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Results for “spatial structure”

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PubMed1999

Structural and energetic determinants of the S1-site specificity in serine proteases.

In recent years the number of determined three-dimensional structures of serine proteases that are accompanied by detailed mutational studies has grown rapidly. In particular, spatial structures have been described for enzymes involved in processes of critical medical significance, often related to severe pathophysiological diseases. There has also been significant progress in the understanding of the structural grounds for the substrate specificity of serine proteases. This review is concerned mainly with primary structural determinants of the S1 specificity, the crucial component of substrate selectivity, often in relation to more distant specificity elements, which cooperatively influence the S1 site.

Amino Acid Sequence↗

PubMed1999

SECOST: sequence-conformation-structure database for amino acid residues in proteins.

The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.

Computational Biology↗

PubMed1999

Variable investment, the Continuous Prisoner's Dilemma, and the origin of cooperation.

Cooperation is fundamental to many biological systems. A common metaphor for studying the evolution of cooperation is the Prisoner's Dilemma, a game with two strategies: cooperate or defect. However, cooperation is rare all or nothing, and its evolution probably involves the gradual extension of initially modest degrees of assistance. The inability of the Prisoner's Dilemma to capture this basic aspect limits its use for understanding the evolutionary origins of cooperation. Here we consider a framework for cooperation based on the concept of investment: an act which is costly, but which benefits other individuals, where the cost and benefit depend on the level of investment made. In the resulting Continuous Prisoner's Dilemma the essential problem of cooperation remains: in the absence of any additional structure non-zero levels of investment cannot evolve. However, if investments are considered in a spatially structured context, selfish individuals who make arbitrarily low investments can be invaded by higher-investing mutants. This results in the mean level of investment evolving to significant levels, where it is maintained indefinitely. This approach provides a natural solution to the fundamental problem of how cooperation gradually increases from a non-cooperative state.

Biological Evolution↗

PubMed2002

Faraday patterns in bose-Einstein condensates.

Temporal periodic modulation of the interatomic s-wave scattering length in Bose-Einstein condensates is shown to excite subharmonic patterns in the atom density through a parametric resonance. The dominant wavelength of the spatial structures is primarily selected by the excitation frequency but also affected by the depth of the spatial modulation via a nonlinear resonance. These phenomena represent analogues of the Faraday patterns excited in vertically vibrated liquids.

Journal Article↗

PubMed2005

Spatial control of high-harmonic generation in hollow fibers.

We demonstrate the control of high-harmonic generation in a hollow fiber by shaping the spatial structure of the generating laser pulse. We use a liquid-crystal-based two-dimensional spatial light modulator to control the spatial phase of the driver pulse. An evolutionary algorithm finds the spatial laser phase distribution that is optimal for reaching maximum total harmonic yield and for selectively enhancing the cutoff region of the spectrum. We show that enhacement of harmonic generation is related to coupling into a single fiber mode. Our results directly show that spatial properties of the laser are important parameters in fully controlling the high-harmonic spectrum. It is thus not possible to derive the controllability of the high-harmonic generation from the single-atom response only.

Journal Article↗

PubMed2002

Structural criteria of biologically active RGD-sites for analysis of protein cellular function - a bioinformatics study.

BACKGROUND: Cell adhesion involves interactions of integrins and extracellular proteins, often facilitated by the RGD motif. Only presence of the RGD in a sequence of a protein may be not sufficient for the biological activity (binding to an integrin) and additional biochemical and/or structural studies are essential. MATERIAL/METHODS: Structural criteria that would allow identification biologically active RGD-sites on the base of a spatial structure may assist analysis of function of a protein in the cell. For the first time, computational analysis of RGD-sites in a large non-redundant set of protein structures was done. RESULTS: Out of 3819 protein chains sequences of about 100 contained RGDs. Analysis of the structures of the RGD-'native' proteins has allowed establishing main determinants of the biologically active conformations of the RGD sites: surface accessibility of the whole RGD-sequence and the secondary structure. The criteria, applied to the remaining proteins of the set, identify 23 proteins ( approximately 25%) with potentially active RGD-sites. The results strongly suggest that RGD has a high propensity for being involved in protein-protein interactions and this may explain occurrence of RGDs in intracellular proteins. Results of the analysis suggest (in some cases, confirm) novel integrin-related activities for 7 membrane/extracellular proteins, as well as confirm RGD-facilitated cell attachment for 5 viral proteins. CONCLUSIONS: Only presence of RGD in a sequence is not sufficient to propose biological activity of this site. The results also suggest that the method can be used on large scale: for example, for identifying potential integrin-interacting proteins in an animal genome.

