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Results for “spatial structure”

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PubMed1978

A 1H nuclear-magnetic-resonance study of the conformation and the molecular dynamics of the glycoprotein cow-colostrum trypsin inhibitor.

The glycoprotein cow colostrum trypsin inhibitor was investigated by high resolution 1H nuclear magnetic resonance (NMR) at 360 MHz and, on the basis of the NMR data, compared with the basic pancreatic trypsin inhibitor (Kunitz) from bovine tissue. Detailed studies of the chemical shifts and the exchange kinetics of the labile protons indicated extensive homologies between the spatial structures of the polypeptide chains in the two compounds. This was further corroborated by comparison of the NMR spectral features and the dynamic properties of the aromatic amino acid residues in the two inhibitors. It thus appears that the covalently attached carbohydrate moiety in the colostrum inhibitor has only very limited effects on the spatial structure of the protein part of the molecule. On the other hand, as evidenced by the NMR line widths, the carbohydrate attachment causes a pronounced restriction of the overall mobility of the molecule, indicating a sizeable increase of the average radius of gyration as compared to the basic pancreatic trypsin inhibitor. Possible spatial arrangements of the globular polypeptide and the carbohydrate moieties in the colostrum inhibitor, which would be compatible with the experimental observations, are discussed.

Amino Acid Sequence↗

PubMed2001

Regional variations in sulfate and nitrate on annual, seasonal, and synoptic time scales.

Ambient data from Interagency Monitoring of Protected Visual Environments (IMPROVE) monitors are analyzed to evaluate the spatial structure of SO4 and NO3 aerosols in the mid-Atlantic region. Sub-weekly, seasonal, and annual data values are compared between the IMPROVE Washington, DC, site and three rural sites. Synoptic perturbations are compared between sites to quantify similarities in short-term temporal perturbations of SO4 and NO3. Based on these comparisons between the rural and urban IMPROVE monitors, the spatial structure of SO4 shows broad regional homogeneity that is recognizable from both the long-term average values and the short-term variations. NO3 data on a seasonal and annual basis show much larger spatial gradients between the urban Washington monitor and the three rural monitors than do SO4 data. Short-term NO3 perturbations at the three rural monitors also differ significantly from those at the Washington site. These dissimilarities in NO3 levels between the rural and urban IMPROVE monitors on both short-term and longer-term time scales indicate little homogeneity of NO3 aerosols in the mid-Atlantic region considered here. The volatility of NO3 aerosols and the removal rate of HNO3 via dry deposition could contribute to the spatial variability differences shown here between SO4 and NO3.

Air Pollutants↗

PubMed1986

Pig kidney Na+,K+-ATPase. Primary structure and spatial organization.

cDNAs complementary to pig kidney mRNAs coding for alpha- and beta-subunits of Na+,K+-ATPase were cloned and sequenced. Selective tryptic hydrolysis of the alpha-subunit within the membrane-bound enzyme and tryptic hydrolysis of the immobilized isolated beta-subunit were also performed. The mature alpha- and beta-subunits contain 1016 and 302 amino acid residues, respectively. Structural data on the peptides from extramembrane regions of the alpha-subunit and on glycopeptides of the beta-subunit underlie a model for the transmembrane arrangement of Na+,K+-ATPase polypeptide chains.

Amino Acid Sequence↗

PubMed2000

Geostatistical analysis of the distribution of NH(4)(+) and NO(2)(-)-oxidizing bacteria and serotypes at the millimeter scale along a soil transect.

Soil is known to be heterogeneous for different activities at several spatial scales. Most studies have focused on macro- and meso-scales but micro-scales are rarely addressed. Hence, the spatial structure of NH(4)(+)- and NO(2)(-)-oxidizers and of various serotypes of the latter was studied along two transects of approximately 10 cm, with two micro-samples taken from each millimeter. The presence of NH(4)(+)- and NO(2)(-)-oxidizers in a micro-sample was detected using colorimetric tests for the presence or absence of NO(2)(-) in cultures of the micro-samples. Geostatistics was used to determine the range of spatial influence of the bacterial types. For both types, semi-variograms indicated a non-random spatial pattern. The spatial dependence ranged from 2 to 4 mm for NO(2)(-)- and NH(4)(+)-oxidizers respectively, and the two bacterial types were not independently spatially located. Among the six serotypes of NO(2)(-)-oxidizers, only one exhibited a spatial dependence. The existence of a spatial structure at the millimeter scale suggests that micro-scale sampling should be employed for soil studies. Therby, data on bacterial populations and activities can be referred to a spatial scale which is meaningful to these organisms.

