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Results for “spatial structure”

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PubMed1998

Spatial structure determination of antiarrhythmic peptide using nuclear magnetic resonance spectroscopy.

The peptide AAP10 was synthesized according to the Merrifield technique following the Fmoc-strategy and its spatial structure in aqueous solution studied with NMR principles. It is known from previous studies that the peptide has antiarrhythmic activity and inhibits cardiac ischemia induced alterations of the activation pattern, decreases the activation-recovery interval (ARI) dispersion and improves cellular coupling via enhancement of gap junction conductance (2, 2, 3, 4). The peptide was synthesized as a peptide amide. Two different semi cyclic conformations were characterized.

Anti-Arrhythmia Agents↗

PubMed2000

Towards the integration of social dominance and spatial structure.

My aim was to show how individual-oriented (or artificial life) models may provide an integrative background for the development of theories about dominance by including effects of spatial structure. Dominance interactions are thought to serve two different, contrasting functions: acquisition of high rank and reduction of aggression. The model I present consists of a homogeneous virtual world inhabited by artificial agents whose actions are restricted to grouping and dominance interactions in which the effects of winning and losing are self-reinforcing. The two functions are implemented as strategies to initiate dominance interactions and the intensity of aggression and dominance perception (direct or memory based) are varied experimentally. Behaviour is studied by recording the same behavioural units as in real animals. Ranks appear to differentiate more clearly at high than at low intensity of aggression and also more in the case of direct than of memory-based rank perception. Strong differentiation of rank produces a cascade of unexpected effects that differ depending on which function is implemented: for instance, a decline in aggression, spatial centrality of dominants and a correlation between rank and aggression. Insight into the origination of these self-organized patterns leads to new hypotheses for the study of the social behaviour of real animals. Copyright 2000 The Association for the Study of Animal Behaviour.

Journal Article↗

PubMedDate not supplied

Spatial structures in a model substrate-inhibition reaction diffusion system.

An important new model universal oscillator proposed by Seelig which depends on substrate inhibition is considered. In a finite spatial domain with zero flux boundary conditions and in which the substrates can diffuse it is shown that diffusion-driven instability is possible and can result in finite amplitude spatial structures. Illustrative numerical results are presented which exhibit this behaviour.

Catalysis↗

PubMed1984

The spatial structure of the axially bound methionine in solution conformations of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c551 by 1H NMR.

A generally applicable method for the determination of the spatial structure of the heme iron-bound methionine in c-type ferrocytochromes at atomic resolution is presented. It relies primarily on measurements of nuclear Overhauser effects between the individual hydrogen atoms of the axial methionine, and between individual hydrogens of the methionine and the heme group. Four different methionine conformers, corresponding to the four possible stereospecific assignments for the methionine methylene proton resonances, are generated by a structural interpretation of the nuclear Overhauser effects with the use of an interactive computer graphics technique. A unique structure and unique stereospecific resonance assignments are then obtained by discriminating between these four conformers on the basis of van der Waals' constraints and heme ring current effects on the chemical shifts. The use of the method is illustrated with studies of horse ferrocytochrome c and Pseudomonas aeruginosa ferrocytochrome c 551. Comparison with the crystal structures shows close coincidence between the methionine conformations in solution and in single crystals of these proteins.

Animals↗

PubMed1979

A colour-dependent abnormality in human visual detection of stimulus motion and spatial structure.

We have studied the wavelength dependence of visual responses in a single human subject, M.W., who has an unusual visual defect. It is shown that for red stimuli, both spatial resolution for grating patterns and detection of target movement are grossly abnormal. On the basis of these and other [8] experimental data, we argue that M.W.'s response pattern implies interdependent central visual processing of colour, movement and spatial structure. We examine this conclusion in relation to recent anatomical and electrophysiological findings.

Color Perception↗

PubMed1988

Incorporating the effects of spatial structure in discrete choice models of migration.

