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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↗
PubMed2004

The evolution of programmed death in a spatially structured population.

Recent studies have identified a number of genes that regulate life span. When these genes are inactivated, organisms live longer, but suffer no obvious adverse effects. These results have generated considerable debate, largely because current evolutionary theory is unable to explain them. In this article, I report results from an individual-based spatial model in which a programmed age of death is allowed to evolve. In a freely mixing population with global dispersal, evolution selects for individuals with ever-increasing life span. However, in a spatially structured population with localized dispersal, a programmed age of death evolves. The exact age of death that evolves depends critically on the scale of dispersal. Within this model, individuals are genetically programmed to die, even though they are still able to reproduce. These results suggest that death can be adaptive and offer an explanation for the evolution of "death genes."

Cell Death↗
PubMed2005

Oligonucleotide arrays: information from replication and spatial structure.

MOTIVATION: The introduction of oligonucleotide DNA arrays has resulted in much debate concerning appropriate models for the measurement of gene expression. By contrast, little account has been taken of the possibility of identifying the physical imperfections in the raw data. RESULTS: This paper demonstrates that, with the use of replicates and an awareness of the spatial structure, deficiencies in the data can be identified, the possibility of their correction can be ascertained and correction can be effected (by use of local scaling) where possible. The procedures were motivated by data from replicates of Arabidopsis thaliana using the GeneChip ATH1-121501 microarray. Similar problems are illustrated for GeneChip Human Genome U133 arrays and for the newer and larger GeneChip Wheat Genome microarray. AVAILABILITY: R code is freely available on request.

Algorithms↗
PubMed1995

[Study of the spatial structure of the product of intracomplex alkylation of the octanucleotide pd(TGTTTGGC) by 4-(N-methyl-N-(2-chloroethyl) amino)benzyl-5'-phosphamide derivative of the heptanucleotide pd(CCAAACA) in an aqueous solution by two-dimensional 1H-NMR spectroscopy and constrained molecular mechanics].

Using one- and two-dimensional 1H NMR spectroscopy (400 MHz), a detailed study of the spatial structure of the covalent adduct, a product of the intracomplex alkylation of octanucleotide pd[TGTTTGGC] by the 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5'-phosphamide derivative of heptanucleotide pd[CCAAACA] in aqueous solution, was continued. The distances between closely spaced protons of oligonucleotides as well as between protons of the benzylamide fragment and protons of the nearest nucleotide units were determined by measurements of the nuclear Overhauser effect. Analysis of effective correlation times for some pairs of protons of the covalent adduct showed that the values of tau c for the benzylamide fragment and nucleotide units C-1 and C-8, which directly interact with it, coincide and are smaller than those for the internal nucleotide units, suggesting the increased rigidity of the structure in the vicinity of the modification region. Using the method of constrained molecular mechanics, a probable state of the covalent adduct in solution is proposed that is in the best agreement with the experimentally obtained set of interproton distances. Problems connected with calculating the distance between a pair of protons with coincident chemical shifts and any third proton are considered.

Alkylation↗
PubMed1984

Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure.

Aspartate aminotransferase is a pyridoxal phosphate-dependent enzyme that catalyses the transamination reaction: L-aspartate + 2-oxoglutarate----oxaloacetate + L-glutamate. The enzyme shuttles between its pyridoxal and pyridoxamine forms in a double-displacement process. This paper proposes a mechanism of action that delineates the dynamic role of the protein moiety of this enzyme. It is based on crystallographically determined spatial structures (at 2.8 A resolution) of the mitochondrial isoenzyme in its unliganded forms and in complexes with substrate analogues, as well as on model building studies. The enzyme is composed of two identical subunits, which consist of two domains. The coenzyme is bound to the larger domain and is situated in a pocket near the subunit interface. The proximal and distal carboxylate group of dicarboxylic substrates are bound to Arg386 and Arg292 , respectively, the latter residue belonging to the adjacent subunit. These interactions largely determine the substrate specificity of the enzyme. They not only position the substrate efficient catalysis but also bring about a bulk movement of the small domain that closes the active site crevice and moves Arg386 about 3 A closer to the coenzyme. The replacement of the epsilon-amino group of Lys258 by the alpha-amino group of the substrate in the aldimine bond to pyridoxal phosphate is accompanied by a tilting of the coenzyme by approximately 30 degrees. The released epsilon-amino group of Lys258 serves as a proton acceptor/donor in the 1,3- prototropic shift producing the ketimine intermediate. At this stage, or after hydrolysis of the ketimine bond, the coenzyme rotates back to an orientation between that in the "external" aldimine intermediate and that in the pyridoxal form. Throughout this process, the protonated pyridine nitrogen atom maintains a hydrogen bond to the beta-carboxylate group of Asp222 . Upon formation of the pyridoxamine form, the small domain moves back to its original position. The proposed mechanism is compatible with the known kinetic and stereochemical features of enzymic transamination.

