecond time-resolved spectra as well as kinetic measurements at specific wavelengths between 490 and 670 nm using 10-fs probe pulses centered at 500 and 620 nm following a 35-fs pump pulse at 500 nm. The expanded spectral window beyond that available (500-570 nm) in our previous study [Schoenlein, R. W., Peteanu, L. A., Mathies, R. A. & Shank, C. V. (1991) Science 254, 412-415] provides the full differential absorption spectrum of the photoproduct as a function of delay time after photolysis. The high time-resolution data presented here contradict an alternative interpretation of the rhodopsin photochemistry offered by Callender and co-workers [Yan, M., Manor, D., Weng, G., Chao, H., Rothberg, L., Jedju, T. M., Alfano, R. R. & Callender, R. H. (1991) Proc. Natl. Acad. Sci. USA 88, 9809-9812]. Our results confirm that the red-shifted (lambda max approximately 570 nm) photo-product of the isomerization reaction is fully formed within 200 fs. Subsequent changes in the differential spectra between 200 fs and 6 ps are attributed to a combination of dynamic ground-state processes such as intramolecular vibrational energy redistribution, vibrational cooling, and conformational relaxation.

Color Perception↗
PubMed2000

Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.

The human retinoic acid receptor (hRAR) is a member of the nuclear receptor superfamily that regulates the transcription of target genes in a ligand-dependent manner. The three hRAR isotypes are targets for retinoids that are used in the treatment of various diseases, including breast cancer and skin diseases. Drug efficiency and safety depend on the pharmacological activity of enantiomers, which can differ because of the chiral environment generated by the target. We report the crystal structures of the hRARgamma ligand-binding domain bound to two enantiomers, the active BMS270394 and the inactive BMS270395, solved at 1.6 A and 1.7 A resolution, respectively. The crystal structures reveal that in both enantiomers, the hydroxyl moiety attached to the chiral center forms a hydrogen bond to the Met-272 sulfur atom, thus imposing a conformation of BMS270395 that differs significantly from that observed for BMS270394 and other known retinoids. BMS270395 adopts an energetically unfavorable conformation, accounting for its inactivity; in contrast, the conformation of BMS270394 is close to an energy minimum. Our high-resolution data allow rationalization of enantiomer discrimination by the receptor and provide a model system for the pharmacological properties of enantiomeric pairs.

Amino Acid Sequence↗
PubMed1998

Subcellular localization of prostaglandin endoperoxide H synthases-1 and -2 by immunoelectron microscopy.

Prostaglandin endoperoxide H synthases-1 and -2 (PGHS-1 and -2) are the major targets of nonsteroidal anti-inflammatory drugs like aspirin and ibuprofen. These enzymes catalyze the committed step in the formation of prostanoids from arachidonic acid. Although PGHS-1 and -2 are similar biochemically, a number of studies suggest that PGHS-1 and PGHS-2 function independently to form prostanoids that subserve different cellular functions. We have hypothesized that these isozymes may reside, at least in part, in different subcellular compartments and that their compartmentation may affect their access to arachidonic acid and serve to separate the functions of the enzymes. To obtain high resolution data on the subcellular locations of PGHS-1 and -2, we employed immunoelectron microscopy with multiple antibodies specific to each isozyme. Both PGHS-1 and -2 were found on the lumenal surfaces of the endoplasmic reticulum (ER) and nuclear envelope of human monocytes, murine NIH 3T3 cells, and human umbilical vein endothelial cells. Within the nuclear envelope, PGHS-1 and -2 were present on both the inner and outer nuclear membranes and in similar proportions. Western blotting data showed a similar distribution of PGHS-1 and -2 in subcellular fractions, and product analysis using isozyme-specific inhibitors suggested that both enzymes generate the same products in NIH 3T3 cells. Thus, we are unable to attribute the independent functioning of PGHS-1 and PGHS-2 to differences in their subcellular locations. Instead, the independent operation of these isozymes may be attributable to subtle kinetic differences (e.g. negative allosteric regulation of PGHS-1 at low concentrations of arachidonate (500-1000 nM)). A further conclusion of importance from a cell biological perspective is that membrane proteins such as PGHS-1 and -2, which are located on the lumenal surface of the ER, are able to diffuse freely among the ER and the inner and outer membranes of the nuclear envelope.

3T3 Cells↗
PubMed2002

Structural model of the regulatory domain of smooth muscle heavy meromyosin.

