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At least 1,333 records · Page 74Linked to original sources
PubMedDate not supplied

Directional shifts in the barber pole illusion: effects of spatial frequency, spatial adaptation, and lateral masking.

We report the results of psychophysical experiments with the so-called barber pole stimulus providing new insights on the neuronal processes underlying the analysis of moving features such as terminators or line-endings. In experiment 1, we show that the perceived direction of a barber pole stimulus, induced by line-ending motion, is highly dependent on the spatial frequency and contrast of the grating stimulus: perceived direction is shifted away from the barber pole illusion at high spatial frequency in a contrast dependent way, suggesting that line-ends are not processed at high spatial scales. In subsequent experiments, we use a contrast adaptation paradigm and a masking paradigm in an attempt to assess the spatial structure and location of the receptive fields that process line-endings. We show that the adapting stimulus that weakens most the barber pole illusion is localized within the barber pole stimulus and not at line-endings' locations. Current models of line-endings' motion processing are discussed in the light of these psychophysical results.

Adaptation, Ocular↗
PubMed1987

Reversible unfolding of ribosomal protein E-L30: an NMR study.

Ribosomal protein E-L30 unfolds reversibly at pH values between 7.0 and 4.5. Unfolding of the protein involves a fast and a slow equilibrium, which depend on the degree of protonation of His19 and His33. Both the fast equilibrium between protonated and deprotonated histidines and the slow equilibrium between folded and unfolded protein could be monitored by means of 500-MHz 1H NMR spectroscopy. The degree of protonation of His19 and His33 appears to be determinant in the unfolding process of the protein. It is shown however that even when the histidines are uncharged, the protein has only limited stability, probably as a result of the presence of all four Glu's of E-L30 in its triple-stranded beta-sheet. At equimolar concentrations of the folded and unfolded form, the rate constant characterizing the transition between these forms is approximately 0.14 s-1. Making use of sequential resonance assignments of the 1H NMR spectrum [van de Ven, F.J.M., & Hilbers, C.W. (1986) J. Mol. Biol. 192, 419-441], the fast equilibrium could be interpreted in terms of alterations in the spatial structure of E-L30 in a specific domain of the molecule. This domain is also affected by temperature although not in exactly the same manner as by pH.

Escherichia coli↗
PubMed1978

Individual assignments of the methyl resonances in the 1H nuclear magnetic resonance spectrum of the basic pancreatic trypsin inhibitor.

In earlier work the resonances of the 20 methyl groups in the basic pancreatic trypsin inhibitor (BPTI) had been identified in the 360-MHz 1H nuclear magnetic resonance (NMR) spectra and most of the methyl lines had from spin-decoupling experiments been assigned to the different types of amino acid residues. The assignments to the different amino acid types were now completed by studies of the saturation transfer between the denatured and the globular forms of the inhibitor and by spin-decoupling experiments in nuclear Overhauser enhancement (NOE) difference spectra. These distinguished between the methyl resonances of Ala and Thr. Furthermore, for most of the methyl resonances, individual assignments to specific residues in the amino acid sequence were obtained from measurements of intramolecular proton-proton NOE's, use of lanthanide NMR shift and relaxation probes, and comparative studies of various chemically modified forms of BPTI. These data provide the basis for individual assignments of the methyl 13C NMR lines in BPTI and for detailed investigations of the relations between the spatial structure of the protein and the chemical shifts of the methyl groups. The methyl groups in BPTI are of particular interest since they are located almost exclusively on the surface of the protein and thus represent potential natural NMR probes for studies of the protein-protein interactions in the complexes formed between BPTI and a variety of proteases.

Alanine↗
PubMed1977

Evidence for topographical analogy between methionine-enkephalin and morphine derivatives.

