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PubMed2004

Molecular modeling of nearly full-length ErbB2 receptor.

Members of the epidermal growth factor receptor family play important roles in various cellular processes, both in physiological and in pathological conditions. Dimerization and autophosphorylation of these receptor tyrosine kinases are key events of signal transduction. Details of the molecular events of the signaling are not entirely known. To facilitate the understanding of receptor structure and function at the molecular level, a molecular model was built for the nearly full-length ErbB2 dimer. Modeling was based on the x-ray or nuclear-magnetic resonance structures of extracellular, transmembrane, and intracellular domains. The extracellular domain was positioned above the cell membrane based on the distance determined from experimentally measured fluorescence resonance energy transfer. Favorable dimerization interactions are predicted for the extracellular, transmembrane, and protein kinase domains in the model of a nearly full-length dimer of ErbB2, which may act in a coordinated fashion in ErbB2 homodimerization, and also in heterodimers of ErbB2 with other members of the ErbB family.

Cell Line, Tumor↗

PubMed2005

Thymosin beta4 induces a conformational change in actin monomers.

Using fluorescence resonance energy transfer spectroscopy we demonstrate that thymosin beta(4) (tbeta(4)) binding induces spatial rearrangements within the small domain (subdomains 1 and 2) of actin monomers in solution. Tbeta(4) binding increases the distance between probes attached to Gln-41 and Cys-374 of actin by 2 A and decreases the distance between the purine base of bound ATP (epsilonATP) and Lys-61 by 1.9 A, whereas the distance between Cys-374 and Lys-61 is minimally affected. Distance determinations are consistent with tbeta(4) binding being coupled to a rotation of subdomain 2. By differential scanning calorimetry, tbeta(4) binding increases the cooperativity of ATP-actin monomer denaturation, consistent with conformational rearrangements in the tbeta(4)-actin complex. Changes in fluorescence resonance energy transfer are accompanied by marked reduction in solvent accessibility of the probe at Gln-41, suggesting it forms part of the binding interface. Tbeta(4) and cofilin compete for actin binding. Tbeta(4) concentrations that dissociate cofilin from actin do not dissociate the cofilin-DNase I-actin ternary complex, consistent with the DNase binding loop contributing to high-affinity tbeta(4)-binding. Our results favor a model where thymosin binding changes the average orientation of actin subdomain 2. The tbeta(4)-induced conformational change presumably accounts for the reduced rate of amide hydrogen exchange from actin monomers and may contribute to nucleotide-dependent, high affinity binding.

Acrylamide↗

PubMed1999

The effect of the Müller-Lyer illusion on map reading.

One important reason for studying visual illusions is that they can influence real-world perception as people interact with human-made displays. Three experiments examined how the Müller-Lyer illusion affects distance judgments and decision-making in the complex graphical context of a map by having subjects estimate the lengths of road segment lines framed by inward-going or outward-going wings in actual maps, in control displays that had the map context removed, and in simulated maps. The experiments showed that (1) outward-going wings led to higher distance estimates than did inward-going wings to the same extent both with and without the map context, (2) decisions based on distances determined from maps were affected by Müller-Lyer elements in the maps, and (3) map readers' measurement behavior influenced the effect of the Müller-Lyer elements in maps. The discussion focuses on how certain display manipulations and task manipulations affect the Müller-Lyer illusion. In addition, the discussion addresses the instances in which using a map might be affected by misestimation due to Müller-Lyer elements.

Adult↗

PubMed2002

Selective reaching: evidence for multiple frames of reference.

Students participated in 3 experiments investigating the use of environment- and action-centered reference frames in selective reaching. They pointed to a green target appearing either with or without a red distractor. Target-distractor distance was manipulated, and distractor interference (difference between distractor trials and no-distractor trials) was measured in reaction time, movement time, and movement endpoint. Target-distractor distance determined the dominant frame of reference. Small distances evoked an environment-centered framework that encoded targets within an external context. Large distances evoked an action-centered framework that encoded targets relative to the start position of the hand. Results support the hypothesis that the brain represents spatial information in multiple frames of reference, with the dominant frame of reference being dependent on the task demands.

Adolescent↗

PubMed1991

An interpretation of the effects of age on migration: Nordic migrants' choice of settlement in Sweden.

A model of the relationship between age and migration is developed and applied to data concerning migrants from other Scandinavian countries who settled in Sweden between 1968 and 1985. The author shows "how changes in Sweden's domestic economic conditions and distance determine the probability for settlement in any of its 24 provinces for migrants of different ages. The results show that in the integrated Nordic labor market, wages at destination do not explain differences in migrants' settlement behavior across ages. Instead they suggest that the major factors to explain the differences are the labor market situation for the different age groups and distance."

