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At least 901 records · Page 50Linked to original sources
PubMed1990

Inter-sulfhydryl distances in plasma fibronectin determined by fluorescence energy transfer: effect of environmental factors.

Human plasma fibronectin, a dimeric glycoprotein, contains two cryptic free sulfhydryl groups per chain. Recent observations revealed that upon binding to a gelatin-coated surface the SH1 site, located between the DNA-binding and cell-binding domains, is partially exposed, while the SH2 site, situated within the carboxyl-terminal fibrin-binding domain, remains buried. Utilizing this newly discovered property of plasma fibronectin, we have developed a procedure to introduce maleimide derivatives of fluorescent probes such as N-(1-pyrenyl)maleimide, 7-(diethylamino)-3-(4'-maleimidylphenyl)-4-methylcoumarin, or fluorescein 5-maleimide selectively into either the SH1 or SH2 site of the fibronectin molecule and have measured the inter-sulfhydryl distances in fibronectin by fluorescence energy transfer methods. The results show that the distance between the SH1 site of one subunit and the SH1 site of the other subunit is between 35 and 44 A, indicating the close proximity of the two subunits near the SH1-containing regions. On the other hand, the distance between the SH2 site of one subunit and the SH2 site of the other subunit is found to be greater than 95 A, suggesting that the two SH2-containing regions are well separated. Additionally, the distance between the SH1 and SH2 sites within each subunit is estimated to be 42-53 A, assuming no intersubunit energy transfer between the probes. Heparin or high salt, which drastically affects the hydrodynamic properties of fibronectin, had virtually no effect on the distance between the SH1-SH1 or the SH1-SH2 pair.(ABSTRACT TRUNCATED AT 250 WORDS)

Energy Transfer↗
PubMed2006

Unfolding of alanine-based peptides using electron spin resonance distance measurements.

We describe a scheme for tagging an alanine-based peptide with a Cu(II) and a nitroxide to measure unfolding transitions. The enhancement in longitudinal relaxation rate of the nitroxide due to the presence of Cu(II) was measured at physiological temperatures by pulsed electron spin resonance (ESR). The change in relaxation rate provided the average interspin distance between the Cu(II) and the nitroxide. Control experiments on a proline-based peptide verify the robustness of the method. The change in interspin distances with temperature for the alanine-based peptide is in accord with the change in helicity measured by circular dichroism. The data provide an opportunity to examine the unfolding process in polyalanine peptides. The distance in the folded state is in concordance with molecular dynamics. However, the ESR experiment measures an average distance of 17 A in the unfolded state, whereas molecular dynamics indicates a distance of 42 A if the unfolded geometry was a polyproline type II helix. Therefore, ESR demonstrates that the unfolded state of this alanine-based peptide is not an ideal extended polyproline type II helix.

Alanine↗
PubMed1997

Troponin T and Ca2+ dependence of the distance between Cys48 and Cys133 of troponin I in the ternary troponin complex and reconstituted thin filaments.

Contraction of vertebrate striated muscle is regulated by the interaction of Ca2+ with the heterotrimeric protein troponin (Tn), composed of troponin-C (TnC), troponin-I (TnI), and troponin-T (TnT). Although much is known about the Ca2+-induced conformational changes in TnC, the Ca2+-binding subunit of Tn, little is known about how TnI, the inhibitory subunit, responds to the binding of Ca2+ to TnC. In this work, we used resonance energy transfer to measure the distance between probes attached at Cys48 and Cys133 in the N- and C-terminal domains, respectively, of TnI. A mutant rabbit skeletal TnI, TnI48/133 (C64S), was constructed by converting Cys64 into Ser. The remaining two thiols at Cys48 and Cys133 were labeled with the fluorescent donor 1,5-IAEDANS, and the nonfluorescent acceptor, DAB-Mal. We found an interprobe distance of approximately 41 A for both uncomplexed TnI and TnI in the binary complex with TnC. This distance increased to 51 A in the ternary Tn complex with TnT. These distances did not change significantly on binding of Ca2+ to TnC. In the reconstituted thin filament, this distance remained to be 50 A in the presence of saturating Ca2+, but increased to approximately 66 A on removing Ca2+ with EGTA in the presence of Mg2+. Our results indicate firstly that while TnC has only small effects on the global conformation of TnI, the presence of TnT in the ternary Tn complex gives rise to an apparent elongation of TnI. Secondly, whereas there is no detectable Ca2+-dependent change in the global conformation of TnI in the Tn complex free in solution, the removal of Ca2+ caused a substantial separation of the N- and C-terminal TnI regions in the reconstituted thin filament, owing to the interaction between the C-terminal region of TnI and actin in the relaxed state.