Discrete-choice theory and logit models are evaluated for their usefulness in analyzing migration patterns in a zonal system. The authors "argue that spatial effects and more specifically the relative location of zones are not taken into account in such analyses. We, therefore, introduce a measure of spatial structure and advocate its usage as a predictor of migration in such models. In an example of intrametropolitan migration in Toronto [Canada], we demonstrate that this variable is not only significant but also it improves the performance of all the other variables with the greatest impact on the distance between zones. In addition, inclusion of this variable improves the overall performance of the model in terms of residuals."

Americas↗

PubMed2003

Ecological and genetic spatial structuring in the Canadian lynx.

The Canadian lynx, distributed all across the northern part of North America, is well known for its regular population cycles-cycles that have different underlying structures in different parts of Canada. Using both nuclear and mitochondrial DNA markers, we report here a close resemblance between the earlier observed spatial ecological structuring of the Canadian lynx and its spatial genetic structuring. Specifically, we demonstrate that the Rocky Mountains represent a barrier to gene flow in western Canada, and, somewhat surprisingly, we detect the presence of a geographically invisible barrier south of Hudson Bay (coinciding with the separation between the ecological Continental and Atlantic regions). No evidence for isolation in different glacial refugia within North America was found. We suggest that ecological factors underlying the spatial dynamic structuring also strongly influence the genetic structuring of the Canadian lynx.

Animals↗

PubMed1992

[Study of the spatial structure of the duplex (Phn-NH(CH2)NH)pd(CCAAACA).pd(TGTTTGGC) with covalently bound 10-(2-hydroxyethyl)phenazine by in aqueous solution by 2D-(1)H-NMR and by limited molecular mechanics].

Detailed investigation of the spatial structure of duplex (Phn-NH(CH2)2NH) x pd(CCAAACA).pd(TGTTTGGC) having a covalently linked N-(2-hydroxyethyl)-phenazine in aqueous solution was continued by means of one- and two-dimensional 1H-NMR spectroscopy. Distances between the protons of the oligonucleotides as well as distances between the phenazinium and the nearest nucleotide groups protons were determined from the series of one-dimensional NOE experiments. The effective correlation time tau c determined for some proton pairs shows the phenazinium fragment to have greater internal motion than the heterocyclic bases. The deoxyribose protons coupling constants show the sugars to be in 2'-endo-conformation. The restrained molecular mechanics have yielded a possible structure of duplex in the aqueous solution fitting the experimental set of interproton distances.

Animals↗

PubMed1988

Solution spatial structure of 'long' neurotoxin M9 from the scorpion Buthus eupeus by 1H-NMR spectroscopy.

1H-NMR spectra of Buthus eupeus neurotoxin M9 (66 amino acid residues, four disulfide bonds) reveal two slowly exchangeable conformations at acidic pH. The spatial structure of the conformer prevailing under physiologically relevant conditions has been determined from two-dimensional 1H-NMR data treated by means of a distance geometry algorithm and refined by molecular modelling. Interrelation between the structure and function of mammalian neurotoxin M9 is discussed by comparing its conformation with those of the scorpion insectotoxins which exhibit different biological specificity (insectotoxins v-2, v-3 and I5A).

Amino Acid Sequence↗

PubMed2002

Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating.

Zervamicin IIB is a 16-amino acid peptaibol that forms voltage-dependent ion channels with multilevel conductance states in planar lipid bilayers and vesicular systems. The spatial structure of zervamicin IIB bound to dodecylphosphocholine micelles was studied by nuclear magnetic resonance spectroscopy. The set of 20 structures obtained has a bent helical conformation with a mean backbone root mean square deviation value of approximately 0.2 A and resembles the structure in isotropic solvents (Balashova et al., 2000. NMR structure of the channel-former zervamicin IIB in isotropic solvents. FEBS Lett 466:333-336). The N-terminus represents an alpha-helix, whereas the C-terminal part has a mixed 3(10)/alpha(R) hydrogen-bond pattern. In the anisotropic micelle environment, the bending angle on Hyp10 (23 degrees) is smaller than that (47 degrees) in isotropic solvents. In the NOESY (Nuclear Overhauser Effect Spectroscopy) spectra, the characteristic attenuation of the peptide signals by 5- and 16-doxylstearate relaxation probes indicates a peripheral mode of the peptaibol binding to the micelle with the N-terminus immersed slightly deeper into micelle interior. Analysis of the surface hydrophobicity reveals that the zervamicin IIB helix is amphiphilic and well suited to formation of a tetrameric transmembrane bundle, according to the barrel-stave mechanism. The results are discussed in a context of voltage-driven peptaibol insertion into membrane.