Analogues of the endogenous opiate-receptor ligand [5-methionine]enkephalin (H-Tyr-Gly-Gly-Phe-Met-OH) were designed and synthesized for the purpose of testing the proposed similarity in spatial structure between this peptide and morphine derivatives. In the bioassay (inhibition of electrically induced contractions of the mouse vas deferens) [1-O-methyltyrosine,5-methionine]enkephalin, [1-N-methyltyrosine,5-methionine]enkephalin, [4-tryptophan,5-methionine]enkephalin, and [5-methionine sulfoxide]enkephalin possess, respectively, 0.4, 21, 27, and 67% activity of [5-methionine]enkephalin. These morphinomimetic activities correlate well with the opiate receptor affinities determined by displacement of [3H]naloxone in a guinea pig brain membrane preparation. The effects of O-methylation of the tyrosine residue and N-methylation of the terminal amino group on biological activity and receptor affinity support the hypothesis that the latter two moieties in the peptide correspond to the phenol group and the tertiary nitrogen, respectively, in morphine. Determination of the efficiency of energy transfer from tyrosine in position 1 to tryptophan in position 4 in [4-tryptophan,5-methionine]enkephalin from both tyrosine fluorescence quenching and relative enhancement of tryptophan fluorescence by means of a modified procedure permitted the calculation of an average intramolecular tyrosine-tryptophan separation of 10.0 +/- 1.1 A. Inspection of CPK models showed excellent agreement between this value and both the intrafluorophore distance in the 4 leads to 1 and 5 leads to 2 hydrogen bonded betaI-bend models of [4-tryptophan,5-methionine]enkephalin (9-11 A) and the phenol-phenyl separation in the potent morphine derivative 7alpha-(1(R)-hydroxy-1-methyl-3-phenylpropyl)-6,14-endo-ethenotetrahydrooripavine (8-10.5 A). The ensemble of these findings suggests an analogous topography for [5-methionine]enkephalin and morphine-oripavine derivatives.

Animals↗
PubMed1975

The association of bovine beta-casein. The importance of the C-terminal region.

Bovine beta-casein exists in the monomer form in solution (pH 6.5, 0.1 M NaCl, 0.5% w/v) at low temperatures, but associates to form polymers at higher temperatures. Gel filtration chromatography at 36 degrees showed that the polymer is large with a hydrodynamic size greater than that of a globular protein with a mol wt of 1.34 times 10(6). Removal of two C-terminal amino acids per molecule decreased the proportion of polymer in the solution, although the chromatographic behavior of the modified beta-casein monomers and polymers was retained. Removal of a 20 amino acid peptide from the C terminus of the beta-casein completely destroyed its ability to form polymers and removed the 8-anilino-1-naphthalenesulfonate binding site. However, deletion of segments of the protein from the N terminus did not decrease the ability of the modified beta-casein to associate, nor did it affect the 8-anilino-1-naphthalenesulfonate binding site greatly. It seems likely that all, or some, of the 20 amino acids at the C terminus are responsible for the associative behavior of beta-casein, possibly by the direct participation of their side chains in hydrophobic bond formation. However, removal of the C-terminal peptides may have disrupted the spatial structure of the native protein so that it could no longer associate normally.

Amino Acid Sequence↗
PubMedDate not supplied

Gelatin blending improves the performance of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) films for biomedical application.

To improve the performance of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx), gelatin was blended with PHBHHx at different ratios. With increasing gelatin content, the weight loss of gelatin/PHBHHx blend in simulated body fluid at 37 degrees C was accelerated. After 2 months, there was about 15% weight loss in PHBHHx blending with 30% gelatin. Scanning electron microscopy and X-ray diffraction results showed that gelatin blending increased the surface porosity and decreased the crystallinity, which may be responsible for the acceleration of the weight loss. Second harmonic generation results indicated that 10% gelatin blending had less disruption to PHBHHx spatial structure, resulting in better tensile mechanical properties. At the same time, increased surface porosity and decreased crystallinity caused by gelatin incorporation may be beneficial for cell growth compared with pure PHBHHx. All these indicated that gelatin incorporation may improve the performances of PHBHHx to meet the need of different situations during medical implantation.

3-Hydroxybutyric Acid↗
PubMed2005

High elongation of polyelectrolyte chains in the osmotic limit of spherical polyelectrolyte brushes: a study by cryogenic transmission electron microscopy.

We investigate the conformation of long polyelectrolyte chains attached to colloidal latex particles by cryogenic transmission electron microscopy (cryo-TEM). The dense grafting of the polyelectrolyte chains ("polyelectrolyte brush") leads to a confinement of the counterions and a concomitantly high osmotic pressure within the polyelectrolyte layer attached to the core particles. Cryo-TEM has provided first model-independent direct proof for the strong stretching of the polyelectrolyte chains by direct visualization. If salt is added, cryo-TEM clearly shows how chains collapse because of the strong screening of the electrostatic interaction. Moreover, the analysis of interacting particles by cryo-TEM shows that the polyelectrolyte chains retract at close contact. Hence, we demonstrate how cryo-TEM can be used to analyze directly the spatial structure of polyelectrolyte brushes in situ.

Journal Article↗
PubMed2005

1,8-Bis(hexamethyltriaminophosphazenyl)naphthalene, HMPN: a superbasic bisphosphazene "proton sponge".

