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Results for “spatial structure”

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PubMed1988

Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli.

The technique of two-dimensional nuclear magnetic resonance (2D-NMR) has recently assumed an active role in obtaining information on structures of polypeptides, small proteins, sugars, and DNA fragments in solution. In order to generate spatial structures from the atom-atom distance information obtained by the NMR method, different procedures have been developed. Here we introduce a combined procedure of distance geometry (DG) and molecular dynamics (MD) calculations for generating 3D structures that are consistent with the NMR data set and have reasonable internal energies. We report the application of the combined procedure on the lac repressor DNA binding domain (headpiece) using a set of 169 NOE and 17 "hydrogen bond" distance constraints. Eight of ten structures generated by the distance geometry algorithm were refined within 10 ps MD simulation time to structures with low internal energies that satisfied the distance constraints. Although the combination of DG and MD was designed to combine the good sampling properties of the DG algorithm with an efficient method of lowering the internal energy of the molecule, we found that the MD algorithm contributes significantly to the sampling as well.

Algorithms↗

PubMed1997

Using Moment Equations to Understand Stochastically Driven Spatial Pattern Formation in Ecological Systems

Spatial patterns in biological populations and the effect of spatial patterns on ecological interactions are central topics in mathematical ecology. Various approaches to modeling have been developed to enable us to understand spatial patterns ranging from plant distributions to plankton aggregation. We present a new approach to modeling spatial interactions by deriving approximations for the time evolution of the moments (mean and spatial covariance) of ensembles of distributions of organisms; the analysis is made possible by "moment closure," neglecting higher-order spatial structure in the population. We use the growth and competition of plants in an explicitly spatial environment as a starting point for exploring the properties of second-order moment equations and comparing them to realizations of spatial stochastic models. We find that for a wide range of effective neighborhood sizes (each plant interacting with several to dozens of neighbors), the mean-covariance model provides a useful and analytically tractable approximation to the stochastic spatial model, and combines useful features of stochastic models and traditional reaction-diffusion-like models. Copyright 1997 Academic Press. Copyright 1997 Academic Press

Journal Article↗

PubMed2006

Small-scale spatial heterogeneity of arbuscular mycorrhizal fungal abundance and community composition in a wetland plant community.

Although it has become increasingly clear that arbuscular mycorrhizal fungi (AMF) play important roles in population, community, and ecosystem ecology, there is limited information on the spatial structure of the community composition of AMF in the field. We assessed small-scale spatial variation in the abundance and molecular diversity of AMF in a calcareous fen, where strong underlying environmental gradients such as depth to water table may influence AMF. Throughout an intensively sampled 2 x 2 m plot, we assessed AMF inoculum potential at a depth of 0-6 and 6-12 cm and molecular diversity of the AMF community using terminal restriction fragment length polymorphism of 18S rDNA. Inoculum potential was only significantly spatially autocorrelated at a depth of 6-12 cm and was significantly positively correlated with depth to water table at both depths. Molecular diversity of the AMF community was highly variable within the plot, ranging from 2-14 terminal restriction fragments (T-RFs) per core, but the number of T-RFs did not relate to water table or plant species richness. Plant community composition was spatially autocorrelated at small scales, but AMF community composition showed no significant spatial autocorrelation. Saturated soils of calcareous fens contain many infective AMF propagules and the abundance and diversity of AMF inoculum is patchy over small spatial scales.

DNA, Fungal↗

PubMed2006

An ESS for the height of a plant population, or an optimal height for an individual?--Rethinking game-theoretic models for plant height.

Plants only interact with neighbors over restricted distances, so local conditions are of great significance for plants. It is therefore important to consider spatial structure and neighborhood effects if we are to understand plants' strategies. We constructed a spatially-explicit, game theory model to explore optimal height growth at the individual-level. In the model, there is no ESS for height growth at the population level, because there is an "instantaneous" optimal height growth strategy for the individual plant that changes depending on the local light environment. The optimal strategy is plasticity in response to local conditions. Game-theoretic models for plant phenotypic traits should move from "mean-field approximations" towards explicit modeling of local interactions.

Ecosystem↗

PubMed2003

On the hemispheric specialization for categorical and coordinate spatial relations: a review of the current evidence.