Age Factors↗

PubMed1992

Cuticular hydrocarbons, isoenzymes and behavior of three populations of Anopheles darlingi from Brazil.

Three populations of Anopheles darlingi were studied for cuticular hydrocarbons, isoenzymes and patterns of peak biting activity. Differences were found in specimens from Costa Marques, a malaria endemic area; Dourado, a site with a very exophilic population and Juturnaíba, located near the type locality. Twelve hour collections from sunset to sunrise showed that An. darlingi from Costa Marques had a bimodal biting activity profile with a major peak at sunset and a minor peak at sunrise. At Dourado, the pattern was trimodal, with peaks at both morning and evening periods of twilight and near midnight. The Juturnaíba population showed a slight increase in activity near 2000 and 0100 h. Nei's genetic distances, determined by isoenzyme electrophoresis between pairs of populations, were low (D < or = 0.049). Using discriminant analysis for the cuticular hydrocarbons, 92.4% of the specimens from Costa Marques, 91.2% of the specimens from Dourado and 61.3% from Juturnaíba were correctly identified. Cuticular hydrocarbon and isoenzyme results matched very well: the smaller the Nei's distance, the more misidentifications occurred in the jackknife estimator used in the cuticular hydrocarbon analysis. This is the first report of cuticular hydrocarbon analysis in combination with isoenzymes to investigate neotropical anopheline species.

Animals↗

PubMed1999

[Interatomic distances of molecule for orthohydrogen and parahydrogen].

The determination of rotational Raman spectra for hydrogen gas at 354.9, 587.4, 814.7 and 1035.1 cm(-1) by FT-Raman spectrometry is described in this paper. The Raman bands at 354.9 and 814.7 cm(-1) were assigned to rotational levels J = 0 --> J = 2 and J = 2 --> J = 4 for parahydrogen, and those at 587.4 and 1035.1 cm(-1) were assigned to rotational levels J = 1 --> J = 3 and J = 3 --> J = 5 for orthohydrogen. The interatomic distances determined for orthohydrogen and parahydrogen molecules with nonrigid rotator model are 75.03 and 74.98 pm, respectively.

English Abstract↗

PubMed1991

Arrangement of the substrates at the active site of brain pyridoxal kinase.

The distances between enzyme-bound paramagnetic CrATP (a stable, beta, gamma-bidentate complex of Cr3+ and ATP) at the active site of sheep brain pyridoxal kinase and the protons of bound inhibitor 4-dPyr (4-deoxypyridoxine) were determined in the ternary enzyme-CrATP.4-dPyr complex by measuring the paramagnetic effects of Cr3+ on the longitudinal relaxation rates (1/T1p) of the protons of 4-dPyr. The correlation time for the Cr(3+)-4-dPyr dipolar interaction on the enzyme was estimated as 1.59 ns by the frequency dependence of 1/T1p of water protons. Temperature dependence of 1/T1p values indicated the fast exchange of 4-dPyr from the paramagnetic enzyme.CrATP.4-dPyr complex; hence the measured 1/T1p values can be used for metalnucleus distance determinations. The distances from the Cr3+ of the enzyme-bound CrATP to the 2-methyl (7.19 A), 4-methyl (7.18 A), and H6 proton (6.18 A) of the 4-dPyr are too great to permit a direct coordination of any group from 4-dPyr. However, these distances can be built into a model in which phosphorus of the gamma-phosphoryl group of ATP is 4 A away from the oxygen atom of the 5-CH2OH group of the 4-dPyr. This suggests that phosphorylation of pyridoxal can occur via direct transfer of the phosphoryl group between the bound substrates at the active site of pyridoxal kinase.

Adenosine Triphosphate↗

PubMed1990

Identification of a beta-turn in the tertiary structure of a peptide fragment of the Alzheimer amyloid protein.

In an attempt to understand the three-dimensional structure of the Alzheimer amyloid protein, a fragment decapeptide was studied by nuclear magnetic resonance spectroscopy. Using two-dimensional techniques, protons close in space were identified and their interproton distances determined. These distances were then used as input data for distance geometry calculations. The resulting three-dimensional structures suggest the presence of a beta-turn in the C-terminus of the decapeptide.

Amino Acid Sequence↗

PubMed1989

Conformation of NAD+ bound to allosteric L-lactate dehydrogenase activated by chemical modification.

