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PubMed1990

Three-dimensional structure of the oligosaccharide terminus of globotriaosylceramide and isoglobotriaosylceramide in solution. A rotating-frame NOE study using hydroxyl groups as long-range sensors in conformational analysis by 1H-NMR spectroscopy.

Spatial structures of the oligosaccharide parts of globotriaosylceramide, Gal(alpha 1-4)Gal(beta 1-4)Glc(beta 1-1)Cer (Cer = ceramide) and isoglobotriaosylceramide, Gal(alpha 1-3)Gal(beta 1-4)Glc(beta 1-1)Cer were investigated in (C2H3)2SO solution by means of laboratory and rotating frame NOE, hydroxyl protons being used as long-range sensors defining the distance constraints. Both oligosaccharides were found to exist in more than one conformation interconverting rapidly on the NMR time scale. The conformation of the Gal(alpha 1-4)Gal(beta 1-4)Glc beta trisaccharide dissolved in 2H2O appeared to be the same as that of the corresponding part of the glycosphingolipid in (C2H3)2SO solution.

Carbohydrate Conformation↗

PubMedDate not supplied

[Biopolymers and evolution].

Biopolymers are usually studied being extracted from the whole system of a cell or of an organism. Some important features are lost during such a procedure. It is necessary to take into account the behavior of proteins and nucleic acids in metabolic networks and to investigate their evolution. The substitutions of amino-acids metabolic networks residues are biologically possible in the polypeptides and proteins if they do not influence their spatial structure and function. The correlations of the primary structure with these properties are degenerate. The protein can be treated as "an edited statistical copolymer" (Ptitsyn). In the process of "edition" an important role is played by the ions of transient metals. Nucleic acids possess similar properties. It can be shown that the deleterious mutations of proteins can be compensated by the changes of their amount, spatial and temporal characteristics of the synthesis. Not only the structure of the protein is important but also the exact answers of the questions: how much, when and where? The contemporary theory of evolution unites phylogeny and onthogeny. The directionality of evolution is determined both by natural selection and by the already existing structure of an organism. Hence many characters are not adaptive. This is valid also for the molecular level of the structure. Thus three independent groups of facts and suggestions are presented, which confirm the neutral theory of evolution (Kimura) and elucidate its physical meaning. The molecular evolution does not coincide with the biological evolution.

Amino Acid Sequence↗

PubMed2005

Exploring the spatial pattern of mental health expenditure.

BACKGROUND: Recent years have witnessed growing interest in cross-sectional variations in municipality mental health expenditure. However, empirical work to date has not examined the links between such variability and demand and supply factors, particularly in the spatial domain. AIMS OF THE STUDY: The aim is to examine whether a local authority's spending decisions in the mental health field respond to neighbouring expenditure decisions. We explore a number of reasons why there might be interdependence between local authorities' decisions, labelling them the demonstrative, market leader, contextual, directive, shared resource and inducement effects. METHODS: Exploratory techniques from spatial data analysis are used to test for the existence of spatial structure. Drawing hypotheses from these initial exploratory analyses, we then adopt a reduced form demand and supply model, extended to incorporate possible policy interaction. The analysis of expenditure and cost variations has traditionally been based on regression models under the classical assumption that the observations are independent. But omitting the recognition that observations are interdependent might lead to erroneous statistical conclusions. Hence, we use spatial econometric techniques that explicitly take into account the potential interdependence of data in order to study the sources of spending variation between municipalities. RESULTS: The exploratory data analyses reveal the presence of positive significant spatial correlation. Per capita mental health spending distributes in clusters, with the highest concentrations in metropolitan areas such as Greater London, Greater Manchester and Birmingham. The estimated spatial regression models indicate that spatial autocorrelation characterises local expenditure decisions, consistent with some degree of policy interdependence between neighbouring municipalities. Comparing the results from our spatial model with those from a classical ('non-spatial') model suggests that the differences in the regression coefficients could be explained by the evident spatial pattern of the phenomenon, since the omission of the lagged dependent variable induces bias in the OLS estimates. IMPLICATIONS FOR HEALTH POLICIES: These results help central and local decision makers understand the factors that influence local spending levels, including variations between municipalities in their achievement of expenditure-related and perhaps other performance targets. The actual patterns of spatial interaction may well be more complex than simple contiguity (the structure assumed here), but there seems little doubt that positive interdependence is an important feature of decision making. IMPLICATIONS FOR FURTHER RESEARCH: Statistical interrogation of a panel dataset would allow exploration of both time-series and cross-municipality variation in mental health expenditure. Subsequent analysis would also benefit from more disaggregated data (e.g. at a census ward level) and the accompanying use of spatial multilevel techniques.

