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PubMed2006

Conformation and mode of membrane interaction in cyclotides. Spatial structure of kalata B1 bound to a dodecylphosphocholine micelle.

Cyclotides are a family of bioactive plant peptides that are characterized by a circular protein backbone and three conserved tightly packed disulfide bonds. The antimicrobial and hemolytic properties of cyclotides, along with the relative hydrophobicity of the peptides, point to the biological membrane as a target for cyclotides. To assess the membrane-induced conformation and orientation of cyclotides, the interaction of the Möbius cyclotide, kalata B1, from the African perennial plant Oldenlandia affinis, with dodecylphosphocholine micelles was studied using NMR spectroscopy. Under conditions where the cyclotide formed a well-defined complex with micelles, the spatial structure of kalata B1 was calculated from NOE and J couplings data, and the model for the peptide-micelle complex was built using 5- and 16-doxylstearate relaxation probes. The binding of divalent cations to the peptide-micelle complex was quantified by Mn2+ titration. The results show that the peptide binds to the micelle surface, with relatively high affinity, via two hydrophobic loops (loop 5, Trp19-Val21; and loop6, Leu27-Val29). The charged residues (Glu3 and Arg24), along with the cation-binding site (near Glu3) are segregated on the other side of the molecule and in contact with polar head groups of detergent. The spatial structure of kalata B1 is only slightly changed during incorporation into micelles and represents a distorted triple-stranded beta-sheet cross-linked by a cystine knot. Detailed structural analysis and comparison with other knottins revealed structural conservation of the two-disulfide motif in cyclic and acyclic peptides. The results thus obtained provide the first model for interaction of cyclotides with membranes and permit consideration of the cyclotides as membrane-active cationic antimicrobial peptides.

Amino Acid Sequence↗
PubMed2006

Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification.

BACKGROUND: Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between projections, the success of any projection method depends on how well its mapping function is able to capture the salient features of protein structure. There is no agreement on what constitutes a good projection technique and the three currently known projection methods utilize very different approaches to the mapping construction, both in terms of what structural elements are included and how this information is integrated to produce a vector representation. RESULTS: In this paper we propose a novel projection method that uses secondary structure information to produce the mapping. First, a diverse set of spatial arrangements of triplets of secondary structure elements, a set of structural models, is automatically selected. Then, each protein structure is mapped into a high-dimensional vector of "counts" or footprint, where each count corresponds to the number of times a given structural model is observed in the structure, weighted by the precision with which the model is reproduced. We perform the first comprehensive evaluation of our method together with all other currently known projection methods. CONCLUSION: The results of our evaluation suggest that the type of structural information used by a projection method affects the ability of the method to detect structural similarity. In particular, our method that uses the spatial conformations of triplets of secondary structure elements outperforms other methods in most of the tests.

Computational Biology↗
PubMed1997

The spatial structure of lipids in human leukocytes: studies by nonradiative energy transfer.

The spatial structure of lipids in living human lymphocytes and granulocytes has been studied using the energy transfer between lipophilic fluorescent probes. One of the probes, an energy donor (DMC), was localized in the lipid interior, whereas another donor (K-68) and an energy acceptor (DSP-12) were near the lipid/water interface. The energy transfer in lymphocytes was the same as in artificial lipid membranes (liposomes). Obviously, in lymphocytes as in liposomes, both donors are localized near the lipid surface (the distance from the donors to the lipid surface is less than Forster's radius R0, i.e., 3.4-5 nm). On the contrary, in granulocytes, the energy transfer from K-68 was 2.2 times more efficient than from the lipid-immersed DMC. It was suggested that a fraction of DMC molecules was immersed into some lipid particles, and the distance from the molecules to the surface of the particles was greater than R0. The positions of the DMC fluorescence spectrum maxima in lymphocytes and in liposomes were the same, but in granulocytes the spectrum was blue-shifted (as in the case of lipoproteins). After subcellular fractionation the DMC fluorescence intensity correlated only with phospholipid concentration in different fractions but not with protein or nucleic acid concentrations. It was suggested that lipid organelles are the main source of the DMC fluorescence. The studies of cell-lipoprotein model mixtures support the suggestion that lipids in lymphocytes are mainly present as lamellar structures (membranes); the presence of lipoprotein-like particles of rather small radius can not be excluded either. On the other hand, in addition to membrane lipids, granulocytes have lipid-containing particles similar to large serum very low density lipoproteins.