On modification of arginine residues with 2,3-butanedione, the Thermus caldophilus L-lactate dehydrogenase is converted to an activated form that is independent of an allosteric effector, fructose 1,6-bisphosphate (Fru-1,6-P2). The conformation of NAD+ bound to the modified enzyme in the absence of Fru-1,6-P2 was investigated by means of proton NMR, analyzing the time dependence of the transferred nuclear Overhauser effect (TRNOE) and TRNOE action spectra. The inter-proton distances determined on TRNOE analysis indicated that both the nicotinamide riboside moiety and the adenosine moiety of NAD+ were in the anti conformation, the ribose rings being in the C3'-endo form. This conformation was almost the same as that of NAD+ bound to the native enzyme-Fru-1,6-P2 complex, rather than that of NAD+ bound to the free native enzyme. These results suggest that the C3'-endo-anti form of the enzyme-bound NAD+ is essential for the activation of the T. caldophilus L-lactate dehydrogenase.

Allosteric Regulation↗

PubMed1985

Nuclear magnetic resonance studies of fructose 2,6-bisphosphate and adenosine 5'-monophosphate interaction with bovine liver fructose-1,6-biphosphatase.

1H and 31P nuclear magnetic resonance was used to investigate the interaction of AMP and fructose 2,6-bisphosphate (Fru-2,6-P2) with bovine liver fructose-1,6-bisphosphatase. Mn2+ bound to fructose-1,6-bisphosphatase was used as a paramagnetic probe to map the active and AMP allosteric sites of fructose-1,6-bisphosphatase. Distances between enzyme-bound Mn2+ and the phosphorus atoms at C-6 of fructose-6-P and alpha-methyl-D-fructofuranoside 1,6-bisphosphate were identical, and the enzyme-Mn to phosphorus distance determined for the C-6 phosphorus atom of Fru-2,6-P2 was very similar to these values. Likewise, the enzyme-Mn to phosphorus distances for Pi, the C-1 phosphorus atom of alpha-methyl-D-fructofuranoside 1,6-bisphosphate, and the C-2 phosphorus atom of Fru-2,6-P2 agreed within 0.5 A. The distance between enzyme-bound Mn2+ and the phosphorus atom of AMP was significantly shorter than the distances obtained for any of the aforementioned ligands, but the presence of Fru-2,6-P2 caused the enzyme-Mn to phosphorus distance for AMP to lengthen markedly. NMR line broadening of AMP protons was studied at various temperatures. The dissociation rate constant was found to be greater than 20 s-1. It was concluded that Fru-2,6-P2 strongly affects the interaction of AMP with fructose-1,6-bisphosphatase and that the sugar most likely acts at the active site of the enzyme.

Adenosine Monophosphate↗

PubMed1986

[Analysis of the reproducibility of conditions of intracavitary irradiation of patients with cervix cancer].

The paper is concerned with the results of an analysis of reproducibility of conditions for intracavitary irradiation of 20 cervical cancer patients using metracolpostat, a combined therapeutic endostat consisting of 3 tubes: the central one to introduce radiation sources into the cervical canal and cavity of the uterus and 2 lateral ones with ovoids to deliver the sources to the vaults of the vagina. Topometric investigations for each patient were performed 4 times: before the first session of fractionated intracavitary irradiation with high activity 252Cf sources using the ANET-B unit and after each session of irradiation. It was shown that discordances between distances from the central endostat to the right and left lateral ovoids determined during roentgenotopometric preparation of each patient and taken as a basis of dosimetric design, and discordances between these distances determined as a result of roentgenotopometric control after each laying, are a random value distributed according to the normal law.

Brachytherapy↗

PubMed1985

[Population genetics of taiga hunters-deer breeders. Characteristics of the prevalence of HLA system markers among the native population of Central Siberia].

The postulated peculiarities of distribution of the HLA antigens in the Evenk population of the Central Siberia indicate this population to be, on the whole, Mongoloid. Prolonged isolated existence of small inbred populations of the Evenks resulted in the number of specific HLA-complex features, such as poor antigen diversity, low level of heterozygosity. Non-homogeneity of gene frequencies was noted, the prevailing genes being A9, B40 with frequencies reaching 50%. Of the remaining alleles found in the Evenks A2, Aw19 in A locus, B5, B15, B17, B27, Bw35 in B locus and Cw2, Cw3, Cw4-in C locus are only widely spread. Similar heterozygosis levels and the HLA-system profiles draw the Evenks and the populations of American Indians and Eskimos closer to one another. On the basis of the fact that significant positive correlation exists between genetic and geographic distances determined for the Evenks and the native populations of America, genetic resemblance of these populations may be considered as evidence for their original relationship. Postulated closeness of native Central-Siberian populations to Americanoids, as regards HLA-system, makes it possible to consider formation of specific complex of HLA-system peculiarities in native American population in the light of their Siberian origin, for the first time.

