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PubMed2003

Molecular simulation of a single-chain antibody against AChE to explore molecular basis of inhibitory effect of 3F3 McAb on enzyme activity.

AIM: To explore the molecular basis of the inhibitory effect of 3F3, a monoclonal antibody against acetylcholinesterase (AChE), by computer-aided molecular simulation. METHODS: The single-chain 3F3 antibody (Sc3F3) was designed by joining VH and VL via a flexible linker (Gly4Ser)3. The amino acid sequence of the recombinant Sc3F3 was then subjected to computer-aided molecular modeling, and docking with the antigen molecule AChE to mimic the immunoactive interaction in a three-dimensional fashion. RESULTS: The modeled structure of Sc3F3 manifested the common features of a classical antibody. Both VH and VL were composed of two ?-sheets and connecting loops. The docking profile of the action between Sc3F3 with AChE demonstrated the formation of a stable structure. The van der Waals force played an important role suggesting that the complex was formed mainly via hydrophobic interactions between Sc3F3 and AChE molecules. CONCLUSION: The spatial structure of the complex of Sc3F3 and AChE showed that Sc3F3 overlaid the entrance of the active center gorge of AChE blocking the access of substrate.

Acetylcholinesterase↗

PubMed2006

Population proteomics: an emerging discipline to study metapopulation ecology.

Proteomics research has developed until recently in a relative isolation from other fast-moving disciplines such as ecology and evolution. This is unfortunate since applying proteomics to these disciplines has apparently the potential to open new perspectives. The huge majority of species indeed exhibit over their entire geographic range a metapopulation structure, occupying habitats that are fragmented and heterogeneous in space and/or through time. Traditionally, population genetics is the main tool used to studying metatopulations, as it describes the spatial structure of populations and the level of gene flow between them. In this Viewpoint, we present the reasons why we think that proteomics, because of the level of integration it promotes, has the potential to resolve interesting issues specific to metapopulation biology and adaptive processes.

Animals↗

PubMed2005

Flicker-induced color and form: interdependencies and relation to stimulation frequency and phase.

Our understanding of human visual perception generally rests on the assumption that conscious visual states represent the interaction of spatial structures in the environment and our nervous system. This assumption is questioned by circumstances where conscious visual states can be triggered by external stimulation which is not primarily spatially defined. Here, subjective colors and forms are evoked by flickering light while the precise nature of those experiences varies over flicker frequency and phase. What's more, the occurrence of one subjective experience appears to be associated with the occurrence of others. While these data indicate that conscious visual experience may be evoked directly by particular variations in the flow of spatially unstructured light over time, it must be assumed that the systems responsible are essentially temporal in character and capable of representing a variety of visual forms and colors, coded in different frequencies or at different phases of the same processing rhythm.

Adult↗

PubMed1992

Population genetics and dynamics of Plasmodium falciparum: an ecological view.

Molecular characterization of the Plasmodium falciparum genome has led to identification of polymorphic loci and the mechanisms generating genetic diversity in this parasite. This information has resulted in the development of molecular methods to type parasite diversity in the field. Consequently, we are now in a position to describe the population genetics and dynamics of P. falciparum. The limited number of field studies that have been conducted to date have revealed an extraordinary degree of genetic diversity in natural parasite populations. Heterozygous recombination which occurs during meiosis appears to be one mechanism for generating genetic diversity. The rate at which such recombination occurs in natural parasite populations defines the genetic structure of the parasite population and can influence the ability of the parasite to respond to selection pressure. The high frequency of single genotype infections and the female-biased gametocyte sex ratios found in hyperendemic malaria areas suggest that self-fertilization occurs frequently. Population-wide surveys of allele frequencies in endemic areas have, however, shown no evidence of linkage disequilibrium and are consistent with a panmictic population structure. We argue that these studies have only sampled symptomatic infections, within which rare or recombinant genotypes may be disproportionately represented. They also take no account of the spatial structure of P. falciparum populations. Systematic investigations of the amount of heterozygosity in small areas as part of population-wide surveys are required to define the genetic structure of P. falciparum populations. Population dynamic studies which consider genetic heterogeneity of P. falciparum have shown fluctuations of different serotypes in space and time. The host immune response appears to play an important role in generating these dynamics. Integrated field and laboratory studies, which consider the interaction between population genetics and dynamics, will be necessary to describe the population biology of P. falciparum.

Animals↗

PubMed2004

Spatial and temporal structure of edge-localized modes.

This Letter provides information on the spatial and temporal structure of periodic eruptions observed in magnetically confined laboratory fusion plasmas, called edge-localized modes (ELMs), and highlights similarities with solar eruptions. Taken together, the observations presented in this Letter provide strong evidence for ELMs being associated with a filamentlike structure. These filaments are extended along a field line, are generated on a 100 micros time scale, erupt from the outboard side, and connect back into the plasma. Such structures are predicted by a theoretical model based on the "ballooning" instability, developed for both solar and tokamak applications.