Journal Article↗

PubMed2006

Cell-cell communication by quorum sensing and dimension-reduction.

Several bacterial taxa change their behavior if the population density exceeds a certain threshold. This phenomenon is the consequence of a communication system between the bacteria and is called quorum sensing (QS). Up to now, this phenomenon is mostly modeled at population level. However, new experimental techniques allow for single cell analysis. We introduce a modeling approach for the description of this QS system, including a discussion of the regulatory network and its bistable behavior. Based on this single-cell model we develop and analyze a spatially structured model for a cell population. Special attention is given to the scaling behavior w.r.t. the cell size (leading to an approximation theorem for stationary solutions) and its consequences for the interpretation of cell communication (QS versus diffusion sensing). Concluding, we apply the modeling approach to spatially structured experimental data.

4-Butyrolactone↗

PubMed1997

[The rational evolution of scorpion toxins].

A theoretical method for the rational design of a "universal" scorpion toxin with a wider spectrum of specificity for K+ channels and a more stable alpha/beta-folding than in its natural homologues is described. On the basis of the analysis of molecular hydrophobic potentials (MHP) of the protein spatial structures, structural features for a family of five short scorpion toxins were revealed. The analysis of the maps of two-dimensional intramolecular MHP contacts allowed the identification of amino acid residues responsible for the folding of the protein and/or for the manifestation of its specific function. The theoretically predicted structure-function roles of the residues were compared with experimental data on the mutagenesis of charybdotoxin. Based on the results of MHP calculations and with the theory of protein molecular evolution used as an additional criterion for the selection of mutations, the amino acid sequence and the spatial structure of a "universal" scorpion toxin were determined.

Amino Acid Sequence↗

PubMed1994

Pathogen invasion and host extinction in lattice structured populations.

We examined the propagation of an infectious disease and the eventual extinction of the host population in a lattice-structured population. Both the host colonization and pathogen transmission processes are assumed to be restricted to act between the nearest neighbor sites. The model is analyzed by an improved version of pair approximation (IPA). Pair approximation is a technique to trace the dynamics of the number of nearest neighbor pairs having particular states, and IPA takes account of the clustering property of lattice models more precisely. The results are checked by computer simulations. The analysis shows: (i) in a one-dimensional lattice population, a pathogen cannot invade a host population no matter how large is the transmission rate; (ii) in a two-dimensional lattice population, pathogens will drive the host to extinction if the transmission rate is larger than a threshold. These results indicate that spatially structured population models may give qualitatively different results from conventional population models, such as Lotka-Volterra ones, without spatial structure.

Biometry↗

PubMed1984

[Conformation analysis of a mixed hemoglobin-glutathione disulfide].

Theoretical conformational analysis was carried out for a mixed disulfide of hemoglobin with glutathione. The conformational mobility of the beta-subunit C-terminal fragment in methemoglobin and deoxyhemoglobin either with free or glutathione-blocked reactive SH-groups was examined. The most stable conformations of the mixed disulfide were delineated. Its spatial structure was shown to be dependent on the hemoglobin state prior to the S-S bond formation: a disulfide made with deoxyhemoglobin had more closely interwoven hemoglobin and glutathione chains than the methemoglobin-derived disulfide. However, in both cases disulfide formation brought about the alterations in the spatial structure of hemoglobin as well as glutathione. The changes in the hemoglobin biochemical properties accompanying the association with glutathione were rationalized in the frames of the mixed disulfide structural analysis.

Disulfides↗

PubMed2001

Investigations of new lead structures for the design of selective estrogen receptor modulators.

Heterocyclic derivatives of (R,S)/(S,R)-1-(2-chloro-4-hydroxyphenyl)-2-(2,6-dichloro-4-hydroxyphenyl)ethylenediamine (L1) were synthesized and tested for estrogen receptor binding. The selection of the heterocycles was based on theoretical consideration. (2R,3S)/(2S,3R)-2-(2-Chloro-4-hydroxyphenyl)-3-(2,6-dichloro-4-hydroxyphenyl)piperazine 2, (4R,5S)/(4S,5R)-4-(2-chloro-4-hydroxyphenyl)-5-(2,6-dichloro-4-hydroxyphenyl)-2-imidazoline 3, and 4-(2-chloro-4-hydroxyphenyl)-5-(2,6-dichloro-4-hydroxyphenyl)imidazole 4 possess a spatial structure with neighboring aromatic rings as is realized in hormonally active [1,2-diphenylethylenediamine]platinum(II) complexes. The 1,2-diphenylethane pharmacophor, however, cannot adapt an antiperiplanar conformation to interact with the estrogen receptor (ER) comparable to synthetic (e.g., diethylstilbestrol (DES)) or steroidal (e.g., estradiol (E2)) estrogens. Due to the different spatial structures, the heterocycles cause only a marginal displacement of E2 from its binding site (relative binding affinity (RBA) < 0.1%). Nevertheless, unequivocally ER mediated gene activation was verified on the MCF-7-2a cell line. Imidazoline 3 as the most active compound reached the maximum effect of E2 (100% activation) in a concentration of 5 x 10(-7) M, while piperazine 2 and imidazole 4 activate luciferase expression only in a small but significant amount of 20% and 27%, respectively. We therefore assigned these heterocyclic compounds to a second class of hormones (type-II-estrogens), which are attached at the ER at different amino acids than DES or E2 (type-I-estrogens).