Actin Cytoskeleton↗
PubMed1997

Real-time measurement of multiple intramolecular distances during protein folding reactions: a multisite stopped-flow fluorescence energy-transfer study of yeast phosphoglycerate kinase.

Understanding the set of rules which dictate how the primary amino acid sequence determines tertiary structure is an unsolved problem in biophysics. If it were possible to simultaneously measure all of the intramolecular distances in a protein (in real time) during a folding reaction, the "second" genetic code problem would be solved. Regrettably, no such technique currently exists. As a first step toward this goal, an optical distance assay system has been developed for a two-domain protein, yeast phosphoglycerate kinase (PGK), using Förster resonance energy transfer [Lillo, M. P., et al. (1997) Biochemistry 36, 11261-11272]. In this study, real-time stopped-flow distance changes are measured using six unique pairs of donor/acceptor fluorescent labels strategically placed throughout the tertiary structure of PGK. These multiple donor/acceptor sites were genetically engineered into PGK by cysteine substitution mutagenesis followed by extrinsic labeling with fluorescent probes, 5-[[[(2-iodoacetyl)amino]ethyl]amino]naphthalenesulfonic acid (as a donor) and 5-iodoacetamidofluorescein (acceptor). The unfolding of PGK is found to be a sequential multistep process (native --> I1 --> I2 --> unfolded) with rate constants of 0.30, 0.16, and 0.052 s-1, respectively (from native to unfolded). Unique to this unfolding study, six intramolecular distance vectors have been resolved for both the I1 and I2 states. With this distance information, it is shown that the transition from the native to I1 state can be modeled as a large hinge-bending motion, in which both domains "swing away" from each other by about 15 A. As the domains move apart, the carboxyl-terminal domain rotates almost 90 degrees about the hinge region connecting the two domains. It is also shown that the amino-terminal domain remains intact during the native --> I1 transition, consistent with our previous site-specific tryptophan fluorescence anisotropy stopped-flow study [Beechem, J. M., et al. (1995) Biochemistry 34, 13943-13948]. Future experiments are proposed which will attempt to resolve in detail the unfolding/refolding transitions in this protein with a resolution of approximately 5-10 A.

Energy Transfer↗
PubMed2004

Apparent decreases in colloid deposition rate coefficients with distance of transport under unfavorable deposition conditions: a general phenomenon.

The transport of polystyrene microspheres was examined in packed glass beads under a variety of environmentally relevant ionic strength and flow conditions. The observed profiles of numbers of retained microspheres versus distance from the column entrance were much steeper than expected based on a constant rate coefficient of deposition acrossthe length of the column, indicating apparent decreases in deposition rate coefficients with transport distance. Deviation in the profile from log-linear decreases with distance was greatest under highly unfavorable conditions (low ionic strength), relatively reduced under mildly unfavorable conditions (high ionic strength), and was eliminated under favorable conditions. The generality of apparent decreases in deposition rate coefficients with distance of transport among microspheres, bacteria, and viruses leads to the conclusion that such effects reflect processes that are fundamental to filtration under unfavorable conditions. Numerical simulations of experiments that were performed under unfavorable conditions utilized a log-normal distribution of deposition rate coefficients among the colloid population in orderto simulate the effluent curves and retained profiles simultaneously. It is shown that while straining could be a significant contributor to the steep retained profiles at low ionic strength, where overall retention is low, distribution in interaction potentials among the population was a viable mechanism that can yield apparent decreases in deposition rate coefficients with distance of transport.

Colloids↗
PubMed2001

Photoinduced electron transfer in hydrogen bonded donor--acceptor systems. Free energy and distance dependence studies and an analysis of the role of diffusion.