Amino Acid Sequence↗

PubMed2005

The role of bivalent metals in hydroxyapatite structures as revealed by molecular modeling with the HyperChem software.

Hydroxyapatite, the major component of bone, demonstrates significant reactivity with metals. Knowledge of spatial structure and energy data of the molecule helps understand the binding of metals by hydroxyapatite and elucidate the chemical and physical properties of such complexes. We used HyperChem software (Hypercube Inc.) to analyze the structure of hydroxyapatite when the central calcium atom is replaced by one of the metal ions (Mg, Cu, Zn, Fe, Cr, Mn) marked by us in bone. Our results show that hetero-ionic exchange affects composition and leads to deformation of hydroxyapatite crystals. Replacement was accompanied by changes in bond lengths between oxygen and calcium atoms in the hydroxyapatite molecule and by displacement of groups of atoms surrounding the central calcium atom. The use of molecular modeling as a computational tool enabled a preliminary and theoretical understanding of chemical structure without the need for laboratory tests.

Durapatite↗

PubMed2003

Atomic resolution structure of obelin: soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine.

The spatial structure of the Ca(2+)-regulated photoprotein obelin has been solved to resolution of 1.1A. Two oxygen atoms are revealed substituted at the C2-position of the coelenterazine in contrast to the obelin structure at 1.73A resolution where one oxygen atom only was disclosed. The electron density of the second oxygen atom was very weak but after exposing the crystals to a trace of Ca(2+), the electron densities of both oxygen atoms became equally intense. In addition, one Ca(2+) was found bound in the loop of the first EF-hand motif. Four of the ligands were provided by protein residues Asp30, Asn32, Asn34, and the main chain oxygen of Lys36. The other two were from water molecules. From a comparison of B-factors for the residues constituting the active site, it is suggested that the variable electron densities observed in various photoprotein structures could be attributed to different mobilities of the peroxy oxygen atoms.

Binding Sites↗

PubMed2001

The impact of habitat fragmentation on dispersal of Cunningham's skink (Egernia cunninghami): evidence from allelic and genotypic analyses of microsatellites.

The effects of habitat fragmentation on processes within and among populations are important for conservation management. Despite a broad spectrum of lifestyles and the conservation significance of many reptiles, very little work on fine-scale population genetics has been carried out on this group. This study examines the dispersal patterns of a rock crevice-dwelling lizard, Cunningham's skink (Egernia cunninghami), in a naturally vegetated reserve and an adjacent deforested site. Both genotypic and genic approaches were employed, using microsatellite loci. The spatial organization of individuals with respect to pairwise relatedness coefficients and allele frequencies, along with assignment tests, were used to infer dispersal characteristics for both sexes in a natural and a cleared area. The distribution of relatedness in both habitats was spatially structured, with E. cunninghami showing high pairwise relatedness within their rocky retreat sites. Analysis of relatedness over different spatial scales, spatial autocorrelation of alleles and assignment tests, all indicated that both sexes in the cleared area show less dispersal than their counterparts in the reserve. Furthermore, deforestation may inhibit female dispersal to a greater extent than that of males. The geographical structuring of allele frequencies for adults in the cleared area, but not the reserve, indicates that habitat fragmentation has the potential to alter at least the microevolution of E. cunninghami populations.

Animals↗

PubMed1989

[Three-dimensional reconstruction of bacterial viruses from electron microscopy data. Subjects and methods of study].

The review summarizes the results of the study of the spatial structure of bacterial viruses (phages) whose tails seem to be the most primitive contracting biological mechanism. Data on the spatial molecular rearrangement are important for understanding the processes of biological mobility. The computer and laser techniques used in order to obtain information on the three-dimensional structure of the object under study by its two-dimensional electron-microphotography are presented in the first part of the review. The second deals with application of the above mentioned techniques for the study of various bacterial viruses.