Aspartate Aminotransferases↗
PubMed1999

Spatial structure of the M2 transmembrane segment of the nicotinic acetylcholine receptor alpha-subunit.

A synthetic peptide corresponding to the transmembrane segment M2 (residues 236-267) of the alpha-subunit of the nicotinic acetylcholine receptor from Torpedo californica has been studied by two dimensional 1H-NMR spectroscopy in a chloroform-methanol (1:1) mixture containing 0.1 M LiClO4. Reconstruction of the spatial structure of M2 from the NMR data resulted in an alpha-helix formed by residues 241-263. Distribution of the molecular hydrophobicity potential on the helix surface is very similar to that in five-helix bundles of proteins with a known three dimensional structure: two hydrophilic bands located on the opposite helix sides separated by strong hydrophobic zones.

Amino Acid Sequence↗
PubMed2005

Modelling antibiotic- and anti-quorum sensing treatment of a spatially-structured Pseudomonas aeruginosa population.

The bacterial cell to cell signalling system known as quorum sensing (QS) is essential for the regulation of virulence in many pathogens and offers a specific biochemical target for novel antibacterial therapies. Expanding on earlier work, in which consideration was given to the primary QS system (lasR system) in a homogeneous population of the common human pathogen Pseudomonas aeruginosa, we build a simple spatial model of an early-stage P. aeruginosa biofilm subject to treatment with topically applied anti-QS drugs (of two specific kinds) and conventional antibiotics. In the case of a slowly growing biofilm we show that both kinds of anti-quorum sensing drug are effective in reducing the level of the relevant signal molecule (3-oxo-C12-homoserine lactone; henceforth AHL), in each case obtaining an explicit bound on the steady-state AHL profile in terms of a prescribed surface drug concentration. Using numerical methods, we are also able to reproduce the hysteretic phenomena exhibited by the homogeneous model, in particular showing that for each kind of anti-QS drug there is a parameter regime in which a catastrophic collapse occurs in the steady-state AHL concentration as the surface drug concentration passes some critical value; an alternative way of interpreting this result is to say that, for a prescribed surface drug concentration, there is a critical biofilm depth such that treatment is successful until this depth is reached, but fails thereafter. In the thick-biofilm limit we show that the critical concentration of each drug increases exponentially with the biofilm thickness (or, conversely, that the critical depth increases logarithmically with surface drug concentration); this is dramatically different to the behaviour observed in the corresponding homogeneous model, where the critical concentrations grow linearly with bacterial carrying capacity, and thus highlights the relative difficulty of treating a large, spatially-structured population with diffusing antibacterials.

4-Butyrolactone↗
PubMed1997

[Spatial structure of bacterioopsin 87-136 fragment].

The [Nle18]-(87-136)-bacterioopsin, a fragment of bacterioopsin from Halobacterium salinarium synthesized by solid phase technique, was solubilized in a 1:1 chloroform-methanol mixture containing 0.1 M LiClO4 and studied by two-dimensional 1H NMR spectroscopy. The complete assignment of proton resonances was performed in the DQF-COSY, TOCSY, and NOESY spectra of this peptide, and its spatial structure was computed. As a result, two helical regions (92-100 and 108-130) were identified, which correspond to the C-terminal part of segment C and to segment D of bacteriorhodopsin, respectively. The 92-100 region forms a right-handed alpha-helix, and the 108-130 region can adopt right-handed alpha-helical, 3(10)-helical, and combined (from the two) conformations. A comparison of the structure computed with the bacteriorhodopsin model deduced from the electron cryomicroscopy data showed good agreement in the 91-100 region (the root-mean-square deviation of the backbone atoms was less than 0.51 A) and considerable differences in the 108-130 region (1.82 A). A dynamic model of the conformation of the D transmembrane segment was suggested, and the accordance of the model to the functional dynamics of bacteriorhodopsin was discussed.

Amino Acid Sequence↗
PubMed1994

Visual acuity and pupillary responses to spatial structure in infants.