Adolescent↗

PubMed1987

Chemistry and biochemistry of metallothionein.

A wealth of chemical, spectroscopic and structural data attest to the uniqueness of the metallothioneins as a group of novel bioinorganic structures. Their earmarking feature is the arrangement of "soft" metal ions in complexes with cysteine side chains to form discrete metal-thiolate clusters. In this review an account is given of the chemical characteristics of the 52 metallothioneins whose primary structures are now known completely or in part. Also included is an up-to-date summary of the spectroscopic properties and of the spatial structure models derived from X-ray diffraction crystallographic analysis and from two-dimensional nuclear magnetic resonance spectroscopy.

Amino Acid Sequence↗

PubMedDate not supplied

Synapses in hippocampus occupy only 1-2% of cell membranes and are spaced less than half-micron apart: a quantitative ultrastructural analysis with discussion of physiological implications.

Relatively little information exists regarding the spatial structure of synaptic neuropil in the brain. The present electron microscopic study employs unbiased stereological techniques and Monte Carlo simulations to characterise quantitatively the spatial organisation of synaptic circuitry in the dentate gyrus of the hippocampus, an area of particular importance in mechanisms of learning and the subject of a number of experimental neurobiological models of synaptic plasticity such as long-term potentiation. Firstly, tissue shrinkage/expansion resulting from embedding was assessed by imaging 300-microm thick hippocampal slices in the course of the entire embedding protocol, giving a value of 94.3 +/- 1.1% for distance measures and 84.3 +/- 2.8% for volumetric measures. Secondly, numeric synaptic density, Nv, was estimated using the disector. Thirdly, accumulated area of post-synaptic densities (PSDs) per tissue volume, Sv, and the overall cell membrane area per tissue volume, Sv*, were assessed using unbiased stereological rules coupled with image analysis of single sections. Finally, the mean area of individual PSDs was derived as a ratio Sv/Nv giving: 0.0394 microm2 for axo-spinous PSDs (thus representing approximately 1.3% of total cell membranes) and 0.0769 microm2 for dendritic shaft PSDs (approximately 0.25% of total cell membranes). From these data, the mean nearest neighbour distance between synapses was estimated using Monte Carlo simulations of a random 3D arrangement of synapses constrained by PSD sizes (a truncated Poisson process), giving a value of 0.48-0.51 microm. The physiological importance of the morphometric data obtained is discussed in terms of assessing (i) the role of synaptic environment in modifying synaptic efficacy and (ii) the plausibility of cross talk between synapses in relation to extrasynaptic neurotransmitter diffusion and transient depletion of extracellular Ca2+.

Animals↗

PubMed2006

Scale invariance and universality of force networks in static granular matter.

Force networks form the skeleton of static granular matter. They are the key factor that determines mechanical properties such as stability, elasticity and sound transmission, which are important for civil engineering and industrial processing. Previous studies have focused on investigations of the global structure of external forces (the boundary condition) and on the probability distribution of individual contact forces. So far, however, precise knowledge of the disordered spatial structure of the force network has remained elusive. Here we report that molecular dynamics simulations of realistic granular packings reveal scale invariance of clusters of particles interacting by means of relatively strong forces. Despite visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, thereby determining a universality class. Unexpectedly, the flat ensemble of force configurations (a simple generalization of equilibrium statistical mechanics) belongs to this universality class, whereas some widely studied simplified models do not. This implies that the elasticity of the grains and their geometrical disorder do not affect the universal mechanical properties.

Journal Article↗

PubMed1997

Design of aromatic inhibitors of influenza virus neuraminidase.

Structure-based drug design, a terminology used to describe rational drug design by complementing the structure, spatially and chemically, of the target macromolecule, is rapidly developing as one of the innovative approaches to drug discovery. A growing volume of protein structure data and new techniques of protein structure determination make this all possible. The method of structure-based drug design and a specific example of the design of influenza virus neuraminidase is briefly presented. A whole new class of influenza virus neuraminidase inhibitors has been designed that can potentially be developed as antiinfluenza drugs.