Binding, Competitive↗

PubMed1998

Visual processing levels revealed by response latencies to changes in different visual attributes.

Visual latencies, and their variation with stimulus attributes, can provide information about the level in the visual system at which different attributes of the image are analysed, and decisions about them made. A change in the colour, structure or movement of a visual stimulus brings about a highly reproducible transient constriction of the pupil that probably depends on visual cortical mechanisms. We measured this transient response to changes in several attributes of visual stimuli, and also measured manual reaction times to the same stimulus changes. Through analysis of latencies, we hoped to establish whether changes in different stimulus attributes were processed by mechanisms at the same or different levels in the visual pathway. Pupil responses to a change in spatial structure or colour are almost identical, but both are ca. 40 ms slower than those to a change in light flux, which are thought to depend largely on subcortical pathways. Manual reaction times to a change in spatial structure or colour, or to the onset of coherent movement, differ reliably, and all are longer than the reaction time to a change in light flux. On average, observers take 184 ms to detect a change in light flux, 6 ms more to detect the onset of a grating, 30 ms more to detect a change in colour, and 37 ms more to detect the onset of coherent motion. The pattern of latency variation for pupil responses and reaction times suggests that the mechanisms that trigger the responses lie at different levels in cortex. Given our present knowledge of visual cortical organization, the long reaction time to the change in motion is surprising. The range of reaction times across different stimuli is consistent with decisions about the onset of a grating being made in V1 and decisions about the change in colour or change in motion being made in V4.

Adult↗

PubMed2000

A new approach for the calculation of the energy of van der Waals interactions in macromolecules of globular proteins.

Van der Waals interaction energy in globular proteins is presented by the interaction energies between regions of protein spatial structure with homogenous medium density distribution. We introduce a notion of the local medium permittivity as a function of absorptance of molecular groups with particular conformation. Proposed theory avoids shortcomings which are typical for the calculations on the basis of the pairwise additive approximation. The approach takes into account local peculiarities of protein spatial structure and physical-chemical characteristics of amino acid residues and molecular groups.

Electromagnetic Fields↗

PubMed1984

Spatial and structural interrelationships between secretory cells of the subcommissural organ and blood vessels. An immunocytochemical study.

In 76 specimens (amphibians, reptilians, mammals) belonging to 25 different vertebrate species, the region of the subcommissural organ (SCO) was investigated with the use of a primary antiserum raised against an extract of bovine Reissner's fiber + the immunoperoxidase procedure according to Sternberger et al. (1970). In the SCO of a toad (Bufo arenarum) and several species of reptiles (lacertilians, ophidians, crocodilians), the ependymal cells were the only type of secretory cell displaying vascular contacts, whereas in mammals ependymal and hypendymal cells established intimate spatial contacts with blood vessels. In Bufo arenarum, but especially in the reptilian species examined, the ependymo-vascular relationship was exerted by a population of ependymal cells having a rather constant location within the SCO and projecting to capillaries that showed a remarkably constant pattern of anatomical distribution. In the SCO of mammals the modality and degree of the structural relationships between secretory cells and blood vessels varied greatly from species to species. In the SCO of the armadillo and dog the secretory tissue was organized as a thick, highly vascularized layer with most of the cells oriented toward the capillaries. A rather opposite situation was found in the SCO of New- and Old-World monkeys, where vascular contacts were restricted to a few ependymal cells.

Animals↗

PubMed1984

Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes.

During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.

Amino Acid Sequence↗

PubMed2003

Visual memory and motor planning in a natural task.