Journal Article↗

PubMed2004

Geographical Information System (GIS) as a tool for monitoring and analysing pesticide pollution and its impact on public health.

Geographical Information System (GIS) combines information from cartography sources (i.e. maps), earthbound surveys, remote sensing (i.e. aerial and satellite imagery) and creates overlapping layers that can be accessed, transformed, and manipulated interactively in one spatial structure. Thanks to the great flexibility of GIS, its possible applications are countless. For example, dynamic databases created by GIS can manage information from various sources and make spatial correlations with epidemiological data about temporal distribution of environmentally-related diseases. GIS has also been increasingly used to monitor, analyse and model pesticide migration in the environment. GIS analysis has proved to be a valuable tool in environmental and public health studies yielding important results that may ultimately help prevent excessive or uncontrolled exposure to xenobiotics, including pesticides. Despite its obvious advantages GIS technology is still not commonly used for such studies, particularly in the developing countries where the knowledge about GIS technology and its accessibility is limited. The presented review briefly explains the basic features of GIS and discusses exemplary studies where this technology has been successfully used for monitoring and analysing pesticide pollution and its impact on public health.

Databases, Factual↗

PubMed1997

Modeling of in vivo proteolytic degradation of hemoglobin.

Based on the amino acid sequences of endogenous peptides and X-ray spatial structure, mechanism of the in vivo proteolly degradation of bovine hemoglobin was analysed. The degradation was shown to be a multi-stage process. Its first stage is determined by the spatial organization of the native protein substrate, and the next stages-by the distribution of the electrostatic field potential of the protein fragments formed at the earlier stage.

Amino Acid Sequence↗

PubMed1995

H2O2-treated actin: assembly and polymer interactions with cross-linking proteins.

During inflammation, hydrogen peroxide, produced by polymorphonuclear leukocytes, provokes cell death mainly by disarranging filamentous (polymerized) actin (F-actin). To show the molecular mechanism(s) by which hydrogen peroxide could alter actin dynamics, we analyzed the ability of H2O2-treated actin samples to polymerize as well as the suitability of actin polymers (from oxidized monomers) to interact with cross-linking proteins. H2O2-treated monomeric (globular) actin (G-actin) shows an altered time course of polymerization. The increase in the lag phase and the lowering in both the polymerization rate and the polymerization extent have been evidenced. Furthermore, steady-state actin polymers, from oxidized monomers, are more fragmented than control polymers. This seems to be ascribable to the enhanced fragility of oxidized filaments rather than to the increase in the nucleation activity, which markedly falls. These facts; along with the unsuitability of actin polymers from oxidized monomers to interact with both filamin and alpha-actinin, suggest that hydrogen peroxide influences actin dynamics mainly by changing the F-actin structure. H2O2, via the oxidation of actin thiols (in particular, the sulfhydryl group of Cys-374), likely alters the actin C-terminus, influencing both subunit/subunit interactions and the spatial structure of the binding sites for cross-linking proteins in F-actin. We suggest that most of the effects of hydrogen peroxide on actin could be explained in the light of the "structural connectivity," demonstrated previously in actin.

Actinin↗

PubMed1998

Elucidation of a new biological function of an old protein: unique structure of the cobra serum albumin controls its specific toxin binding activity.

Although few proteins have been studies as thoroughly as serum albumin, a new biological property of this evolutionary ancient protein was recently discovered: The ability of cobra serum albumin (CSA) to specifically sequester lethal endogenous toxins. A study of the structural basis of this property is reported in this contribution. Two independent approaches were used to alter the structure of the CSA at defined positions: Directed mutagenesis and limited proteolysis. The conserved pattern of the disulfide linkages in the primary structure of the serum albumins showed in the case of the cobra snake (Naja naja kaouthia) an anomaly at C11 and C502, which suggested the existence of a unique spatial structure in this protein. The two cysteine residues were singly replaced with the consensus residue, i.e. C11-->F and C502-->T. The former substitution increased the specific neurotoxin binding capacity of the CSA by the factor 1.7 +/- 0.2, whereas the latter replacement reduced it to (25 +/- 2)%. The limited proteolysis yielded the large tryptic peptides T60, T40, T30 and T18, which after isolation by PAGE followed by HPLC had retained a strong toxin affinity. The location of these peptides in the amino-acid sequence was identified by Edman degradation and suggested the order of their release. On the basis of these data, a model of the unfolding and of the activity changes of the CSA caused by the structural perturbations was composed and the kinetic parameters associated with the process were evaluated. The results support the hypothesis of the existence of a structure of multiple homologous domains with a disulfide linkage between C11 and C502 in the native CSA that joins the chain ends to form a dense conformation.