The free energy dependence of electron transfer in a few small-molecule donor--acceptor systems having hydrogen-bonding appendages was studied to evaluate the role of diffusion in masking the inverted region in bimolecular PET reactions. A small fraction of the probe molecules associate and this led to the simultaneous observation of unimolecular and diffusion-mediated quenching of the probe fluorescence. Free energy dependence studies showed that the unimolecular electron transfer obeys Marcus behavior and the diffusion-mediated electron transfer obeys Rehm--Weller behavior. The absence of an inverted region in bimolecular PET reactions is thus attributed to diffusion. The results of the free energy dependence studies suggest that distance dependence of electron transfer plays a role in masking the inverted region. To ascertain this aspect we have carried out a study of the distance dependence of electron transfer in the hydrogen-bonded donor--acceptor systems. For a system in the normal region an exponential rate decrease was observed. For a system in the inverted region it was observed that the rate depends very feebly on distance. Thus distance dependence studies did not confirm the prediction of enhanced rates at larger distances in the inverted region.

Journal Article↗
PubMed2000

Inter- and intramolecular distance measurements by solid-state MAS NMR: determination of gramicidin A channel dimer structure in hydrated phospholipid bilayers.

Distance constraints are an important complement to orientational constraints. While a high-resolution monomer structure of the ion channel forming polypeptide, gramicidin A, has been solved with 120 orientational constraints, the precise geometry of the dimer interface has not been characterized. Here, using both 13C and 15N labeled gramicidin A samples in hydrated phospholipid bilayers, both inter- and intramolecular distances have been measured with a recently developed simultaneous frequency and amplitude modulation (SFAM) solid-state NMR scheme. Using this approach 15N-13C1 residual dipolar couplings across a hydrogen bond as small as 20+/-2 Hz have been characterized. While such distances are on the order of 4.2+/-0.2 A, the spectroscopy is complicated by rapid global motion of the molecular structure about the bilayer normal and channel axis. Consequently, the nominal 40 Hz dipolar coupling is averaged depending on the orientation of the internuclear vector with respect to the motional axis. The intermolecular distance confirmed the previously described monomeric structure, while the intramolecular distance across the monomer-monomer interface defined this junction and confirmed the previous model of this interface.

Bacillus↗
PubMed2001

A 5-year follow-up study for distance visual acuity after low dose radiation on subfoveal choroidal neovascularization in age-related macular degeneration.

In a prospective study with a 5-year follow-up, we assessed the effect of a single series of low-dose radiation on the distance visual acuity in eyes with angiographically confirmed subfoveal choroidal neovascularization (CNV) in age-related macular degeneration (ARMD). The posterior pole of 12 eyes was treated with 5 Gy (4 x 1.25 Gy), and 34 eyes treated with 8 Gy (4 x 2 Gy). The best corrected distance visual acuity was measured at the time of treatment, and annually thereafter for 5 years. The study obtained complete follow-up for 11 patients in the 5-Gy group (nine classic, two occult CNVs), and 29 patients in the 8-Gy group (12 classic, 17 occult CNVs). At baseline, the mean distance visual acuity of the treated eyes was 0.16 (20/125) in the 5-Gy group, and 0.2 (20/100) in the 8-Gy group. Five years later, an average loss of 3.2 lines was present in the 5-Gy group, and 4 lines in the 8-Gy group. After 5 years, an average loss of 2 lines was found in a control group consisting of 18 second eyes with low stage dry ARMD, with a mean distance visual acuity of 0.5 (20/40) at baseline. Statistical analyses with Wilcoxon and Mann-Whitney U-tests showed that a single series of low dose radiation with either 5 Gy or 8 Gy was not able to stabilize the distance visual acuity of eyes with subfoveal CNV in ARMD during a 5-year follow-up.

Aged↗
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↗
PubMed2002

Patchy distribution fields: sampling distance unit of a zigzag survey and reconstruction adequacy.