This article reviews current evidence on the hemispheric specialization hypothesis for two types of spatial relations representations; categorical versus coordinate [Psychol. Rev. 94 (1987) 148; J. Exp. Psychol.: Percept. Perform. 15 (1989) 723]. Categorical representations capture general properties of the spatial structure of a visual stimulus, without defining the exact metric properties. Coordinate representations specify precise spatial locations of objects or parts in terms of metric units. It is claimed that a hemispheric difference in contribution to the computation of both types of spatial relations representations exists, in which the left hemisphere is specialized for the computation of categorical spatial representations while the right hemisphere is specialized for the computation of coordinate ones. Several forms of research (experimental, computer simulations, patient studies and neuroimaging studies) are reviewed. In general, there is convergent evidence for a conceptual separation of coordinate and categorical processing, with strongest indications for a relative right hemisphere advantage in encoding coordinate spatial relations, and weaker support for left hemispheric categorical specialization. The pattern appears to be critically linked to receptive field properties of the two hemispheres and as such is modulated by certain elementary visual characteristics of the displayed stimuli.

Brain Diseases↗

PubMed2002

(4R,5S)/(4S,5R)-4,5-Bis(4-hydroxyphenyl)-2-imidazolines: ligands for the estrogen receptor with a novel binding mode.

(4R,5S)/(4S,5R)-4,5-Bis(4-hydroxyphenyl)-2-imidazolines 1-7 were synthesized by the reaction of the methoxy-substituted (1R,2S)/(1S,2R)-1,2-diarylethylenediamines 1b-7b with triethyl orthoformate and subsequent ether cleavage with BBr(3). All compounds were tested for estrogen receptor (ER) binding in a competition experiment with [(3)H]-estradiol and for gene activation in a luciferase assay using ER positive MCF-7-2a breast cancer cells stably transfected with the plasmid ERE(wtc)luc. The relative binding affinities of the 2-imidazolines were very low (RBA < 0.1%). Nevertheless, 4-7 possessed full agonistic activity in the luciferase assay. The relative transcription potency increased in the order 5 (2,2'-I) < 6 (2,6-Cl(2), 2'-F) < 4 (2,2'-Cl) < 7 (2,6-Cl(2), 2'-Cl). These data together with spectroscopic and molecular modeling studies were used to investigate the preferred binding mode adopted by the imidazoline ligands. The 1,2-diarylethane pharmacophor takes a Z-stilbene-like structure with pseudoaxially oriented phenyl rings at the planar heterocyclic ring. Because of this unusual spatial structure, the (4R,5S)/(4S,5R)-4,5-bis(4-hydroxyphenyl)-2-imidazolines have to be assigned to a second class of estrogenically active compounds (type II estrogens). In contrast to type I estrogens, e.g., estradiol (E2), diethylstilbestrol (DES), and meso-hexestrol (HES), which are connected to His 524 in the binding site, type II estrogens are very likely H-bonded to Asp 351 in a hydrophobic side pocket.

Animals↗

PubMed2002

The role of parasites in sympatric and allopatric host diversification.

Exploiters (parasites and predators) are thought to play a significant role in diversification, and ultimately speciation, of their hosts or prey. Exploiters may drive sympatric (within-population) diversification if there are a variety of exploiter-resistance strategies or fitness costs associated with exploiter resistance. Exploiters may also drive allopatric (between-population) diversification by creating different selection pressures and increasing the rate of random divergence. We examined the effect of a virulent viral parasite (phage) on the diversification of the bacterium Pseudomonas fluorescens in spatially structured microcosms. Here we show that in the absence of phages, bacteria rapidly diversified into spatial niche specialists with similar patterns of diversity across replicate populations. In the presence of phages, sympatric diversity was greatly reduced, as a result of phage-imposed reductions in host density decreasing competition for resources. In contrast, allopatric diversity was greatly increased as a result of phage-imposed selection for resistance, which caused populations to follow divergent evolutionary trajectories. These results show that exploiters can drive diversification between populations, but may inhibit diversification within populations by opposing diversifying selection that arises from resource competition.

Animals↗

PubMed2006

Web-ware bioinformatical analysis and structure modelling of N-terminus of human multisynthetase complex auxiliary component protein p43.

Human multisynthetase complex auxiliary component, protein p43 is an endothelial monocyte-activating polypeptide II precursor. In this study, comprehensive sequence analysis of N-terminus has been performed to identify structural domains, motifs, sites of post-translation modification and other functionally important parameters. The spatial structure model of full-chain protein p43 is obtained.

Amino Acid Motifs↗

PubMed1986

[The structure of Buthus eupeus neurotoxin M9 in a solution studied by 1H-NMR spectroscopy].