Anisotropy↗

PubMed1996

Metapopulations and equilibrium stability: the effects of spatial structure.

Recently, there has been a great deal of interest in the dynamics of metapopulations, where a number of local populations are coupled via dispersal. The importance of movement for the persistence of an ensemble of locally unstable patches has been established in many studies. In this paper, we present analytical and simulation results concerning the effects of spatial structure on the equilibrium stability of individual populations. We conclude that for general single-species and two-species competition models, the introduction of the spatial dimension in a biologically sensible way has no effect on the overall stability properties. In host-parasitoid models, however, strong host or parasitoid over-dispersal may be destabilizing.

Animals↗

PubMed1999

NMR spatial structure of alpha-conotoxin ImI reveals a common scaffold in snail and snake toxins recognizing neuronal nicotinic acetylcholine receptors.

A 600 MHz NMR study of alpha-conotoxin ImI from Conus imperialis, targeting the alpha7 neuronal nicotinic acetylcholine receptor (nAChR), is presented. ImI backbone spatial structure is well defined basing on the NOEs, spin-spin coupling constants, and amide protons hydrogen-deuterium exchange data: rmsd of the backbone atom coordinates at the 2-12 region is 0.28 A in the 20 best structures. The structure is described as a type I beta-turn (positions 2-5) followed by a distorted helix (positions 5-11). Similar structural patterns can be found in all neuronal-specific alpha-conotoxins. Highly mobile side chains of the Asp-5, Arg-7 and Trp-10 residues form a single site for ImI binding to the alpha7 receptor. When depicted with opposite directions of the polypeptide chains, the ImI helix and the tip of the central loop of long chain snake neurotoxins demonstrate a common scaffold and similar positioning of the functional side chains, both of these structural elements appearing essential for binding to the neuronal nAChRs.

Amino Acid Sequence↗

PubMed2003

Analysis on sensitivity and landscape ecological spatial structure of site resources.

This article establishes a set of indicators and standards for landscape ecological sensitivity analysis of site resources by using the theories and approaches of landscape ecology. It uses landscape diversity index (H), evenness (E), natural degree (N), contrast degree (C) to study spatial structure and landscape heterogeneity of site resources and thus provides a qualitative-quantitative evaluation method for land planning and management of small, medium scale areas. The analysis of Yantian District, Shenzhen of China showed that Wutong Mountain belonged to high landscape ecological sensitivity area, Sanzhoutian Reservoir and Shangping Reservoir were medium landscape sensitivity and high ecological sensitivity area; Dameisha and Xiaomeisha belonged to medium sensitivity area caused by the decline of natural ecological areas. Shatoujiao, Yantian Pier belonged to low sensitivity area but urban landscape ecological development had reshaped and influenced their landscape ecological roles in a great extent. Suggestions on planning, protection goals and development intensity of each site or district were raised.

China↗

PubMed2001

Increased coupling between subpopulations in a spatially structured environment can lead to population outbreaks.

Destruction and fragmentation of habitats is widely considered as a major threat to biological diversity. A theoretical framework aimed at understanding and predicting species responses to these destructive processes is still lacking, however. In this paper, the species dynamics in a spatially structured, two-habitat, patchy environment is considered subject to changes in individual migration intensity, i.e. coupling between the habitats. The subpopulation dynamics inside each habitat is assumed to be bistable but with different parameter values. By using space-discrete/continuous metapopulation dynamic models and computer simulations, we show that there can be two principally different regimes of metapopulation dynamics. With increasing intensity in the interplay between subpopulations, the total abundance can either gradually decrease or experience a sudden burst-like increase. This result is shown to be robust to the choice of mathematical models (discrete or continuous). Particularly, both the "self-excitation" and "self-inhibition" regimes of the metapopulation system are robust to variation in habitat size; however, when one of the habitats is much smaller than the other, the "self-excitation" regime can give way to the "self-inhibition" regime and vice versa.