A mathematical model was used to examine the effects of choosing various units of sampling distance of a zigzag survey on the adequacy of reconstructing patchy distribution fields. The model simulates fish or plankton patches (or gaps) of different shapes and spatial orientations, and an acoustic survey by zigzag or parallel transects along which a unit of sampling distance is set. Adequacy of the reconstructed fields to those originally generated is evaluated by calculating their correlations (r). A priori information on the autocorrelation radii for the field in the directions of the survey (Rs) and perpendicular direction (Rp) allows optimisation of the survey design and the algorithm of data analysis. A field can be reconstructed properly (r2 > 0.70) if the distance between transects D < (1.0-1.5)Rs and the unit of sampling distance d < (1.0-1.5)Rp. A posteriori determination of patch orientation allows reconstruction of the best field attainable on the basis of the survey data. In cases of field movement, if the dimension of patches in the direction of movement exceeds that of a surveyed area, a survey in the opposite direction gives best results; in contrast, if the dimension of moving patches is smaller than that of a surveyed area, it is reasonable to carry out a survey in the same direction. The criterion remains valid when a survey is carried out by zigzag transects and a unit of sampling distance is set along them. The results obtained indicate that, for a fixed transect spacing and a given number of sampling points on each full transect, zigzag pattern allows less adequate reconstruction of an original distribution field (in cases of both immovable and movable fields) than corresponding parallel pattern.

Animals↗
PubMed1999

Interpupillary distance in a normal black population.

This report expands on a study by Pryor [Pryor HB. Objective measurement of interpupillary distance. Pediatrics 1969: 44: 973 977] that related normal values of inner canthal distance (ICD), outer canthal distance (OCD) and interpupillary distance (IPD) for Whites, Asians and Mexican Americans. To date, no similar values have been reported for Blacks. Utilizing a sample (n = 931: 485 males; 446 females) of black people (range, birth 24 years), OCD, ICD, and head circumference (HC) were measured and tabulated. We calculated mean IPD according to Pryor's formulation and report that the general mean OCD and ICD in our sample differed significantly from, and were consistently higher than, Pryor's reported measurements for White males and females at each age level (p < 0.001). However, ICD in our sample was significantly lower at birth in both sexes, appeared to increase at a more rapid rate relative to Whites during the first 3 months of life, and reached and maintained a higher value beyond the age of 3 months, with most age groups showing a significant difference in mean ICD measurements. At each age level, the mean IPD values in Whites and Blacks were significantly higher (p < 0.001). Based upon these findings, we suggest that interpupillary distance of Black children and adults be assessed according to the mean proportions for their race.

Age Factors↗
PubMed1980

Recognition of transposed melodies: a key-distance effect in developmental perspective.

Four experiments examined the possibility of a key-distance effect in a transposition detection task. Subjects heard standard melodies followed by comparison melodies presented in the same key, a musically near key or a musically far key. The task was to recognize comparisons that were exact transpositions of the standards, rejecting nontranspositions. Results suggested a largely invariant key-distance effect with nontransposition comparisons (lures); same- and near-key lures evoked more false alarms than far-key lures. The variables of musical experience, age of subject, and familiarity of melody affected the level of transposition-recognition performance but did not consistently affect the size of the key-distance effect. The results support the psychological reality of key distance and are consistent with both musical and nonmusical-auditory theories of its effects. The key-distance effect was not found with transposition comparisons (targets), a result with implications for the separability of key and interval information in short-term memory for melodies.

Adult↗
PubMed2000

The contribution of nonvisual information to simple place navigation and distance estimation: an examination of path integration.

In Experiment 1, participants walked without vision to a target location they had either previously viewed, were led to and from blindfolded, or both viewed and were led to and from blindfolded. A course to the target could be set and held without vision only if prior vision of its location was available. The locomotor group reproduced the heading and distance to the target less accurately than the other groups, which did not differ significantly. However, when nonvisual information accompanied vision of the target location, it served to subtly influence performance. Participants in Experiment 2 estimated the distance of a target they either viewed or were led to blindfolded. When vision was available, men overestimated target distance and women underestimated it. When target distance was learned nonvisually, no sex differences in distance estimations emerged. Our findings suggest that deriving navigation information from nonvisual locomotion is difficult and may be dependent on prior visual information.

Adult↗
PubMed1991

Sliding distance between actin and myosin filaments per ATP molecule hydrolysed in skinned muscle fibres.

Muscle contraction is generally thought to be driven by tilting of the 19-nm-long myosin head, part of the thick filament, while attached to actin, part of the thin filament. This motion would produce about 12 nm of filament sliding. Recent estimates of the sliding distance per ATP molecule hydrolysed by actomyosin in vitro vary widely from 8 nm to greater than or equal to 200 nm. The latter value is incompatible with a power stroke incorporating a single tilting motion of the head. We have measured the isotonic sliding distance per ATP molecule hydrolysed during the interaction between myosin and actin in skinned muscle fibres. We directly estimated the proportion of simultaneously attached actomyosin complexes and their ATP use. We report here that at low loads the interaction distance is at least 40 nm. This distance corresponds to the length of the power stroke plus the filament sliding while actomyosin crossbridges bear negative drag forces. If the power stroke is 12 nm, then our results indicate the drag distance to be at least 28 nm. Our results could also be explained by multiple power strokes per ATP molecule hydrolysed.