Chalcone↗
PubMed1990

Carcinoembryonic antigen, its spatial structure and localization of antigenic determinants.

The effects of temperature and pH on the spatial structure of carcinoembryonic antigen (CEA) and its various derivatives are studied by circular dichroic spectroscopy and differential UV spectroscopy. The spatial organization of the protein portion of CEA and its derivatives as revealed by spectroscopic evidence is discussed with respect to the antigenic activity of the species studied. We conclude that the protein portion of CEA consists mainly of a beta-structural type. Using the various modifications of the sugar moiety and the protein portion, antigenic determinants of CEA are shown to possess the main conformational character of the molecule while participation of the sugars in the formation and orientation of the carbohydrate chains relative to the protein core of the antigen appear to be important.

Carbohydrate Conformation↗
PubMedDate not supplied

[Statistical criteria for evaluating the spatial structure, used in the reverse case of forming protein globules].

Statistical requirements to spatial structure representation used in the inverse folding problem have been considered. The representation by the distance from centers of side chaines to center of backbone of the molecule has been elaborated. It allows to select residue position and environmental properties and thus to improve computer methods for estimation 3D-1D compatibility.

Protein Conformation↗
PubMed2000

The evolution of parasite virulence and transmission rate in a spatially structured population.

If the transmission occurs through local contact of the individuals in a spatially structured population, the evolutionarily stable (ESS) traits of parasite might be quite different from what the classical theory with complete mixing predicts. In this paper, we theoretically study the ESS virulence and transmission rate of a parasite in a lattice-structured host population, in which the host can send progeny only to its neighboring vacant site, and the transmission occurs only in between the infected and the susceptible in the nearest-neighbor sites. Infected host is assumed to be infertile. The analysis based on the pair approximation and the Monte Carlo simulation reveal that the ESS transmission rate and virulence in a lattice-structured population are greatly reduced from those in completely mixing population. Unlike completely mixing populations, the spread of parasite can drive the host to extinction, because the local density of the susceptible next to the infected can remain high even when the global density of host becomes very low. This demographic viscosity and group selection between self-organized spatial clusters of host individuals then leads to an intermediate ESS transmission rate even if there is no tradeoff between transmission rate and virulence. The ESS transmission rate is below the region of parasite-driven extinction by a finite amount for moderately large reproductive rate of host; whereas, the evolution of transmission rate leads to the fade out of parasite for small reproductive rate, and the extinction of host for very large reproductive rate.

Animals↗
PubMed2001

Self-organized dynamics in spatially structured populations.

Self-organization and pattern formation represent the emergence of order in temporal and spatial processes. Self-organization in population ecology is gaining attention due to the recent advances concerning temporal fluctuations in the population size of dispersal-linked subunits. We shall report that spatially structured models of population renewal promote the emergence of a complex power law order in spatial population dynamics. We analyse a variety of population models showing that self-organization can be identified as a temporal match in population dynamics among local units, and how the synchrony changes in time. Our theoretical results are concordant with analyses of population data on the Canada lynx.

Animals↗
PubMed2001

High-resolution speckle-microscopy: study of the spatial structure of a bioflow.

Perspectives of velocity measurements of a random bioflow and its spatial structure by speckle-methods are studied in this paper. The mechanism of output signal formation and the optical scheme of the speckle-microscope are described. Amplitude, phase and frequency characteristics of this measuring system are investigated. The main types of signal distortions in the speckle-microscope are considered. Results of the analysis of output characteristics are applied to measurements of the spatial distribution of the refractive index of a blood flow in a small single microvessel. It is shown that the minimal size of flow inhomogeneities (with fluctuations in the optical path of the investigated object, less than 0.01 lambda) that can be resolved by the speckle-microscope is about a quarter of the waist beam diameter.

Algorithms↗
PubMed1987

Evaluating the aggregate spatial structure of Canadian metropolitan areas.

"Few attempts have been made to develop and test a conceptual framework for the comparative analysis of urban spatial structure and growth. This paper offers one aggregate approach as well as a series of empirical tests based on Canada's 27 largest urban areas. Six composite indices are introduced: population densities, rates of change, intraurban population redistribution, mobility rates, incidence of low-income populations, and degree of social polarization. Regression analyses reveal that differences among urban areas in spatial patterning and structural change are consistent with the hypothesized effects of city size, age, transport usage, social heterogeneity, production base, and physical setting. Yet immense regional and intraurban diversity remains. No single model of urban structure is sufficient to capture this diversity." (SUMMARY IN FRE)

Americas↗
PubMed2001

Evolution in a spatially structured population subject to rare epidemics.