Animals↗

PubMed1999

Microspatial genetic structure in the land snail helix aspersa (Gastropoda: helicidae)

The microspatial genetic structure of allele frequencies at seven isozyme loci was examined for 15 populations of the land snail Helix aspersa sampled in a village from Brittany (north-western France). Spatial heterogeneity of allele frequencies was highly significant (P < 0.001). Fixation indices reflected nonrandom mating within neighbourhoods and a slight but consistent differentiation between colonies (FST=0.044; P < 0.01). Analyses of gene flow or genetic distances failed to reveal a significant relationship with geographical distance, probably because of the complexity of environmental heterogeneity. However, matrix comparisons between genetic distances and connectivity networks among adjacent colonies (Gabriel-connected graph) yielded a significant correlation in every case, indicating a 'step-by-step' relationship between neighbouring localities. Moreover, most of the allozymes were spatially structured and showed (i) a gradual isolation of colonies with increasing geographical distances, and (ii), for some correlogram profiles, a circular gradient illustrating a multidirectional colonization of the village. The probable existence of disperser individuals allowed us to suggest a metapopulation model which would explain the maintenance of such animals in fragmented habitats where anthropogenic disturbances and extinction/recolonization events are commonly observed.

Journal Article↗

PubMedDate not supplied

A spatial analysis of 100 surnames in England and Wales.

Spatial patterns are described and analysed for the 84 most common surnames in England and Wales, as well as 16 others selected for various reasons. At least three-quarters of the surname frequencies show spatial structure and are heterogeneous over the area of study. While they do not exhibit clines extending over the entire area of study, they do divide into four characteristics patterns. Spatial autocorrelation, while significant, is relatively low; similarity in surname frequency does not extend much beyond 100 km. Correlograms could be clustered to yield groups of surfaces denoting partial clines, isolation by distance, and differentiation at far distances. A method for detecting zones of rapid change found 21 such zones, mostly near the periphery of the study area. These boundaries do not indicate barriers to gene flow, but appear to be patterns brought about by historical factors. There are diffusion patterns between areas that differ greatly in surname composition, such as Wales and central England. There is little evidence of long-distance movements involving several surnames. At least three characteristic migration patterns, east-west and north-south diffusion and local dispersal, were found.

England↗

PubMed2003

Peptidylprolyl cis/trans isomerases (immunophilins): biological diversity--targets--functions.

Information recovered from genome sequencing projects, multiple sequence alignments, structural analyses of PPIase and published records were used in deciphering the biological diversity, functions and targets of four groups of proteins encoded by dissimilar sets of sequences whose spatial representations exhibit peptidylprolyl cis/trans isomerase activity (PPIase). In the human genome there are encoded fifteen proteins whose segments have significant homology with the sequence of 12 kDa protein which is the target of the potent immunosuppressive macrolides FK506 or rapamycin. The 12 kDa archetype of the FK506-binding protein (FKBP), known as FKBP-12a, is an abundant intracellular protein whereas other FKBPs possessing from one to four FK506-like binding domains (FKBDs) have nominal masses varying from 13 to 135 kDa. The human genome contains at least sixteen genes encoding proteins comprising one cyclosporin-A (CsA) binding domain (CLD) called cyclophilins whose nominal masses vary from 17 to 324 kDa and multiple coding segments for small cyclophilins (17-19 kDa) whose transcription levels and functions remain unknown. The third group of PPIases encoded in the genome comprises two proteins (hPin1 and hParv14) where hPin1 is an important PPIase for cell cycle. The A. thaliana, C. elegans, D. melanogaster and S. cerevisiae genomes encode a less diverse spectrum of PPIases whereas the prokaryotic genomes contain from none to three cyclophilins, from none to four genes encoding FKBPs, one distant homologue of the Pin1 protein named parvulin and the fourth group of PPIases known as trigger factors. PPIases are discretely distributed to different cellular compartments and interact with a number of targets that control a range of cellular processes. Analyses of the sequence alignments of the two groups of PPIases, namely cyclophilins and FKBPs from diverse phyla, show that in each group their sequences diverge but the amino acid residues which form the PPIase activity site and macrolide binding cavity remain well conserved in the majority of them which suggests that the spatial structures and functions of each group of PPIases remain conserved.

Amino Acid Sequence↗

PubMed1989

[Amino acid sequence of Ondatra myoglobin (Ondatra zibethica). Characteristic features of myoglobins from semiaquatic animals].