PURPOSE: To determine the age of onset of the pupil grating response (PGR). To compare estimates of resolution acuity obtained by pupillometric and behavioral methods in early infancy. METHODS: Dynamic infrared pupillometry was undertaken on 19 newborn infants while they fixated a uniform background upon which a 0.1 c/deg sine wave grating was briefly presented. Pupillary responses were also recorded to an increment in luminance of a spatially homogeneous target. Longitudinal measurements of PGRs were obtained from a subset of eight infants between 3.5 and 38 weeks of age. In this group, behavioral estimates of visual resolution obtained using the acuity card procedure were compared with the highest spatial frequency grating to elicit a PGR. RESULTS: When presented with the pattern stimulus, newborn infants did not show any pupil reaction indicative of a PGR. This finding could not be attributed to immaturity of pupillomotor function: All infants showed marked pupillary construction to diffuse light stimulation. By 1 month of age, pupillary responses to pattern stimuli were reliably present. For these and older infants, the spatial frequency of the finest grating to elicit a PGR was comparable to the behaviorally determined resolution threshold: mean difference (+/- 95% confidence interval) = 0.28 +/- 0.23 octaves. CONCLUSIONS: A PGR could not be detected in newborn infants. From 1 month of age, responses to spatial structure can provide objective estimates of visual acuity comparable to those determined by established methods.

Age of Onset↗
PubMed2004

Using geographical information techniques to quantify the spatial structure of endolithic boring processes within sediment grains of marine stromatolites.

Marine stromatolites are generated through the interactions of environmental parameters and specific microbial processes. The activities of endolithic bacteria, that bore canals through calcium carbonate (CaCO(3)) sand grains (ooids) and reprecipitate the CaCO(3) as a single layer (i.e. micritic laminae) are especially important in the longer term stability of the stromatolite macrostructure. Image analysis and classification approaches have been used previously, but only seldom as a quantitative microscopic tool. Here, we develop a new approach that enables the quantification of microscale (i.e. micrometers to millimeters) spatial structure within marine stromatolites. To demonstrate our approach, images were acquired from two different layers of a stromatolite: "orange layers", where microboring of canals within ooids was relatively abundant, and "white layers" where microboring was greatly reduced or lacking. Images were then transformed into spatial maps. Computation of canal and ooid grain areas within each image was conducted and statistically compared between replicate samples from the two stromatolite layers. This allowed quantification of the areas of ooid grains that were microbored. Based on our results, we suggest that our method could be widely applicable to sedimentary environments, and other areas of fundamental research.

Bacteria↗
PubMed2003

Dispersion movements in ants: spatial structuring and density-dependent effects.

This paper examines whether the characteristics of individual dispersion movements in ants are changed when workers are moving solitarily or in a group. We analyzed the trajectories of workers of the species Messor sancta moving solitarily or in groups of different size (5, 10, 15 individuals), tested for density-dependent effects on their trajectory characteristics and investigated through resampling techniques whether ants are able to spatially structure their movements through direct (e.g. contact) or indirect (pheromone deposited on the ground) interactions. In addition to group size, the effects of the nutritional state of the colony and of the state of the area on which ants were dispersing were also examined. Solitary ants moved faster and had more sinuous trajectories than ants moving in a group. We found however no significant differences in trajectory characteristics between groups of different size. Whatever the group size, ants from starved colonies moved more slowly and had more direct trajectories than their counterpart coming from fed colonies. On the other hand, the state of the area on which ants were moving had no direct significant effect on dispersion movement. Ants dispersing in a group moved independently and did not coordinate their movements through direct or indirect interactions. However, the geometry of their path was changed not only through the effect of random encounters with other workers but also through an active modification of their movement when they perceived directly or indirectly the presence of nearby workers.

Journal Article↗
PubMed1985

[Study of the spatial structure of des-Gly9-[Arg8]vasopressin by two-dimensional NMR spectroscopy and theoretical conformation analysis].