Actins↗
PubMed2003

Modelling the impact of colonisation on genetic diversity and differentiation of forest trees: interaction of life cycle, pollen flow and seed long-distance dispersal.

It was shown previously that the long lifespan and juvenile phase of trees strongly attenuate founder effects during colonisation in a diffusive dispersal model. However, this model yielded too slow a colonisation rate in comparison with palynological data for temperate forest trees. Since rare long-distance dispersal events have been shown to increase considerably colonisation rates in population dynamics models, we investigate here the impact of long-distance dispersal on within-population diversity (H(S)) and among-population differentiation (F(ST)) during the colonisation process. We use a stochastic approach and compare several dispersal strategies, ranging from very rare dispersal events of large amplitude to more frequent events of smaller amplitude. Using a simulation approach, which takes into account tree life-history traits, we show that long-distance dispersal events increase colonisation speed, and yield much larger founder effects in comparison with the diffusive model. The two models that include intermediate- and long-distance dispersal events show stronger deviations from experimental F(ST) values during and at the end of the colonisation process than the model with more frequent events of smaller dispersal variance. Furthermore, the introduction of a high level of pollen flow has a much more limited impact on models that include long-distance dispersal than on a diffusive dispersal model. The relatively high H(S) values that were obtained in all models are discussed according to the assumed mutation rate and effective population size. This study is an example of how observed genetic data can provide additional evidence on the best demographic model for a given species or group of species.

Computer Simulation↗
PubMed1988

Estimation of the distance between the divalent cation binding site of des-1-41-light chain-activated bovine plasma protein C and a nitroxide spin label attached to the active-site serine residue.

The paramagnetic effect of Mn2+ on the electron paramagnetic resonance spectrum of a nitroxide spin label covalently attached to the active-site serine residue of des-1-41-light chain bovine plasma-activated protein C, and situated at a distance of approximately 1.2 nm from this amino acid, has been utilized to estimate the distance on the enzyme surface between the single Mn2+ site and the free electron of the spin label. This distance has been found to be approx. 1.12 nm. A significant paramagnetic effect of Mn2+ on the spectrum of this same nitroxide spin label bound to activated protein C (APC) has been found. However, in this case distance calculations are complicated by the existence of a multiplicity of Mn2+ sites on APC. If it is assumed that a single Mn2+ site is responsible for the paramagnetic effect on the spectrum of the spin label, the interelectron distance on APC would be approx. 0.90 nm.

Animals↗
PubMed1989

Conformational changes in human serum albumin studied by fluorescence and absorption spectroscopy. Distance measurements as a function of pH and fatty acids.

pH- and fatty acid-induced conformational changes in human serum albumin were investigated by fluorescence-energy transfer, determining the distance between Trp-214 and bound bilirubin at 25 degrees C. This distance changes significantly with the pH, being 2.52 +/- 0.01 nm at pH 6, 2.31 +/- 0.04 nm at pH 9, 2.13 +/- 0.07 nm at pH 11.0 and 2.77 nm at pH 11.9. The influence of different fatty acids on the distance was also determined. At pH 7.4 medium-chain fatty acids seem to increase this distance, whereas long-chain fatty acids, at low concentrations, decrease the distance between the two chromophores. The contraction of the protein carrying long-chain saturated fatty acids is even more pronounced at pH 9.

Bilirubin↗
PubMed1997

Supportive learning in distance education.

This paper argues that tutorial support should enhance the learning experience of students who enrol on a distance education programme. A rationale for such support is given as well as a definition of support for distance learners. The complex role of the tutor in distance learning is described which suggests the need for tutor preparation, particularly for tutors adapting to this mode of course delivery. The paper reports on two existing models used within distance education which have focused on the outcome of study. The paper introduces an alternative model of supportive learning which focuses on the development of the educational experience throughout the length of a distance-learning course.

Education, Nursing↗