Animal Husbandry↗

PubMed1984

Photometric oculometry. II. Measurement of axial ocular distances with slit-lamp microscopy. Clinical evaluation, and comparison with ultrasonography.

Photometric oculometry is a slit-lamp technique, which makes possible an estimation of intraocular axial distances and axial length. The technique is based on a transformation of a sagittal slit-lamp movement into intraocular axial distances when the slit-lamp focal plane is moved in the optical axis from retina to cornea. Determination of the axial length in 50 eyes (refractive range +4.75 to -5.25 D) showed that the axial length varied from 21.9 mm in hypermetropic eyes to 26.0 mm in myopic eyes, with the emmetropic eyes being approximately 24 mm. A comparison of intraocular axial distances determined by photometric oculometry and by ultrasonography on a small series of eyes showed no significant differences between the axial length, the length of the vitreous body, and the lens thickness, whereas a significant difference between the anterior chamber depth was observed (photometry giving slightly larger values than ultrasound).

Adult↗

PubMed1995

Monte Carlo study of electron spectra and dose from backscattered radiation in the vicinity of media interfaces for monoenergetic photons of 50-1250 keV.

In the present paper electron fluence spectra and backscatter dose factors for monoenergetic photons (50, 100, 250 and 1250 keV) are presented. The influence of the atomic number of the backscatter materials glass, bone, steel and titanium is studied. For all radiations increases in dose were found in the immediate vicinity of the interface in a region extending over a distance determined by the photon energy. In a thin layer extending several tens of micrometers from the interface, a large increase in dose was found for 50 and 100 keV photons. The largest backscatter dose factor (3.5) was found for 50 keV photons and a steel interface. This large effect was found to be due largely to backscattered photoelectrons. K-shell fluorescent photons from titanium and steel were also included but were found to have almost no effect on backscatter dose factors or electron spectra. With both K-shell fluorescence and sampling of the photoelectron angular distribution switched off, much smaller backscatter factors were obtained. Beyond the thin region near the interface where the dose is increased, significant dose depressions were found for photons of these energies in a region extending several centimeters from the interface. The effect was maximum for 50 keV photons, for which dose depressions of about 35% for steel and titanium and 15% for glass and bone were obtained. For 250 and 1250 keV photons a more modest dose enhancement was found close to the interface (40-50%) but extending over a larger region (e.g. 5 mm for 1250 keV photons). Small differences in radiation quality nearer to the interface were found as expressed by track-averaged and dose-averaged restricted linear energy transfer, LET100,T and LET100,D, with a maximum effect for the 100 keV photons. For this radiation quality a decrease of 50% in LET100,T was found close to the interface.

Dose-Response Relationship, Radiation↗

PubMed1994

Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.

The effect of araC incorporation into the dodecamer duplex [d(CGCGAATT) (araC)d(GCG)]2 was examined by comparing its nuclear magnetic resonance (NMR)-determined solution structure with that of the control duplex d[(CGCGAATTCGCG)]2. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H NMR and a 3-D 31P-1H heteroTOCSY-NOESY experiment. Proton-proton distances (determined from NOESY data) and sugar dihedral angles (from NOESY and COSY data) were used in restrained molecular dynamics simulations starting from canonical A- or B-form DNA models. Both the control and araC sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures which were in excellent agreement (R1/6 < 0.05) with the observed NOE intensities. A detailed comparison of the final control and araC structures revealed a global similarity (overall RMSD approximately 1.3 A), with significant differences localized at the araC site and neighboring bases. These included changes in sugar pucker, backbone torsion angles, base stacking, and other helical parameters. These findings are in general agreement with the previously published X-ray structure of a decamer duplex containing araC. One intriguing feature of the NMR solution structure not found in the crystal structure is the presence of an intramolecular hydrogen bond between the 2' hydroxyl on the araC sugar and the 3' phosphate group.

Base Composition↗

PubMed1997

Public housing and migration: a multi-level modelling approach.

"This paper...[analyzes] the distance moved by one-year migrants using a multi-level modelling approach. Controlling for a range of socio-economic variables, derived from the 1991 British Census Sample of Anonymised Records (SAR), at both the individual and area level, the distance moved by household heads in public, privately rented and owner-occupied housing within Britain is assessed.... It is confirmed that migrants in public housing are less likely to migrate long distances than owner-occupiers and that the proportion of public housing in a SAR area, and the absolute reduction in public housing in a SAR area between 1981 and 1991, does not have a significant effect on the distance that in-migrants have moved."

Demography↗