PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “spatial structure”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
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↗
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↗
PubMed2002

Spatial structure and symmetry of simple-cell receptive fields in macaque primary visual cortex.

I present measurements of the spatial structure of simple-cell receptive fields in macaque primary visual cortex (area V1). Similar to previous findings in cat area 17, the spatial profile of simple-cell receptive fields in the macaque is well described by two-dimensional Gabor functions. A population analysis reveals that the distribution of spatial profiles in primary visual cortex lies approximately on a one-parameter family of filter shapes. Surprisingly, the receptive fields cluster into even- and odd-symmetry classes with a tendency for neurons that are well tuned in orientation and spatial frequency to have odd-symmetric receptive fields. The filter shapes predicted by two recent theories of simple-cell receptive field function, independent component analysis and sparse coding, are compared with the data. Both theories predict receptive fields with a larger number of subfields than observed in the experimental data. In addition, these theories do not generate receptive fields that are broadly tuned in orientation and low-pass in spatial frequency, which are commonly seen in monkey V1. The implications of these results for our understanding of image coding and representation in primary visual cortex are discussed.

Animals↗
PubMed1987

The two-dimensional spatial structure of simple receptive fields in cat striate cortex.

1. A reverse correlation (6, 8, 25, 35) method is developed that allows quantitative determination of visual receptive-field structure in two spatial dimensions. This method is applied to simple cells in the cat striate cortex. 2. It is demonstrated that the reverse correlation method yields results with several desirable properties, including convergence and reproducibility independent of modest changes in stimulus parameters. 3. In contrast to results obtained with moving stimuli, we find that the bright and dark excitatory subregions in simple receptive fields do not overlap to any great extent. This difference in results may be attributed to confounding the independent variables space and time when using moving stimuli. 4. All simple receptive fields have subregions that vary smoothly in all directions in space. There are no sharp transitions either between excitatory subregions or between subregions and the area surrounding the receptive field. 5. Simple receptive fields vary both in the number of subregions observed, in the elongation of each subregion, and in the overall elongation of the field. In contrast with results obtained using moving stimuli, we find that subregions within a given receptive field need not be the same length. 6. The hypothesis that simple receptive fields can be modeled as either even symmetric or odd symmetric about a central axis is evaluated. This hypothesis is found to be false in general. Most simple receptive fields are neither even symmetric nor odd symmetric. 7. The hypothesis that simple receptive fields can be modeled as the product of a width response profile and an orthogonal length response profile (Cartesian separability) is evaluated. This hypothesis is found to be true for only approximately 50% of the cells in our sample.

Animals↗
PubMedDate not supplied

[Spatial structure of cro-repressor in a solution. II. Effect of ionized groups].

The technique of 1H NMR spectroscopy and absorption UV spectroscopy were used to study the ionization of the tyrosine phenol cycles and the effect of ionizable groups on the chemical shifts of signals from protons in the side chains of several amino acid residues. The microenvironment of these residues was established by analysing the titration curves. The mutual orientation of two functionally important adjacent alpha-helical protein regions was determined in solution. The signals from methionine residues belonging to different regions of the secondary structure were assigned in the NMR spectrum. The results indicate that the spatial structure of the repressor is similar in solution an in the crystal. They confirm the model proposed for the cro repressor interaction with DNA and based on the data of X-ray diffraction analysis.

Bacteriophage lambda↗
PubMed1995

[Spatial structure of bacterioopsin transmembrane segments C, E, and G from two-dimensional 1H-NMR data].

The spatial structure of synthetic peptides with transmembrane segment sequences C (residues 67-106), E (128-162), and G (190-233) of bacterioopsin from Halobacterium halobium solubilized in methanol-chloroform 1:1 containing 0.1 M LiClO4 was computed based on 2D 1H NMR data. Segment C forms a right alpha-helix between Pro77 and Val101. The residue Pro91 within the alpha-helix induces a 25 degrees "kink". Segment E forms a right alpha-helix between Val136 and Ser158. Segment G includes alpha-helical region, which begins from CO of Ile198 and ends at N alpha-H of Arg227. The torsion angles, chi 1, of the side chains were unambiguously determined for most of the residues within the alpha-helical regions. Conformations of some side chains of the transmembrane segment residues in the solution were found to differ from their previously reported conformations determined by electron microscopy. Conformations of the sites terminating the C and E segment alpha-helices were refined.

Amino Acid Sequence↗
PubMed1985

Evidence for spatial structure in the cortical input to the monkey lateral geniculate nucleus.

We combined visual stimulation of the corticogeniculate pathway with cryogenic blockade of area 17 to examine the visual spatial structure of the cortical influence on single macaque LGN cells. Excitatory central areas surrounded by inhibitory regions and vice versa were found with equal frequency. Unstructured influences were also seen. The structure of the influence suggests that modulation of the spatial parameter may be an important function for the corticogeniculate pathway.

Animals↗
PubMedDate not supplied

[The distribution of direct interactions in the spatial structures of globular proteins].

The hydrogen bond distributions in 123 protein structures with the atom coordinates established at a resolution of less than 2 A were analyzed. The peculiarities of hydrogen bond distributions with respect to the lengths and remoteness of contacting residues in the primary structure were established. A hierarchy of H-bond energy distribution in the spatial structure of protein globules was demonstrated. The role of hydrogen bonds in the formation of domain structure and their special properties in proteins with different types of secondary structure are discussed.