Animals↗

PubMed1999

Spatial structure of the human alpha rhythm: global correlation in adults and local correlation in children.

OBJECTIVE: The maturation of the neocortex during childhood and adolescence involves dramatic increases in white-matter volume. EEG recordings from children and adults were examined to determine whether there are associated changes in spatial properties of dynamic processes in the neocortex. METHODS: Spontaneous eyes-closed and eyes-open EEG were recorded at 128 electrodes in 20 children aged 6-11 years and 23 adults aged 18-23 years. The surface Laplacian algorithm was applied to improve the spatial resolution of each electrode. Power and coherence were used to characterize the spatial structure of the alpha rhythm. A stochastic field model was used to eliminate coherences that are inflated due to volume conduction. RESULTS: In adults, the alpha rhythm is characterized by very high coherence between distant electrodes. The children demonstrated reduced anterior power and coherence between anterior and posterior electrodes at the peak alpha frequency in comparison to the adults. The Laplacian alpha rhythm demonstrated much higher power in the children at both anterior and posterior electrodes, but was weakly correlated between electrodes. CONCLUSIONS: The maturation of neocortex in late childhood involves increased global correlation by long-range corticocortical connections. The local correlation that contributes power to each electrode, independent of other electrodes, is reduced as the global correlation increases.

Adolescent↗

PubMed2002

Continuous B-epitope maps of cytochrome P450cam (CYP101) obtained by peptide scanning: correlation to spatial structure.

Protein continuous B-epitopes can be revealed using short synthetic peptides that overlap a known protein sequence. Since the whole protein surface is considered to possess antigenic properties, a question that arises is whether a set of linear B-epitopes determined by peptide scanning correlates with a protein spatial structure. We have chosen cytochrome P450cam (CYP101) of Pseudomonas putida, with known 3D structure, as a template. Sera of two rabbits and antibody egg yolk preparations from three chickens were produced against the P450cam molecule. These polyclonals were analyzed separately in ELISA with 409 overlapping P450cam hexapeptides. The whole set of continuous antigenic sites of P450cam covered about 45% of the P450cam sequence. However, immunodominant sites (those revealed with more than 50% antibody preparations), the so-called "antigenic core," represent only 9% of the protein sequence. While the amount of water-accessible residues in the total antigenic map (42%) was close to that in the whole native P450cam molecule (39%), the amount of water-accessible residues in the antigenic core was significantly higher (64%). These results led to the conclusion that antigenic core epitopes can be associated to the molecular surface, whereas epitopes with low detection frequency may partly correspond to unfolded regions of the protein molecule.

Animals↗

PubMed2000

[Spatial structure of a Fab-fragment of a monoclonal antibody to human interleukin-2 in two crystalline forms at a resolution of 2.2 and 2.9 angstroms].

The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 was determined in two crystal forms by the X-ray method of molecular replacement at 2.2 and 2.9 A resolutions. The spatial structure of the protein and the stereochemistry of its antigen-binding site were analyzed.

Amino Acid Sequence↗

PubMedDate not supplied

[Isolation, biological properties, and spatial structure of an antibiotic loloatin A].

Peptide antibiotic with cyanolytic activity was isolated from the IGM52 strain of the Brevibacillus laterosporus Gram-positive spore-forming bacteria. By 1H NMR spectroscopy, this antibiotic was identified as loloatin A, a cyclic decapeptide cyclo(-Asn-Asp-Tyr-Val-Orn-Leu-DTyr-Pro-Phe-DPhe-). The spatial structure of loloatin A in solution was determined. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.

Amino Acid Sequence↗