We study a model that gives rise to spatially inhomogeneous population densities in a system of host individuals subject to rare, randomly distributed disease events. For stationary hosts that disperse offspring over short distances, evolutionary dynamics can lead to persistent populations with a variety of spatial structures. A mean-field analysis is shown to account for the behavior observed in simulations of a one-dimensional system, where the evolutionarily stable state corresponds to the solution of a straightforward optimization problem. In two dimensions, evolution drives the system to a stable critical state that is less well understood.

Animals↗
PubMedDate not supplied

[Fluorescent probe study of the spatial structure of membranes and lipoproteins].

A review is devoted to principles of studies in spatial structure of the model and biological membranes and lipoproteins on the basis of measuring radiationless energy transfer between fluorescent probes and from proteins to the probes. Recently the theory has been developed for energy transfer in membranes of various geometry and in lipoproteins of different size and structure. Special fluorescent probes are designed and made. The measurement procedure was tested in simulated systems and used to study a series of membranes as well as blood plasma lipoproteins of main classes. Everything above-mentioned resulted in obtaining data on the size of protein molecules in membranes and lipoproteins, proteins location relative to the lipid phase, on the surface area of the membranes (isolated and directly in a cell), association of protein molecules, state of near-protein lipid layer, membrane asymmetry, spreading of proteins on the lipoprotein surface, on the cholesterol effect on the lipid bilayer size etc.

Animals↗
PubMed2004

Spatial structure and genetic diversity of two tropical tree species with contrasting breeding systems and different ploidy levels.

Analyses of the spatial distribution pattern, spatial genetic structure and of genetic diversity were carried out in two tropical tree species with contrasting breeding systems and different ploidy levels using a 50-ha demographic plot in a lowland dipterocarp forest in Peninsular Malaysia. Shorea leprosula is a diploid and predominantly outcrossed species, whereas S. ovalis ssp. sericea is an autotetraploid species with apomictic mode of reproduction. Genetic diversity parameters estimated for S. leprosula using microsatellite were consistently higher than using allozyme. In comparisons with S. leprosula and other tropical tree species, S. ovalis ssp. sericea also displayed relatively high levels of genetic diversity. This might be explained by the lower pressure of genetic drift due to tetrasomic inheritance, and for autotetraploids each locus can accommodate up to four different alleles and this allows maintenance of more alleles at individual loci. The observed high levels of genetic diversity in S. ovalis ssp. sericea can also be due to a random retention of more heterogeneous individuals in the past, and the apomictic mode of reproduction might be an evolutionary strategy, which allows the species to maintain high levels of genetic diversity. The spatial distribution pattern analyses of both species showed significant levels of aggregation at small and medium but random distribution at the big diameter-class. The decrease in magnitude of spatial aggregation from small- to large-diameter classes might be due to compensatory mortality during recruitment and survival under competitive thinning process. Spatial genetic structure analyses for both species revealed significant spatial genetic structure for short distances in all the three diameter-classes. The magnitude of spatial genetic structure in both species was observed to be decreasing from smaller- to larger-diameter classes. The high spatial genetic structuring observed in S. ovalis ssp. sericea at the small-diameter class is due primarily to limited seed dispersal and apomictic mode of reproduction. The similar observation in S. leprosula, however, can be explained by limited seed and pollen dispersal, which supports further the fact that the species is pollinated by weak fliers, mainly of Thrips and Megalurothrips in the lowland dipterocarp forest.

Age Factors↗
PubMed2005

Determination of the spatial structure of glutathione by residual dipolar coupling analysis.

The approach based on analysis of the residual 1H-13C dipolar couplings in molecules partially aligned in a lyotropic liquid crystalline medium was used in the NMR investigation of the reduced glutathione (Glu-Cys-Gly; GSH) structure in a lyotropic medium (cetylpyridinium chloride-n-hexanol). The spatial structure of GSH in solution was established on the basis of the experimental data for observed couplings only.

Carbon Isotopes↗
PubMed1992

Spatial structure of (34-65)bacterioopsin polypeptide in SDS micelles determined from nuclear magnetic resonance data.