Antiviral Agents↗

PubMed1978

Characterisation of a local structure in the synthetic parathyroid hormone fragment 1--34 by 1H nuclear-magnetic-resonance techniques.

Previous studies had shown that the molecular conformation of the synthetic human parathyroid hormone fragment 1--34 in dilute aqueous solution contained a local non-random structure formed by the four consecutive residues--Val-21--GIn-22--Trp-23--Leu-24--. This paper gives a detailed description of this local spatial structure obtained from high resolution 1H NMR studies at 360 MHZ of several peptide analogs of the partial sequence 20--24. The most important spectral parameters were high-field shifts of the alpha and gamma protons of Val-21, the spin-spin coupling constants related to the rotamer populations of the side-chains of Val-21 and Trp-23, and pH titration shifts of the amide proton resonances. It was found that the backbone fragment 20--24 is so arranged that the side-chain of Val-21 is located next to the indole ring plane of Trp-23; evidence is presented that this non-random structure is mainly stabilized by hydrophobic interactions between the side-chains of Val-21 and Trp-23. The thermal population of the observed molecular structure at room temperature was estimated from the nuclear magnetic resonance data to be approximately 20%.

Amino Acid Sequence↗

PubMed1995

Global dimensional complexity of the EEG in healthy volunteers.

In contrast to the single-channel dimensional complexity, the global dimensional complexity is calculated from a multichannel EEG. The intention with the method is to measure the spatial distribution of information processing in the brain. The method seems to be of interest in psychopharmacological research, but the interpretation of the results in physiological terms is rather difficult. To get a more detailed information on the physiological significance of the EEG complexity measures, the influence of well-known physiological factors was studied in a group of 14 healthy subjects aged from 1.5 to 61 years. It was found that the correlation dimension was somewhat higher in older individuals, but the correlation with age was not statistically significant. However, the global correlation dimension was significantly lower during full alertness than during drowsiness. These results might reflect the changes in spatial structure of information processing, a high complexity suggesting a 'disorganisation' during drowsiness. As regards the age-dependent changes of the correlation dimension, the spatial 'flexibility' of information processing was also studied, using the differences between the 'alert' and 'drowsy' parts of the same EEG as indicator. It was found that the differences 'drowsy minus alert' were significantly related to age. A plausible interpretation seems to be that the spatial distribution of information processing is more changeable, or more flexible, in adults than in children.

Adolescent↗

PubMed2000

Effect of ethanol on structural transitions of DNA and polyphosphates under Ca2+ ions action in mixed solutions.

In the present work using the IR spectroscopy method the effect of ethanol on structural transitions of DNA and polyphosphates under the action of Ca2+ ions in mixed solutions containing ethanol (0-25 vol.%) was studied. It was shown that, on its interaction with Ca2+ ions, in aqueous and mixed solutions DNA becomes transformed into compact form. With the increase of concentration of ethanol the degree of Ca2+-induced DNA compactisation rises. It was found that, in mixed solutions containing ethanol, Ca2+-induced DNA compactisation depends not only on the solution's dielectric permeability but also on the solution structure. On stabilisation of the water structure in the presence of low ethanol concentrations a stabilisation of the DNA macromolecule occurs that leads to the increase of the Ca2+ ion concentration necessary for DNA compactisation. Comparison of the effects of ethanol on Ca2+-induced structural transitions in DNA and polyphosphates in mixed solvents permits to suppose that at alcohol concentrations in solution resulting in disruption of the water spatial structure, some peculiarities are observed in the behavior of those molecules whose hydrophobic interactions are essential.

Calcium↗

PubMed2003

Spatial channels of visual processing in cortical blindness.

Blindsight is the ability of some cortically blind patients to discriminate visual events presented within their field defect. We have examined a fundamental aspect of visual processing, namely the detection of spatial structures presented within the field defect of 10 cortically blind patients. The method outlined is based on the detection of high-contrast stimuli and is effective in flagging a 'window of detection' in the spatial frequency spectrum, should it exist. Here we report on the presence of a narrowly tuned psychophysical spatial channel optimally responding to frequencies less than 4 cycles/ degrees in eight out of 10 patients tested. The two patients who did not show any evidence of blindsight appear to have intact midbrain structures, but have lesions that extend from the occipital cortex to the thalamus. In addition, we have recorded subjective reports of awareness of the visual events in each trial. Detection scores of eight blindsight patients were subsequently subdivided based on the subjective reports of awareness. It appears that the psychophysical spatial channel-mediating responses in the absence of any awareness of the visual event have a narrower frequency response than those involved when the patients report some awareness of the visual event. The findings are discussed in relation to previous reports on the incidence of blindsight and performance on tasks involving spatial processing.