Neurotoxin M9 isolated from the venom of Central Asian scorpion Buthus eupeus (66 amino acid residues, 4 disulfide bridges) has two slowly exchangeable conformations at the acidic pH. 2D-1H-NMR spectroscopy has been used to determine the polypeptide backbone foiding in the conformer that dominates under physiological conditions. The conformer contains the right alpha-helix (residues 22-31) and the antiparallel beta-sheet, which consists of the three strands (residues 1-5, 46-52, 35-40). All five Xxx-Pro bonds are in the trans configuration. Comparison of the obtained data with the crystal structure of the homologous scorpion toxin v-3 Centruroides sculpturatus (65 residues) and the solution spatial structure of the "short" type insectotoxin I5A Buthus eupeus (35 residues) shows close similarity in the first case and similarity of the types and mutual disposition of the regular secondary structure elements in the second case.

Amino Acid Sequence↗

PubMedDate not supplied

[Stereochemical theory of the 3-dimensional structure of globular proteins. III. Prediction of the tertiary structure].

A prediction is made of the tertiary structure of parvalbumin, the variable part of the immunoglobulin molecule, carboxypeptidase and the trypsin inhibitor. The structures obtained theoretically coincide completely with the native ones. In the case of the trypsin inhibitor molecule, the theoretical sequence of disulfide bridge formation completely coincides with the experimental data. Elements of symmetry were found in highly helical intermediate structures of the four proteins studied. The theory developed can be successfully applied for assembling the quaternary protein structure. Proceeding from this theory the mechanisms of the increased rate of assembly of protein spatial structure in conditions in vivo as compared with their assembly in vitro are analysed.

Animals↗

PubMed1982

[Vital cycle, mitotic capacity, and genomic restoration].

We define a theoretical model for clonal reproduction and we describe how the accumulation of mutations induces an ineluctable decline of the "mitotic capacity". During the vital cycle of organisms, meïosis and fecundation may have the function of making up for this fall. This should allow us to understand the temporal structure or the sexualisation of the vital cycle as well as some peculiarities of the spatial structure of the genome.

Clone Cells↗

PubMedDate not supplied

A contribution of sparse matrices tools to matrix population model analysis.

When one wants to study the dynamics of structured populations, matrix type models are widely used. The complexity of such models increases with the number of classes of individuals considered, and a mathematical analysis becomes difficult to perform when a further heterogeneous spatial structure is introduced. The use of efficient computational tools is also required for numerical simulations. In this note we deal with the contribution of sparse matrices tools which allow to numerically simulate and to numerically perform stability analysis of large sized structured population models including density dependence and spatial heterogeneities. Our main motivation through this work is to show that such numerical tools can be useful when mathematical methods become difficult to employ.

Age Factors↗

PubMed1998

[Structural organization of 2C-terminal region and its analogs in a subunit of ribonucleotide reductase from herpes virus].

By means of conformational analysis, the spatial structure and conformational potential of the H-Tyr-Ala-Gly-Ala-Val-Val-Asn-Asp-Leu-OH molecule, which corresponds to sequence 329-337 of the subunit 2 C-terminal region of the herpes virus ribonucleotide reductase, were studied. It was shown that its spatial organization can be described by a set of 17 low-energy conformations of the backbone. The "reverse conformational problem" for this molecule was solved to enable the prediction of a series of synthetic analogues matching the set of low-energy, potentially physiologically active conformations.

Amino Acids↗

PubMed2002

C-terminal domain of gyrase A is predicted to have a beta-propeller structure.

Two different type II topoisomerases are known in bacteria. DNA gyrase (Gyr) introduces negative supercoils into DNA. Topoisomerase IV (Par) relaxes DNA supercoils. GyrA and ParC subunits of bacterial type II topoisomerases are involved in breakage and reunion of DNA. The spatial structure of the C-terminal fragment in GyrA/ParC is not available. We infer homology between the C-terminal domain of GyrA/ParC and a regulator of chromosome condensation (RCC1), a eukaryotic protein that functions as a guanine-nucleotide-exchange factor for the nuclear G protein Ran. This homology, complemented by detection of 6 sequence repeats with 4 predicted beta-strands each in GyrA/ParC sequences, allows us to predict that the GyrA/ParC C-terminal domain folds into a 6-bladed beta-propeller. The prediction rationalizes available experimental data and sheds light on the spatial properties of the largest topoisomerase domain that lacks structural information.

Amino Acid Sequence↗

PubMedDate not supplied

Spatial variation of natural radiation and childhood leukaemia incidence in Great Britain.