Bacteriophages↗

PubMed2000

Recent Changes in the Near-Infrared Structure of eta Carinae.

Near-infrared imaging at two phases in the 5 yr spectroscopic cycle of eta Carinae reveals changes in the spatial structure of the inner core that may be related to recently reported near-infrared photometric variability. The central source changed from a pointlike object to a more extended, bipolar or shell structure. This behavior is reminiscent of changes observed in the radio continuum. NICMOS images show a toroidal distribution of dust and gas around the central star and confirm the morphology of several other structures observed in ground-based images of the Homunculus. The morphological variations appear to be confined to the central core of the nebula.

Journal Article↗

PubMed2000

Spatial mixture modeling of fMRI data.

Recently, Everitt and Bullmore [1999] proposed a mixture model for a test statistic for activation in fMRI data. The distribution of the statistic was divided into two components; one for nonactivated voxels and one for activated voxels. In this framework one can calculate a posterior probability for a voxel being activated, which provides a more natural basis for thresholding the statistic image, than that based on P-values. In this article, we extend the method of Everitt and Bullmore to account for spatial coherency of activated regions. We achieve this by formulating a model for the activation in a small region of voxels and using this spatial structure when calculating the posterior probability of a voxel being activated. We have investigated several choices of spatial models but find that they all work equally well for brain imaging data. We applied the model to synthetic data from statistical image analysis, a synthetic fMRI data set and to visual stimulation data. Our conclusion is that the method improves the estimation of the activation pattern significantly, compared to the nonspatial model and to smoothing the data with a kernel of FWHM 3 voxels. The difference between FWHM 2 smoothing and our method were more modest.

Brain↗

PubMed2004

Decision tree algorithm for detection of spatial processes in landscape transformation.

The conversion of landscapes by human activities results in widespread changes in landscape spatial structure. Regardless of the type of land conversion, there appears to be a limited number of common spatial configurations that result from such land transformation processes. Some of these configurations are considered optimal or more desirable than others. Based on pattern geometry, we define ten processes responsible for pattern change: aggregation, attrition, creation, deformation, dissection, enlargement, fragmentation, perforation, shift, and shrinkage. A novelty in this contribution is the inclusion of transformation processes causing expansion of the land cover of interest. Consequently, we propose a decision tree algorithm that enables detection of these processes, based on three parameters that have to be determined before and after the transformation of the landscape: area, perimeter length, and number of patches of the focal landscape class. As an example, the decision tree algorithm is applied to determine the transformation processes of three divergent land cover change scenarios: deciduous woodland degradation in Cadiz Township (Wisconsin, USA) 1831-1950, canopy gap formation in a terra firme rain forest at the Tiputini Biodiversity Station (Amazonian Ecuador) 1997-1998, and forest regrowth in Petersham Township (Massachusetts, USA) 1830-1985. The examples signal the importance of the temporal resolution of the data, since long-term pattern conversions can be subdivided in stadia in which particular pattern components are altered by specific transformation processes.

Algorithms↗

PubMed1985

Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry.

A determination of the solution conformation of the proteinase inhibitor IIA from bull seminal plasma (BUSI IIA) is described. Two-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) was used to obtain a list of 202 distance constraints between individually assigned hydrogen atoms of the polypeptide chain, to identify the positions of the three disulfide bridges, and to locate the single cis peptide bond. Supplementary geometric constraints were derived from the vicinal spin-spin couplings and the locations of certain hydrogen bonds, as determined by nuclear magnetic resonance (n.m.r.). Using a new distance geometry program (DISGEO) which is capable of computing all-atom structures for proteins the size of BUSI IIA, five conformers were computed from the NOE distance constraints alone, and another five were computed with the supplementary constraints included. Comparison of the different structures computed from the n.m.r. data among themselves and with the crystal structures of two homologous proteins shows that the global features of the conformation of BUSI IIA (i.e. the overall dimensions of the molecule and the threading of the polypeptide chain) were well-defined by the available n.m.r. data. In the Appendix, we describe a preliminary energy refinement of the structure, which showed that the constraints derived from the n.m.r. data are compatible with a low energy spatial structure.