Adult↗

PubMed1999

Solution of the nerve cable equation using Chebyshev approximations.

The propagation of excitation along the dendrites and the axon of a neurone is described by a partial differential equation which is nonlinear when voltage-gated conductances are present. In this case, numerical methods are employed to obtain a solution: the evolution of the membrane potential in space and time. Even when the membrane is passive (linear), numerical methods might still be preferred to analytical ones that are often too cumbersome to obtain. In this paper, we present the Chebyshev pseudospectral or collocation method as an alternative to the hitherto commonly used finite difference schemes (compartmental models) that are based on sufficiently fine equidistant subdivisions of the spatial structure (dendrites or axon). In the Chebyshev method, solutions are approximated by finite Chebyshev series. The solutions have uniform, usually high, numerical accuracy at any spatial point, not only at the original collocation points. Often, truncation errors become negligible, hence, the total error is essentially the rounding error of the computations. Furthermore, quantities involving spatial derivatives, and in particular the axial current, can be computed exactly from the solution, i.e. the membrane potential. Space-dependent parameter distributions (channel densities, non-uniform dendritic geometries), as well as mixed linear boundary conditions can easily be implemented, and can be chosen from the large class of piecewise smooth functions.

Animals↗

PubMed1997

Self-organization of microtubules and motors.

Cellular structures are established and maintained through a dynamic interplay between assembly and regulatory processes. Self-organization of molecular components provides a variety of possible spatial structures: the regulatory machinery chooses the most appropriate to express a given cellular function. Here we study the extent and the characteristics of self-organization using microtubules and molecular motors as a model system. These components are known to participate in the formation of many cellular structures, such as the dynamic asters found in mitotic and meiotic spindles. Purified motors and microtubules have previously been observed to form asters in vitro. We have reproduced this result with a simple system consisting solely of multi-headed constructs of the motor protein kinesin and stabilized microtubules. We show that dynamic asters can also be obtained from a homogeneous solution of tubulin and motors. By varying the relative concentrations of the components, we obtain a variety of self-organized structures. Further, by studying this process in a constrained geometry of micro-fabricated glass chambers, we demonstrate that the same final structure can be reached through different assembly 'pathways.

Animals↗

PubMed1998

Learning from the pupil: a spatial visual channel in the absence of V1 in monkey and human.

The pupil of the normal human subject constricts in response not only to average increases in light energy, but also selectively to the spatial structure of a visual stimulus even when there are no energy changes. This enables one to measure visual acuity and sensitivity as a function of spatial frequency. It is known that pupillometric measures of acuity correlate well with those determined psychophysically for normal human observers. The purpose of the present study was to measure pupillary changes with stimuli delivered to the 'blind' hemifields of monkeys with unilateral V1 removal, and also with stimulation of a human subject (G.Y.) with putative V1 destruction. The results show that there are small but reliable pupillary changes to flux-equated gratings in the blind fields both in monkeys and human. The response profile in both species is very similar: it is narrowly tuned, with a peak at approximately 1 cycle/degree and a cut-off acuity of approximately 7 or 8 cycles/degree, a significant reduction compared with the intact hemifield. The result also maps well onto the psychophysically determined spatiotemporal response profile to gratings in the blind field, as determined independently for G.Y. Thus, there is a narrowly tuned spatial visual channel that does not require the integrity of V1 in monkey or human. There was no evidence under these particular conditions in either monkeys or subject G.Y. of a pupillary response to an equiluminant change from white to green or red in the hemianopic field. The pupil holds promise as a non-verbal, indirect method for determining the spatial profile, sensitivity and other properties of residual visual capacity, both in animals and humans.

Adult↗

PubMed2006

A continuum mechanical model of mechanoreceptive afferent responses to indented spatial patterns.