The spatial structure of a synthetic 32-residue polypeptide, an analog of the membrane-spanning segment B (residues 34-65) of bacterioopsin of Halobacterium halobium, incorporated into perdeuterated sodium dodecyl sulfate micelles, was determined from 1H NMR data. The structure determination included the following steps: (1) local structure analysis; (2) structure calculations using the distance geometry program DIANA; (3) systematic search for energetically allowed side-chain rotamers consistent with NOESY cross-peak volumes; (4) random generation of peptide conformations in allowed conformational space. The obtained structure has a right-handed alpha-helical region from Lys41 to Leu62 with a kink of 27 degrees at Pro50. The C-cap Gly63 adopts a conformation with phi = 87 +/- 6 degrees, psi = 43 +/- 10 degrees typical to a left-handed helix. The N-terminal part (residues 34-40) is exposed to the aqueous phase and lacks an ordered conformation. The secondary structure of segment B in micelles is consistent with the high-resolution electron cryomicroscopy model of bacteriorhodopsin (Henderson et al. (1990) J. Mol. Biol., 213, 899-929).

Bacteriorhodopsins↗
PubMed1980

Computer studies of the spatial structure and temporal growth of tumor cells.

In the present paper we attempt to determine the spatial structure and the time behaviour of cell renewal systems, continuing previous studies in which tumor diseases were interpreted as unstable control loops. A computer model wa developed for the two-dimensional cell space, which is described by a set of specifications and growth statements. Selected case studies are then simulated by means of a digital computer (CYBER 76). In the development of this model special emphasis was given to (i) the existence of several cell systems with different mean life spans, growing in competition; (ii) the variability of the mean life spans of a cell and of the initial configuration of cell patterns; (iii) the description of the cell-to-cell interactions; (iv) the perturbation of normal cell growth by tumor cells and their elimination in medicine comparable with a direct irradiation or removal by surgery; (v) the consideration of the loss of tumor cells. The development of this model enables a deeper insight into the structure and function of disturbed cell renewal processes. Systematic studies were made on the influence of the size of a tumor nucleus and the mean life span of a tumor cell on the tumor growth assuming constant cell loss. Furthermore it is possible with this computer model to simulate simple basic cases which are difficult to test in real life.

Cell Division↗
PubMed2003

Accumulation of Dobzhansky-Muller incompatibilities within a spatially structured population.

A simple, deterministic analysis predicts that accumulation of Dobzhansky-Muller incompatibilities by a spatially structured population strongly depends on the number of negative interactions of an allele. If an allele can be incompatible with alleles at only one locus, incompatibilities accumulate linearly with time. In contrast, if an allele can participate in multiple pairwise incompatibilities with alleles at different loci, the expected number of incompatibilities eventually increases quadratically.

Alleles↗
PubMedDate not supplied

[Spatial structure of (1-36)bacterioopsin solubilized in a methanol-chloroform mixture with sodium dodecylsulfate micelles].

Spatial structures of proteolytic segment A (sA) of bacterioopsin of Halobacterium halobium (residues 1-36) solubilized in the mixture of methanol-chloroform (1:1), 0.1 M LiClO4 or in perdeuteriated sodium dodecyl sulfate (SDS) micelles, were determined by 2D 1H-NMR techniques. Most of the resonances in 1H-NMR spectra of fragment A were assigned using DQF-COSY, TOCSY and NOESY spectra. Deuterium exchange rates for amide protons were measured in series of NOESY spectra. 324 and 400 NOESY cross-peak volumes were measured in NOESY spectra of sA in mixture of organic solvents and SDS micelles, respectively. The sA structure was determined by local structure analysis, distance geometry calculation with program DIANA and systematic search for energetically allowed side chain rotamers consistent with NOESY cross-peak volumes. The structures of sA are similar in both milieus. These structures have the right-handed alpha-helical region from Pro-8 to Met-32 with root mean square deviation (RMSD) of 0.25 A between back bone heavy atoms and fit well with Pro-8 to Met-32 alpha-helical region in electron cryo-microscopy (ECM) model of bacteriorhodopsin [4]. The C-terminal region Gly-33-Asp-36 is disordered in both milieus, while N-terminal region Ala-2-Gly-6 in organic solvents has a fixed structure (RMSD of 0.25 A) stabilized by the Thr-5 NH...O=C Gln-3 and Ile-4 NH...O = C Ala-2 hydrogen bonds. This region of sA in SDS micelles has disordered structure with RMSD of 1.44 A for back bone heavy atoms. Torsion angles chi 1 of sA were unequivocally determined for 72% of side chains in the alpha-helical region and are identical in both milieus.

Amino Acid Sequence↗