Amino Acid Sequence↗

PubMed2006

Spatially extended host-parasite interactions: the role of recovery and immunity.

Techniques for determining the long-term dynamics of host-parasite systems are well established for mixed populations. The field of spatial modelling in ecology is more recent but a number of key advances have been made. In this paper, we use state-of-the-art approximation techniques, supported by simulations, in order to investigate the role of recovery and immunity in spatially structured populations. Our approach is to use correlation models, namely pair-wise models, to capture the spatial relationships of contacts and interactions between individuals. We use the pair-wise framework to address a number of key ecological questions; including, the persistence of endemic limit cycles and regions of parasite-driven extinction--features which differentiate spatial from non-spatial models--and the effects on invasion fitness. We demonstrate a loss of limit cycle behaviour, in addition to an increase in the critical transmissibility and extinction thresholds, when recovery is included. This approach allows for a better analytical understanding of the dynamics of host-parasite interactions and demonstrates the importance of recovery and immunity in local interactions.

Animals↗

PubMed2004

Model for spreading of liquid monolayers.

Manipulating fluids at the nanoscale within networks of channels or chemical lanes is a crucial challenge in developing small scale devices to be used in microreactors or chemical sensors. In this context, ultrathin (i.e., monolayer) films, experimentally observed in spreading of nanodroplets or upon extraction from reservoirs in capillary rise geometries, represent an extreme limit which is of physical and technological relevance since the dynamics is governed solely by capillary forces. In this work we use kinetic Monte Carlo (KMC) simulations to analyze in detail a simple, but realistic model proposed by Phys. Rev. Lett. 76, 86 (1996)]] for the two-dimensional spreading on homogeneous substrates of a fluid monolayer which is extracted from a reservoir. Our simulations confirm the previously predicted time dependence of the spreading, X ( t--> infinity ) =A square root of t, with X (t) as the average position of the advancing edge at time t, and they reveal a nontrivial dependence of the prefactor A on the strength U0 of interparticle attraction and on the fluid density C0 at the reservoir as well as an U0 -dependent spatial structure of the density profile of the monolayer. The asymptotic density profile at long time and large spatial scale is carefully analyzed within the continuum limit. We show that including the effect of correlations in an effective manner into the standard mean-field description leads to predictions both for the value of the threshold interaction above which phase segregation occurs and for the density profiles in excellent agreement with KMC simulation results.

Computer Simulation↗

PubMed2005

Controlling chaos in a weakly coupled array of Bose-Einstein condensates.

The spatial structure of a Bose-Einstein condensate loaded into an optical lattice potential is investigated and the spatially chaotic distributions of the condensates are revealed under the tight-binding approximation. Adding a laser pulse on a proper site of the lattice and treating it as a control signal, control of the chaos in the system is carried out by using the Ott-Grebogi-Yorker scheme. For an appropriate laser pulse, we can suppress the chaos and push the system onto a stable manifold of a target orbit. After the control, a regular distribution, which may be expected in experiments or practical applications, of the condensates in the coordinate space is obtained.

Journal Article↗

PubMed2000

[Biological role of a neurotrophic factor fragment from pigment epithelium: structure-functional homology with a differentiation factor for the HL-60 cell line].

It was shown that the full-size neurotrophic factor from pigment epithelium (PEDF) induces the cell differentiation of the human promyelocyte leukemia cell line HL-60. A structural analysis of PEDF revealed in its C-terminal region a six-membered peptide fragment PEDF-(352-357) (PEDF-6) whose sequence is highly homologous to the 41-46 fragment of the active site of the human leukocyte differentiation factor HLDF (HLDF-6). The biological effect of PEDF and synthetic peptides PEDF-6 and HLDF-6 on the HL-60 cells and the early gastrula ectoderm of Xenopus laevis embryos was studied. On the basis of the structural and functional homologies of HLDF, PEDF, and their homologous peptides and the computer models of the spatial structures of the full-size PEDF and the PEDF with the C-terminal fragment split off tby the cleavage of the Leu380-Thr381 bond in the serpin loop, a hypothesis on the functional role of the serpin loop in PEDF was put forward.

Amino Acid Sequence↗