2D 1H-NMR spectra of des-Gly9-[Arg8]vasopressin in dimethylsulfoxide have been taken and the 1H resonances have been assigned. The coupling constants and amide proton temperature coefficients (delta delta/delta T) have been measured and the NOE cross-peaks in the NOESY spectrum have been analyzed. The most essential information on the spatial structure of des-Gly9-[Arg8]vasopressin is extracted from the low delta delta/delta T value for Asn5 amide proton and from the NOE between the Cys1 and Cys6 alpha-protons. A diminished accessibility of the Asn5 NH proton for the solvent is ascribed to the presence of a beta-turn in the fragment 2-5. The distance between the Cys1 and Cys6 C alpha H protons seems to be less than 4 A. These constraints were taken into account in the conformational analysis of the title peptide. The derived set of the low-energy backbone conformations was analyzed against the background of the all available NMR data. The most probable conformation of the cyclic moiety in des-Gly9-[Arg8]vasopressin was found to be the type III beta-turn. The corner positions are occupied by the residues 3, 4, while the residues 1-2 and 5-6 are at the extended sites. Some NMR data indicate that this structure is in a dynamic equilibrium with other minor conformers.

Amino Acid Sequence↗
PubMed1996

Formation of polymeric chelate bridges between double-stranded DNA molecules fixed in spatial structure of liquid-crystalline dispersions.

The formation of cholesteric liquid-crystalline dispersions from DNA-daunomycin complexes in water-salt polyethyleneglycol-containing solutions was investigated. In the case of nonclassical complex formation between DNA and daunomycin (DAU), reactive groups of DAU were used for the formation of polymeric chelate complex with divalent copper ions (-DAU-Cu-...-Cu-DAU-), located between neighboring double-stranded DNA molecules, fixed in spatial structure of liquid-crystalline dispersions. The formation of polymeric chelate complex does not depend upon the sense of helicoidal twist of DNA cholesterics. A many-fold increase in the CD band in the DAU absorption region is specific to this process. A reduction of the divalent copper ions as a result of a redox-process is accompanied by destroying of structure of polymeric chelate complex between DNA molecules and by disappearance of the abnormal CD band in daunomycin absorption region.

Ascorbic Acid↗
PubMed2004

Multilocus microsatellite typing system for Penicillium marneffei reveals spatially structured populations.

For eukaryotic pathogens that have low levels of genetic variation, multilocus microsatellite typing (MLMT) offers an accurate and reproducible method of characterizing genetic diversity. Here, we describe the application of an MLMT system to the emerging pathogenic fungus Penicillium marneffei. Isolates used for this study were those held in the culture collections of the Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and the Chiang Mai University Department of Microbiology, Chang Mai, Thailand. High genetic diversity and extensive spatial structure were observed among clinical isolates, with the geographical area of origin for each isolate strongly correlating with the occurrence of two deeply divided clades. Within each clade, multilocus linkage associations were highly significant and could be explained by genetically differentiated populations or by an exclusively clonal reproductive mode, or both. Our results show that southeast Asian penicilliosis is caused by a fungus with a complex population genetic structure. Furthermore, this MLMT system generates digital data that can be easily queried against a centrally held database via the internet (http://pmarneffei.multilocus.net/); this provides a powerful epidemiological tool for analyzing the underlying parameters that are responsible for the emergence of P. marneffei in human immunodeficiency virus-positive populations.

AIDS-Related Opportunistic Infections↗
PubMed2005

The spatial structure of epidemic emergence: geographical aspects of poliomyelitis in north-eastern USA, July-October 1916.

The great epidemic of poliomyelitis which swept New York City and surrounding territory in the summer of 1916 eclipsed all previous global experience of the disease. We draw on epidemiological information that is included in the seminal US Public Health Bulletin 91, 'Epidemiologic studies of poliomyelitis in New York City and the northeastern United States during the year 1916' (Washington DC, 1918), to re-examine the spatial structure of the epidemic. For the main phase of transmission of the epidemic, July-October 1916, it is shown that the maximum concentration of activity of poliomyelitis occurred within a 128-km radius of New York City. Although the integrity of the poliomyelitis cluster was maintained up to approximately 500 km from the metropolitan focus, the level and rate of propagation of disease declined with distance from the origin of the epidemic. Finally, it is shown that the geographical transmission of the epidemic in north-eastern USA probably followed a process of mixed contagious-hierarchical diffusion.

Journal Article↗
PubMedDate not supplied

[Effect of forest fires on the population count and spatial structure of the taiga tick (Ixodidae)].

Results of two large-scale surveys of Ixodes persulcatus distribution were compared. Surveys were conducted in a south taiga forest area in the Khabarovsk region two and ten years after a great fire. The direct inhibiting effect of the fire on the population of I. persulcatus was not continuous though apparent. By the moment of pyrogenic small forests formation on slash fires, i.e. during the period not exceeding 2-3 complete developmental cycles of I. persulcatus, the abundance and spatial structure of its population are restored completely.

Animals↗