It is shown that a combination of Schwesinger's phosphazene base concept and the idea of the disubstituted 1,8-naphthalene spacer, first introduced by Alder in paradigmatic 1,8-bis(dimethylamino)naphthalene (DMAN), yields a new superbase, HMPN, which represents the up to date most basic representative of this class of "proton sponges", as evidenced by the theoretically estimated proton affinity PA = 274 kcal/mol and the measured pK(BH+) (MeCN) 29.9 +/- 0.2. HMPN is by nearly 12 orders of magnitude more basic than Alder's classical 1,8-bis(dimethylamino)naphthalene (DMAN). The title compound, HMPN, is prepared and fully characterized. The spatial structure of HMPN and its conjugate acid is determined by X-ray technique and theoretical DFT calculations. It is found that monoprotonated HMPN has an unsymmetrical intramolecular hydrogen bridge (IHB). This cooperative proton chelating effect renders the bisphosphazene more basic than Schwesinger's set of "monodentate" P1 phosphazene bases. The density functional calculations are in good accordance with the experimental results, providing some complementary information. They conclusively show that the high basicity of HMPN is a consequence of the high energy content of the base in its initial neutral state and the intramolecular hydrogen bonding in the resulting conjugate acid with contributions to proton affinity of 14.1 and 9.5 kcal/mol, respectively.

Journal Article↗
PubMed2006

Water density in the electric double layer at the insulator/electrolyte solution interface.

I studied the spatial structure of the thick transition region between n-hexane and a colloidal solution of 7-nm silica particles by X-ray reflectivity and grazing incidence small-angle scattering. The interfacial structure is discussed in terms of a semiquantitative interface model wherein the potential gradient at the n-hexane/sol interface reflects the difference in the potentials of "image forces" between the cationic Na(+) and anions (nanoparticles) and the specific adsorption of surface charge at the interface between the adsorbed layer and the solution, as well as at the interface between the adsorbed layer and n-hexane. The X-ray scattering data revealed that the average density of water in the field approximately 10(9)-10(10) V/m of the electrical double layer at the hexane/silica sol interface is the same as, or only few percent higher (1-7%) than, its density under normal conditions.

Colloids↗
PubMed2006

Mass transfer limitations at crystallizing interfaces in an atomic force microscopy fluid cell: a finite element analysis.

Although atomic force microscopy (AFM) has emerged as the preeminent experimental tool for real-time in situ measurements of crystal growth processes in solution, relatively little is known about the mass transfer limitations that may impact these measurements. We present a continuum analysis of flow and mass transfer in an atomic force microscope fluid cell during crystal growth, using data acquired from calcium oxalate monohydrate (COM) crystal growth measurements as a comparison. Steady-state flows and solute concentration fields are computed using a three-dimensional, finite element method implemented on a parallel supercomputer. Steady-state flow results are compared with flow visualization experiments to validate the model. Computations of the flow field demonstrate how nonlinear momentum transport alters the spatial structure of the flow with increasing flow volume, altering mass transport conditions near the AFM cantilever and tip. The simulations demonstrate that the combination of solute depletion from crystal growth and mass transfer resistance lowers the solute concentration in the region between the tip and the crystal compared with the solute concentration at the inlet of the AFM cell. For example, using experimentally measured growth rates for COM, the solute concentration in this region is 3.1% lower than the inlet value because the solute consumed by crystal growth beneath the AFM tip cannot be replenished fully due to mass transport limitations. The simulations also reveal that increasing the flow rate through the cell does not affect this difference significantly because of the inherent shielding by the AFM tip in proximity with the crystal surface. Models such as the one presented here, used in conjunction with AFM measurements, promise more precise interpretations of measurement data.

Journal Article↗
PubMed1998

Wave propagation mediated by GABAB synapse and rebound excitation in an inhibitory network: a reduced model approach.

A reduction method is used to analyze a spatially structured network model of inhibitory neurons. This network model displays wave propagation of postinhibitory rebound activity, which depends on GABAB synaptic interactions among the neurons. The reduced model allows explicit solutions for the wavefronts and their velocity as a function of various parameters, such as the synaptic coupling strength. These predictions are shown to agree well with the numerical simulations of the conductance-based biophysical model.

Electric Conductivity↗
PubMed2001

Mechanism of oxidation of oxymyoglobin by copper ions: comparison of sperm whale, horse, and pig myoglobins.