Information about the spatial structure of tactile stimuli is conveyed by slowly adapting type 1 (SA1) and rapidly adapting (RA) afferents innervating the skin. Here, we investigate how the spatial properties of the stimulus shape the afferent response. To that end, we present an analytical framework to characterize SA1 and RA responses to a wide variety of spatial patterns indented into the skin. This framework comprises a model of the tissue deformation produced by any three-dimensional indented spatial pattern, along with an expression that converts the deformation at the receptor site into a neural response. We evaluated 15 candidate variables for the relevant receptor deformation and found that physical quantities closely related to local membrane stretch were most predictive of the observed afferent responses. The main outcome of this study is an accurate working model of SA1 and RA afferent responses to indented spatial patterns.

Action Potentials↗

PubMed2006

Dispersal limitation and environmental heterogeneity shape scale-dependent diversity patterns in plant communities.

Understanding the large-scale distribution of species diversity requires distinguishing two of the primary factors that cause compositional differences: dispersal limitation and environmental variation. In a community with a naturally discontinuous spatial structure, we asked (1) at what scale(s) nonrandom variation in species composition occurs and (2) at what scale(s) such variation is associated with spatial separation, indicative of dispersal limitation, and at what scale(s) variation is associated with environmental heterogeneity? We sampled 50 seeps (small wetlands) on five serpentine outcrops. Using a randomization model, we showed that additive beta diversity (a measure of community dissimilarity) was lower than random within seeps and higher than random among both seeps and outcrops. Using Mantel tests, we showed that plant community dissimilarity, in both the full seep assemblage as well as in a subset of seep endemics, at the two larger scales was associated with different forms of environmental heterogeneity and, at the largest scale, was also associated with geographic distance. We conclude that diversity in this system is shaped by multiple scales of heterogeneity and by dispersal limitation at the largest scale.

Biodiversity↗

PubMedDate not supplied

[Tertiary structure of myelopeptides. II. Conformational analysis of Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro, Val-Val-Tyr-Pro-Asp, and Val-Asp-Pro-Pro].

Theoretical conformational analysis was used to study the spatial structure and conformational properties of myelopeptides, bone marrow peptide mediators. The low-energy conformations of myelopeptides MP-4 (Phe-Arg-Pro-Arg-Ile-Met-Thr-Pro), MP-5 (Val-Val-Tyr-Pro-Asp), and MP-6 (Val-Asp-Pro-Pro) were found; the values of dihedral angles of backbone and side chains of the amino acid residues were determined; and the energies of intra- and interresidual interactions were estimated.

Amino Acid Sequence↗

PubMed1983

Conformation of glucagon in a lipid-water interphase by 1H nuclear magnetic resonance.

A determination of the spatial structure of the polypeptide hormone glucagon bound to perdeuterated dodecylphosphocholine micelles is described. A map of distance constraints between individually assigned hydrogen atoms of the polypeptide chain was obtained from two-dimensional nuclear Overhauser enhancement spectroscopy. These data were used as the input for a distance geometry algorithm for computing conformations that would be compatible with the experiments. In the region from residues 5 to 29 the mobility of the polypeptide backbone and most of the amino acid side-chains was found to be essentially restricted to the overall rotational tumbling of the micelles. The secondary structure in this region includes three turns of irregular alpha-helix in the segment of residues 17 to 29 near the C terminus, a stretch of extended polypeptide chain from residues 14 to 17, an alpha-helix-like turn formed by the residues 10 to 14 and another extended region from residues 5 to 10. In the N-terminal tetrapeptide H-His-Ser-Gln-Gly- the two terminal residues are highly mobile, indicating that they extend into the aqueous phase, and the mobility of the residues Gln3 and Gly4 appears to be only partially restricted by the binding to the micelle. The absence of long range nuclear Overhauser effects between the peptide segments 5-9 and 11-29, and between 5-16 and 19-29 shows that the polypeptide chain does not fold back on itself and hence that micelle-bound glucagon does not adopt a globular tertiary structure. Previously it was shown that the polypeptide backbone of glucagon is located close to and runs roughly parallel to the micelle surface. Combination of these observations suggests that the overall spatial arrangement of the glucagon polypeptide chain in a lipid-water interphase is largely determined by the topology of the lipid support, in the present case the curvature of the dodecylphosphocholine micelles. The tertiary structure is further characterized by the formation of two hydrophobic patches by the side-chains of Phe6, Tyr10 and Leu14, and the side-chains of Ala19, Phe22, Val23, Trp25 and Leu26, respectively.

Amino Acid Sequence↗