Animals↗
PubMed1987

[Spatial structure of gramicidin A in organic solvents. 1H-NMR analysis of conformation heterogeneity in ethanol].

Structural features of double helices formed by polypeptides with alternating L- and D-amino acid residues were analysed. It was found that the map of short distances (less than 4 A) between protons of the two backbones is unique for each double helix type and even its fragment implies unambiguously parameters of the helix (i.e. parallel or antiparallel, handedness, pitch of helix, relative shift of polypeptide chains). By analysis of two-dimensional 1H-NMR spectra (COSY, RELSY, HOHAHA, NOESY), proton resonances of [Val1]gramicidin A (GA) in the ethanol solution were assigned. The results obtained show that the solution contains five stable conformations of GA in comparable concentrations. Monomer of GA is in a random coil conformation. Specific maps of short interproton distances for the other four species (1-4) were obtained by means of two dimensional nuclear Overhauser effect spectroscopy. The maps as well as spin-spin couplings of the H-NC alpha-H protons and solvent accessibilities of the individual amide groups correspond to four types of double helices pi pi LD 5,6 with 5.6 residues per turn. The double helices are related to the Veatch species 1-4 of GA. Species 1 and 2 are left-handed parallel double helices increase increase pi pi LD 5,6 with different relative shift of polypeptide chains. Species 3 is a left-handed antiparallel double helix increase decrease pi pi LD 5,6 and species 4 is a right-handed parallel double helix increase increase LD 5,6. In the dimers helices are fixed by the maximum number (28) of interbackbone hydrogen bonds NH...O = C possible for these structures. Species 1, 3 and 4 have C2 symmetry axes. Relationship between gramicidin A spatial structures induced by various media is discussed.

Ethanol↗
PubMed1985

Impaired spatial structures.

Our knowledge of the very early processes of human development, such as how the body becomes experienced as a three-dimensional spatial structure containing different functional cavities that communicate with the outer world via bodily orifices which are regulated by appropriate sphincter control, is far from being complete. Analysing spatial aspects of psychodynamic phenomena can bring us closer to understanding the nature of internal and external spaces and their role in harmonious and disturbed psychic development. In the paper attention is called to special symbolic connexions between open and strictly closed spaces, malfunctioning boundaries in the outside world and insufficient-containing functions and respective disorders in the development of the ego and ego boundaries. Specific defensive manoeuvres, aimed at annihilating inner spaces and bringing the organism to a 'thing-like', two-dimensional way of existence, are demonstrated in the material of patients with severe psychosomatic diseases and identity problems.

Adult↗
PubMed2001

The spatial structure of sexual and cytonuclear polymorphism in the gynodioecious Beta vulgaris ssp. maritima: I/ at a local scale.

We have analyzed the spatial distribution of the sex phenotypes and of mitochondrial, chloroplast, and nuclear markers within two gynodioecious populations of Beta vulgaris ssp. maritima. Within both populations, sexual phenotype variation is controlled mainly by the cytoplasmic genotype, although in one study population a joint polymorphism of cytonuclear factors is clearly involved. In spite of contrasts in the ecology (mainly due to different habitats), a clear common feature in both populations is the highly patchy distribution of cytoplasmic haplotypes, contrasting with the wide distribution of nuclear diversity. This high contrast between cytoplasmic vs. nuclear spatial structure may have important consequences for the maintenance of gynodioecy. It provides opportunities for differential selection since nuclear restorer alleles are expected to be selected for in the presence of their specific cytoplasmic male sterile (CMS) type, but to be neutral (or selected against if there is a cost of restoration) in the absence of their CMS type. Selective processes in such a cytonuclear landscape may explain the polymorphism we observed at restorer loci for two CMS types.

Cell Nucleus↗
PubMed1995

The features of the spatial structure of the gramicidine A-cesium complex.

Earlier obtained two-dimensional 1H-NMR spectroscopy data were used to analyze the spatial structure and conformational mobility of the double right increases decreases pi pi 7.2 LD helix of the complex formed by gramicidine A and Cs+ ions in an organic solvent (a chloroform-methanol mixture). Analysis of the experimental data permitted the determination of a set of conformations for each of the high-mobility residue side chains in the solution. The energy refinement of the most probable conformation of the double right increases decreases pi pi 7.2 LD helix was made and conformational rearrangements of the tryptophan residue side chain were studied in detail.

Cesium↗
PubMed1992

[Spatial structure and antigenic activity of non-glycosylated forms of embryonal prealbumin-1 (EPA-1NG)].

The influence of temperature and pH on the spatial structure of EPA-1NG has been studied by means of circular dichroism and differential UV-spectroscopy, indicating the molecule to consist mainly of beta-structures. A conformational transition in the molecule was observed within the range of 40-50 degrees C. The further temperature elevation (up to 70 degrees C) was accompanied to the complete distortion of the parent conformation, which is reversed after cooling down to 20 degrees C. A correlation of the spectral data with the antigenic activity of genuine EPA-1NG and its carboxymethylated, heat-degraded and pH-denatured derivatives demonstrates that some antigenic determinants of EPA-1NG appear to be topographic.

Antigens↗