The influence of Cu2+ concentration, pH, and ionic strength of the solution as well as redox-inactive zinc ions on the rate of oxidation of sperm whale, horse, and pig oxymyoglobins (oxy-Mb) by copper ions has been studied. These myoglobins have homologous spatial structures and equal redox potentials but differ in the number of histidines located on the surface of the proteins. It was shown that oxy-Mb can be oxidized in the presence of Cu2+ through two distinct pathways depending on which histidine binds the reagent and how stable the complex is. A slow pH-dependent catalytic process is observed in the presence of equimolar Cu2+ concentration for sperm whale and horse oxymyoglobins. The curves of pH dependence in both cases are sigmoid with pK(eff) corresponding to the ionization. The process is caused by the strong binding of Cu2+ to His113 and His116, an analogous His residue being absent in pig Mb. In contrast, rapid oxidation of 10-15% of pig oxy-Mb is observed under the same conditions (fast phase), which is not accompanied by catalysis because the reduced copper is apparently not reoxidized. The complexing of Cu2+ with His97 situated near the heme is probably responsible for the fast phase of the reaction. The affinity of His97 for Cu2+ must be significantly lower than those of the "catalytic" His residues since the fast phase does not contribute markedly to the rate of sperm whale and horse oxy-Mb oxidation. Increasing copper concentration does not produce a proportional growth in the oxidation rate of sperm whale and horse oxy-Mbs. Which Cu2+ binding sites of Mb make main contributions to the His reaction rate at different Cu2+/Mb ratios from 0.25 to 10 is discussed.

Animals↗
PubMedDate not supplied

[Efficient synthesis of natural alpha-conotoxins and their analogs].

An efficient scheme for the synthesis of alpha-conotoxins, containing 12-18 amino acid residues and two disulfide bridges, was proposed. Its advantages are: (1) the avoidance of orthogonal protections of Cys residues; (2) a lower number of stages in a cycle of the peptide chain elongation by the method of solid phase synthesis; (3) the linear product is sufficiently pure for being used at the next stage of the disulfide bond formation without additional purification; and (4) a substantially reduced time of oxidation to disulfides at pH 10, which led to the target product in a high yield. A number of natural alpha-conotoxins (GI, ImI, EI, MII, and SIA), affecting the muscle and neuronal nicotinic acetylcholine receptors of various types, and several new analogues of these conotoxins (in particular, [Tyr10]ImI, [Gln12]GI, and [Ser1]GI) were synthesized by this scheme. They were used for elucidating the spatial structure of alpha-conotoxins by 1H NMR spectroscopy and for studying the ligand-binding sites of their receptors.

Amino Acid Sequence↗
PubMedDate not supplied

[ESR study of the interaction of cytotoxin II with model membranes].

Cytotoxin II from the venom of the Central-Asian cobra Naja oxiana spin-labeled at Lys35 (SLCT II) was studied by ESR spectroscopy in aqueous solution and upon interaction with phospholipid vesicles from egg phosphatidylcholine or its mixture with dimyristoylphosphatidylglycerol (molar ratio 9:1). The distribution of SLCT II between the aqueous and lipid phases depended on the toxin and lipid concentrations and on the solution ionic strength. It was analyzed using the modified Gouy-Chapman equation that takes into account different charges of the cytotoxin in solution and in membrane. The analysis revealed two states of the cytotoxin-lipid complex. The first state corresponds to monomeric SLCT II hydrophobically interacting with the lipid membrane [a binding constant of (8 +/- 3) x 10(3) M-1] and carrying the charge of 4.4 +/- 0.3. On the basis of these parameters and the spatial structure of cytotoxin II in dodecylphosphocholine micelles, we concluded that the cytotoxin is mainly incorporated into the region of polar groups of the lipid bilayer. The second state of SLCT II is realized at high cytotoxin concentrations in the membrane and corresponds to the formation of toxin-lipid complexes that destruct the membrane bilayer structure.

Algorithms↗
PubMedDate not supplied

Turning on and off with excitation: the role of spike-timing asynchrony and synchrony in sustained neural activity.