This paper investigates the temporal dependencies of natural vision by measuring eye and hand movements while subjects made a sandwich. The phenomenon of change blindness suggests these temporal dependencies might be limited. Our observations are largely consistent with this, suggesting that much natural vision can be accomplished with "just-in-time" representations. However, we also observe several aspects of performance that point to the need for some representation of the spatial structure of the scene that is built up over different fixations. Patterns of eye-hand coordination and fixation sequences suggest the need for planning and coordinating movements over a period of a few seconds. This planning must be in a coordinate frame that is independent of eye position, and thus requires a representation of the spatial structure in a scene that is built up over different fixations.

Fixation, Ocular↗

PubMed2006

Modeling species-habitat relationships with spatially autocorrelated observation data.

Spatial autocorrelation in wildlife observation data arises when extrinsic environmental processes and patterns that influence the spatial distribution of wildlife are themselves spatially structured, or when species are subject to intrinsic population processes, causing contagion or dispersion effects. Territoriality, Allee effects, dispersal limitations, and social clustering are examples of intrinsic processes. Both forms of autocorrelation can violate the assumptions of generalized linear regression models, resulting in biased estimation of model coefficients and diminished predictive performance. Such consequences may be avoided for extrinsic autocorrelation when autocorrelated environmental variables are available for use as model covariates, whereas intrinsic spatial autocorrelation requires an alternative modeling approach. The autologistic model provides an approach suited to the binary observations often obtained in wildlife surveys, but its performance has not been tested across widely varying sampling intensities or strengths of intrinsic spatial structure. Here we use simulated data to test the autologistic model under a range of sampling conditions. The autologistic model obtains better fits and substantially better predictive performance than the standard logistic regression model over the full range of sampling designs and intensities tested. We provide a simple Bayesian implementation of the autologistic model, which until now has not been achieved with standard statistical software alone. A step-by-step procedure is given for characterizing and modeling spatial autocorrelation in binary observation data, along with computer code for fitting autologistic models in WinBUGS, a freeware Bayesian analysis package. This approach avoids normal approximations to the pseudo-likelihood, in contrast to previous Bayesian applications of the autologistic model. We provide a sample application of the autologistic model, fitted to survey data for a gliding marsupial in southeastern Australia.

Bayes Theorem↗

PubMedDate not supplied

Electronic structure and spatial arrangement of C2v-coordinated ferric iron in metmyoglobin, metmyoglobin fluoride, and methemoglobin.

The electronic term scheme of ferric iron in metmyoglobin, metmyoglobin fluoride, and methemoglobin is evaluated by a Hamiltonian which involves the Coulomb repulsion of the 3d electrons, their interaction with the C2v-coordinated ligands, and spin-orbit coupling. The adjustable parameters of the theory were determined by a least squares fit to experimental EPR, susceptibility, and far-infrared data reported in the literature. According to these results, the structural properties of the ferric ion and its neighboring ligands were discussed by means of group theoretical arguments: An increasing out of plane position of the ferric ion is found in the sequence metHb--metMb--MbF which corresponds to an increasing binding strength with the axial ligands.

Computers↗

PubMed1986

Class structure and spatial polarization: an assessment of recent urban trends in Latin America.

"In this paper, we review those major trends characteristic of peripheral urbanization as they are reflected in the recent Latin American experience. Such trends include: urban primacy and the relative absence of secondary city systems, the character and dynamics of the informal sector, housing deficiencies and state housing policy, and the recent rise of popular organizations oriented toward self-sufficiency or militant demand-making. These trends are important because they represent the form in which continuity and change of peripheral class structures are reflected in space, both at the national and local levels....[The authors conclude that] the political economy of Latin American cities is one where the resolution to the plight of underdevelopment promised by accelerated capitalist industrialization has not materialized. Instead, the process has produced a more complex and more contradictory social fabric."

Americas↗

PubMed1980

High-resolution 1H-NMR studies of self-aggregation of melittin in aqueous solution.

4 mM melittin solution in 0.05 M sodium phosphate buffer at p2H 7.0 and 30 degrees C was shown by ultracentrifugation to contain tetrameric melittin. Using the spectra of this species and the previously characterized monomeric melittin as references, high-resolution 1H-NMR at 360 MHz was used to investigate self-aggregation of melittin at variable temperatures, pH and ionic strength. The NMR parameters show that the spatial structure of aggregated melittin is different from monomeric mellitin in aqueous solution but resembles closely the conformation adopted by melittin bound to detergent micelles. Comparison of melittin bound to different detergent micelles and self-aggregated melittin in different aqueous media indicates that the mellitin monomers adopt similar conformations in all these systems. The present data suggest that melittin assumes an amphiphilic spatial structure which is stabilized both by the formation of mixed micelles with detergents or by self-aggregation.

Amino Acid Sequence↗