The goal of this study was to provide structural information about the regulatory domains of double-headed smooth muscle heavy meromyosin, including the N terminus of the regulatory light chain, in both the phosphorylated and unphosphorylated states. We extended our previous photo-cross-linking studies (Wu, X., Clack, B. A., Zhi, G., Stull, J. T., and Cremo, C. R. (1999) J. Biol. Chem. 274, 20328-20335) to determine regions of the regulatory light chain that are cross-linked by a cross-linker attached to Cys(108) on the partner regulatory light chain. For this purpose, we have synthesized two new biotinylated sulfhydryl reactive photo-cross-linking reagents, benzophenone, 4-(N-iodoacetamido)-4'-(N-biotinylamido) and benzophenone, 4-(N-maleimido)-4'-(N-biotinylamido). Cross-linked peptides were purified by avidin affinity chromatography and characterized by Edman sequencing and mass spectrometry. Labeled Cys(108) from one regulatory light chain cross-linked to (71)GMMSEAPGPIN(81), a loop in the N-terminal half of the regulatory light chain, and to (4)RAKAKTTKKRPQR(16), a region for which there is no atomic resolution data. Both cross-links were to the partner regulatory light chain and occurred in unphosphorylated but not phosphorylated heavy meromyosin. Using these data, data from our previous study, and atomic coordinates from various myosin isoforms, we have constructed a structural model of the regulatory domain in an unphosphorylated double-headed molecule that predicts the general location of the N terminus. The implications for the structural basis of the phosphorylation-mediated regulatory mechanism are discussed.

Amino Acid Sequence↗
PubMed2004

Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.

Unsaturated glucuronyl hydrolase (UGL) is a novel glycosaminoglycan hydrolase that releases unsaturated d-glucuronic acid from oligosaccharides produced by polysaccharide lyases. The x-ray crystallographic structure of UGL from Bacillus sp. GL1 was first determined by multiple isomorphous replacement (mir) and refined at 1.8 A resolution with a final R-factor of 16.8% for 25 to 1.8 A resolution data. The refined UGL structure consists of 377 amino acid residues and 478 water molecules, four glycine molecules, two dithiothreitol (DTT) molecules, and one 2-methyl-2,4-pentanediol (MPD) molecule. UGL includes an alpha(6)/alpha(6)-barrel, whose structure is found in the six-hairpin enzyme superfamily of an alpha/alpha-toroidal fold. One side of the UGL alpha(6)/alpha(6)-barrel structure consists of long loops containing three short beta-sheets and contributes to the formation of a deep pocket. One glycine molecule and two DTT molecules surrounded by highly conserved amino acid residues in UGLs were found in the pocket, suggesting that catalytic and substrate-binding sites are located in this pocket. The overall UGL structure, with the exception of some loops, very much resembled that of the Bacillus subtilis hypothetical protein Yter, whose function is unknown and which exhibits little amino acid sequence identity with UGL. In the active pocket, residues possibly involved in substrate recognition and catalysis by UGL are conserved in UGLs and Yter. The most likely candidate catalytic residues for glycosyl hydrolysis are Asp(88) and Asp(149). This was supported by site-directed mutagenesis studies in Asp(88) and Asp(149).

Amino Acid Sequence↗
PubMed2001

3-Dimensional organization of the N-terminal vinculin head fragment.

The cytoskeleton-associated protein vinculin is composed of a globular head and an elongated tail domain. The protein can be cleaved by V8 protease treatment into two fragments with apparent molecular masses of 90 and 29/27 kDa, respectively. So far, no high-resolution data on the tertiary structure of the N-terminal 90-kDa fragment are available. We analyzed the 90-kDa fragment in detail, using electron spectroscopic imaging in conjunction with modelling experiments. The front view projection of this fragment appears roughly rhomboidal, with 4 intensity maxima arranged at the vertices and a stain-filled region in the center. Based on a detailed examination of different particle projections, a 3-dimensional model was constructed which appears as a flattened tetrahedron. A comparison of the 90-kDa fragment with the intact protein allows for a correlation between the subdomain organization of the vinculin head and the biochemically defined V8 protease cleavage sites (aa 851 and 857).

Animals↗
PubMed1986

Energy minimized structures of carcinogen-DNA adducts: 2-acetylaminofluorene and 2-aminofluorene.

Energy minimized structures of DNA modified by the aromatic amines 2-acetylaminofluorene (AAF) and 2-aminofluorene (AF), for which no experimental atomic resolution data exist, are presented. These have been computed with a new molecular mechanics program specifically designed to define distortions imposed by such adducts, and employing a rational strategy for searching the conformation space of a DNA molecule with covalently linked carcinogen. In alternating G-C sequences, the AAF adduct prefers to reside at the exterior of an undeformed Z-helix. It can also induce base displacement with attendant denaturation and helix bending in sequences that disfavor the Z form, but undeformed B helices are excluded. The AF adduct, by contrast, prefers the major groove of an unperturbed B-helix, but can also induce carcinogen-base stacking in single stranded regions of the DNA, such as at the replication fork. The different biological properties of these two adducts may be related to their distinct

2-Acetylaminofluorene↗
PubMed1992

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies.

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as--intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96--a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Bacteriorhodopsins↗