This paper describes an analysis of the geographical variation of childhood leukaemia incidence in Great Britain over a 15 year period in relation to natural radiation (gamma and radon). Data at the level of the 459 district level local authorities in England, Wales and regional districts in Scotland are analysed in two complementary ways: first, by Poisson regressions with the inclusion of environmental covariates and a smooth spatial structure; secondly, by a hierarchical Bayesian model in which extra-Poisson variability is modelled explicitly in terms of spatial and non-spatial components. From this analysis, we deduce a strong indication that a main part of the variability is accounted for by a local neighbourhood 'clustering' structure. This structure is furthermore relatively stable over the 15 year period for the lymphocytic leukaemias which make up the majority of observed cases. We found no evidence of a positive association of childhood leukaemia incidence with outdoor or indoor gamma radiation levels. There is no consistent evidence of any association with radon levels. Indeed, in the Poisson regressions, a significant positive association was only observed for one 5-year period, a result which is not compatible with a stable environmental effect. Moreover, this positive association became clearly non-significant when over-dispersion relative to the Poisson distribution was taken into account.

Air Pollution, Indoor↗

PubMed1989

Arthroscopy and arthrography. A combined procedure.

Arthrography and arthroscopy are invasive diagnostic procedures performed on all main joints of the human body. Both procedures are effective, with differing methods of visualizing intra-articular structures. Whereas the arthrogram reproduces a black-and-white, two-dimensional picture of a spatial structure (an indirect procedure), arthroscopy provides a colored picture facilitating a three-dimensional assessment of the joint cavity, palpation, and the arthroscopic operation. However, both procedures have their weaknesses. False-positive and false-negative results may occur in arthrographic techniques, whereas in arthroscopy, the inability to visualize particular joint regions resulting from the anatomical features of the joints is known. Arthroscopy and arthrography are complementary procedures in joint diagnosis. The present paper is based on experience gathered in 5188 arthroscopies of the six large human joints. Prior to all hand and hip arthroscopies, arthrographic examinations were performed. They provided essential information in 30% of all ankle-joint arthroscopies and in 10% of all knee arthroscopies, but in only a few elbow and shoulder arthroscopies.

Ankle Joint↗

PubMed2004

Diversity of arbuscular mycorrhizal fungi across a fragmented forest in Panama: insular spore communities differ from mainland communities.

It is now understood that alterations in the species composition of soil organisms can lead to changes in aboveground communities. In this study, we assessed the importance of spatial scale and forest size on changes in arbuscular mycorrhizal fungal (AMF) spore communities by sampling AMF spores in soils of forested mainland and island sites in the vicinity of Gatun Lake, Republic of Panama. We encountered a total of 27 AMF species or morphospecies, with 17, 8, 1 and 1 from the genera Glomus, Acaulospora, Sclerosystis, and Scutellospora, respectively. At small scales (<100 m2), we found little evidence for spatial structuring of AMF communities (decay of Morisita-Horn community similarity with distance). However, at large spatial scales, we found that the AMF spore community of a mainland plot was more similar to other mainland plots several kilometers (>5) away than to nearby island plots (within 0.7 km). Likewise, most island plots were more similar to other island plots regardless of geographic separation. There was no decay in AMF species richness (number of species), or Shannon diversity (number of species and their spore numbers) either with decreasing forest-fragment size, or with decreasing plant species richness. Of the six most common species that composed almost 70% of the total spore volume, spores of Glomus "tsh" and G. clavisporum were more common in soils of mainland plots, while spores of Glomus "small brown" and Acaulospora mellea were more abundant in soils of island plots. None of these common AMF species showed significant associations with soil chemistry or plant diversity. We suggest that the convergence of common species found in AMF spore communities in soils of similar forest sizes was a result of forest fragmentation. Habitat-dependent convergence of AMF spore communities may result in differential survival of tree seedlings regenerating on islands versus mainland.

Analysis of Variance↗

PubMed2004

Tyrosine residues modification studied by MALDI-TOF mass spectrometry.

Amino acid residue-specific reactivity in proteins is of great current interest in structural biology as it provides information about solvent accessibility and reactivity of the residue and, consequently, about protein structure and possible interactions. In the work presented tyrosine residues of three model proteins with known spatial structure are modified with two tyrosine-specific reagents: tetranitromethane and iodine. Modified proteins were specifically digested by proteases and the mass of resulting peptide fragments was determined using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Our results show that there are only small differences in the extent of tyrosine residues modification by tetranitromethane and iodine. However, data dealing with accessibility of reactive residues obtained by chemical modifications are not completely identical with those obtained by nuclear magnetic resonance and X-ray crystallography. These interesting discrepancies can be caused by local molecular dynamics and/or by specific chemical structure of the residues surrounding.

Amino Acid Substitution↗