Delay-related sustained activity in the prefrontal cortex of primates, a neurological analogue of working memory, has been proposed to arise from synaptic interactions in local cortical circuits. The implication is that memories are coded by spatially localized foci of sustained activity. We investigate the mechanisms by which sustained foci are initiated, maintained, and extinguished by excitation in networks of Hodgkin-Huxley neurons coupled with biophysical spatially structured synaptic connections. For networks with a balance between excitation and inhibition, a localized transient stimulus robustly initiates a localized focus of activity. The activity is then maintained by recurrent excitatory AMPA-like synapses. We find that to maintain the focus, the firing must be asynchronous. Consequently, inducing transient synchrony through an excitatory stimulus extinguishes the sustained activity. Such a monosynaptic excitatory turn-off mechanism is compatible with the working memory being wiped clean by an efferent copy of the motor command. The activity that codes working memories may be structured so that the motor command is both the read-out and a direct clearing signal. We show examples of data that is compatible with our theory.

Action Potentials↗
PubMed1997

Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: comparison with distance geometry calculations.

The three-dimensional spatial structure of a methylene-acetal-linked thymine dimer present in a 10 basepair (bp) sense-antisense DNA duplex was studied with a genetic algorithm designed to interpret NOE distance restraints. Trial solutions were represented by torsion angles. This means that bond angles for the dimer trial structures are kept fixed during the genetic algorithm optimization. Bond angle values were extracted from a 10 bp sense-antisense duplex model that was subjected to energy minimization by means of a modified AMBER force field. A set of 63 proton-proton distance restraints defining the methylene-acetal-linked thymine dimer was available. The genetic algorithm minimizes the difference between distances in the trial structures and distance restraints. A large conformational search space could be covered in the genetic algorithm optimization by allowing a wide range of torsion angles. The genetic algorithm optimization in all cases led to one family of structures. This family of the methylene-acetal-linked thymine dimer in the duplex differs from the family that was suggested from distance geometry calculations. It is demonstrated that the bond angle geometry around the methylene-acetal linkage plays an important role in the optimization.

Algorithms↗
PubMedDate not supplied

[1H-NMR analysis of the heteroassociation of caffeine with the antibiotic actinocyl-bis(3-dimethylaminopropylamine) in aqueous solution].

The heteroassociation of caffeine (CAF) and the synthetic antibiotic actinocyl-bis(3-dimethylaminopropylamine) (ACT) was studied in aqueous solution by one- and two-dimensional 1H NMR spectroscopy at 500 MHz. The equilibrium reaction constants, thermodynamic parameters (delta H and delta S) of ACT heteroassociation with CAF, the limiting values of proton chemical shifts of their molecules in the heteroassociation complex, and the spatial structure of the ACT-CAF complex were determined from the experimental dependences of proton chemical shifts of the aromatic molecules on concentration and temperature. The parameters of CAF heteroassociation with the phenoxazone antibiotic actinomycin D and its synthetic analogue ACT were comparatively analyzed and conclusions were made on the crucial role of stacking interactions of the chromophores of CAF and the phenoxazone antibiotics in the formation of the heterocomplexes in aqueous solution.

Antineoplastic Agents↗
PubMed2002

Characterization of soil organic matter content of two sample size populations along a climatic transect.

Soil organic matter (SOM) content was determined in two populations of soil samples that were taken from 0-2 soil depth. One population represented soil samples that were taken from a square of 25 cm2 in size (small-S population) and the other population represented soil samples that were taken from a square of 2500 cm2 in size (large-L population). The samples were collected on hillslopes in different climatic regions: Mediterranean (GIV), semi-arid (MAL), mildly-arid (MIS) and arid (KAL). The results of both S and L populations showed decreasing SOM mean and variance from the Mediterranean site to the arid site. Statistical and spatial characteristics of each population were compared between the climatic regions. In addition, comparison between the two populations was made for each site. The difference in sample size did not significantly affect the mean values of SOM of the two populations in sites GIV, MAL and KAL, but did affect the mean at site MIS. At all study sites, except for site MAL, the variance increased with decreasing sample size. At sites GIV and KAL the coefficient of variation of S population was higher (more than 1.5 times) than that of L population, whereas at sites MAL and MIS, the differences were negligible. The relationships between the values of S and L samples at the individual sampling points defined the background of the study sites, which reflects the effect of vegetation (type), grazing, biological crust and soil properties. It was found that at the extreme sites GIV and KAL the background was characterized by relatively low SOM content with small areas of high organic matter content. At site MIS the background was characterized by relatively high SOM with small areas of low organic matter content. At site MAL the background was not dominated by high values of SOM nor by low ones. The spatial pattern of L population became more simple with increasing aridity. At the relatively wet sites the spatial pattern did not depend on the sample size while in the more arid sites it was sample size dependent. It was indicated that the spatial structure of SOM at the semi-arid and mildly arid sites is anisotropic whereas at the Mediterranean and arid sites it is isotropic.

Climate↗