Based on the amino acid composition of globin, amino acid analysis and N-terminal sequencing of peptides as well as a comparative analysis of the primary structure of beaver, coypu rat and otter myoglobins with the use of the fingerprinting technique, the amino acid sequence of the major component of ondatra myoglobin including 153 amino acid residues was reconstructed. The results of a comparative analysis of the primary structure of myoglobin and the peculiarities of the functional morphology of myoglobins from semi-aquatic animals and sperm whale and the role of amino acid substitutions in the spatial structure of ondatra myoglobin are discussed.

Amino Acid Sequence↗

PubMed2001

[Landscape structure and greenland spatial pattern in workshop district of Wuhan Iron and Steel Company].

The landscape structure and greenland spatial pattern in the workshop district of Wuhan Iron and Steel Company were investigated and analyzed on the basis of landscape ecological theory. The results showed that the main parts of the landscape structure were the artificial landscape elements such as building and concrete covering patches, highway and railway bed corridors, and industrial reservations. All of these artificial landscape elements accounted for 74.37% of patch area and 57.70% of patch dominance. In the landscape, the building and concrete covering land had the maximum percentage of patch area (56.43%) and the maximum dominance (35.59%). The special purpose greenlands had the highest fragmentation index (5.0591 ind.hm-2) and the wide-ranging distribution. The corridor density (13.78 km.km-2) was high, and the highway had more effects on landscape than the railway. All the results reflected not only the essential landscape features of industrial region, but also the rational trend of landscape structure in the workshop district of Wuhan Iron and Steel Company. In the greenland, the road greenbelts had the maximum patch number, area percentage (66.07%), and dominance (75.31%), the shelter forests being mainly composed of tree species had high patch average area (8454.45 m2) and environmental benefit, and the ornamental greenlands had abundant plant species and varied scenery. The greenland system was initially formed by four afforestation districts, using shelter forests and ornamental greenlands in large patch as a center connected by road greenbelts. It should be attached importance to the relatively high dominance of wild grasslands, the low area percentage of shelter forests and the imperfect road greenbelts to develop the uncovered lands and to improve the quality of the greenland system.

China↗

PubMed2005

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology.

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.

Analysis of Variance↗

PubMedDate not supplied

[Semiempirical calculations of the structure of apamine].

Conformational properties of the neurotoxin apamine were investigated starting from the known amino acid sequence. Nonvalent and electrostatic interactions, hydrogen bonding and torsional energies were computed by variation of all backbone and side chain dihedral angles. In a search for the spatial structure of the molecule, di-, tri-, tetra- etc. fragments were subsequently analyzed. As the result, the apriori calculations of the 15-residue apamine fragment revealed strong energy differentiations of forms. The lowest energy conformation has a folded backbone, with an orientation of Cys-1--Cys-11 and Cys-3--Cys-15 side chain pairs favoring the formation of disulfide bridges.

Apamin↗

PubMed1995

Purification and characterization of human pancreatic polypeptide expressed in E. coli.

The region of cDNA encoding human pancreatic polypeptide (hPP) was obtained by polymerase chain reaction (PCR) and subcloned into an expression vector. The pancreatic polypeptide gene was expressed in Escherichia coli in two versions: as a cleavable fusion protein with IgG-binding synthetic ZZ domains of protein A from Staphylococcus aureus or with the 1-48 fragment of lambda Cro repressor. Site-specific hydrolysis by hydroxylamine was used to cleave the fusion protein, releasing the human polypeptide. The structure of the obtained hPP has been studied by scanning microcalorimetry and circular dichroism spectrometry. It has been shown that hPP in solutions close to neutral has a compact and unique spatial structure with an extended hydrophobic core. This structure is stable at 20 degrees C and co-operatively breaks down upon heating from this temperature.

Base Sequence↗

PubMed2002

Imaging of electrochemical enzyme sensor on gold electrode using surface plasmon resonance.

Three types of imaging, namely layer structure, electrochemical reaction, and enzyme sensor response, were achieved by applying surface plasmon resonance (SPR) measurement to an electrochemical biosensor. We constructed glucose oxidase based mediator type sensors on a gold electrode by spotting the mediator that contained horseradish peroxidase and spin coating the glucose oxidase film. The layer structure of the sensor was imaged by means of angle scanning SPR measurement. The single sensor spot (about 1 mm in diameter) consisted of about 100 x 100 pixels and its spatial structure was imaged. The multilayer structure of the enzyme sensor had a complex reflectance-incident angle curve and this required us to choose a suitable incident angle for mapping the redox state. We chose an incident angle that provided the most significant reflection intensity difference by using data obtained from two angle scanning SPR measurements at different electrode potentials. At this incident angle, we controlled the electrochemical states of the spotted mediator in cyclic voltammetry and imaged the degree to which the charged site density changed. Finally, we mapped the enzymatic activity around the mediator spot by the enzymatic reoxidation of pre-reduced mediator in the presence of glucose.

Biosensing Techniques↗