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At least 595 records · Page 33Linked to original sources
PubMed2001

Distributions of intramolecular distances in the reduced and denatured states of bovine pancreatic ribonuclease A. Folding initiation structures in the C-terminal portions of the reduced protein.

The purpose of this investigation is to characterize the reduced state of RNase A (r-RNase A) in terms of (i) intramolecular distances, (ii) the sequence of formation of stable loops in the initial stages of folding, and (iii) the unfolding transitions induced by GdnHCl. This is accomplished by identifying specific subdomain structures and local and long-range interactions that direct the folding process of this protein and lead to the native fold and formation of the disulfide bonds. Eleven pairs of dispersed sites in the RNase A molecule were labeled with fluorescent donor and acceptor probes, and the distributions of intramolecular distances (IDDs) were determined by means of time-resolved dynamic nonradiative excitation energy transfer (TR-FRET) measurements. The mutants were designed to search for (a) a possible nonrandom fold of the backbone in the collapsed state and (b) possible loops stabilized by long-range interactions. It was found that, under folding conditions, (i) the labeled mutants of r-RNase A in refolding buffer (the R(N) state) exhibit features of specific (nonrandom) compact but very dispersed subdomain structures (indicated by short mean distances, broad IDDs, and a weak dependence of the mean distances on segment length), (ii) the backbone fold in the C-terminal beta-like portion of the molecule appears to adopt a native-like overall fold, (iii) the N-terminal alpha-like portion of the chain is separated from the C-terminal core by very large intramolecular distances, larger than those in the crystal structure, and (iv) perturbations by addition of GdnHCl reveal several conformational transitions in different sections of the chain. Addition of GdnHCl to the native disulfide-intact protein provided a reference state for the extent of expansion of intramolecular distances under denaturing conditions. In conclusion, r-RNase A under folding conditions (the R(N) state) is poised for the final folding step(s) with a native-like trace of the chain fold but a large separation between the two subdomains which is then decreased upon introduction of three of the four native disulfide cross-links.

Animals↗
PubMed1986

Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG).

The three-dimensional structure of d(CGCGTTTTCGCG) in solution has been determined from proton NMR data by using distance geometry methods. The rate of dipolar cross-relaxation between protons close together in space is used to calculate distances between proton pairs within 5 A of each other; these distances are used as input to a distance geometry algorithm that embeds this distance matrix in three-dimensional space. The resulting refined structures that best agree with the input distances are all very similar to each other and show that the DNA sequence forms a hairpin in solution; the bases of the loop region are stacked, and the stem region forms a right-handed helix. The advantages and limitations of the technique, as well as the computer requirements of the algorithm, are discussed.

DNA↗
PubMed1987

Distance estimate of the active center of D-beta-hydroxybutyrate dehydrogenase from the membrane surface.

D-beta-Hydroxybutyrate dehydrogenase (EC 1.1.1.30) is a membrane-bound, lipid-requiring enzyme which has a reactive sulfhydryl in the vicinity of the active center. The spin-probe-spin-label technique has been used to estimate the distance of separation of the reactive sulfhydryl of D-beta-hydroxybutyrate dehydrogenase from the bilayer surface. The reactive sulfhydryl of the enzyme was derivatized with the maleimide spin-label reagent 4-maleimido-2,2,6,6-tetramethylpiperidinyl-1-oxy in the presence of the cofactor NAD+. The derivatized enzyme, inserted (inlaid orientation) into phospholipid vesicles, was titrated with spin probes, either Mn2+ or Gd3+, until the spin-label EPR spectrum was reduced in amplitude to its residual (limiting) value. From this limiting amplitude, the dipolar interaction coefficient was obtained, which is related to the reciprocal of the distance to the sixth power. The radial distances of closest approach of the paramagnetic Mn2+ and Gd3+ ions to the spin-label nitroxide on the enzyme were found to be 18 and 16 A, respectively. These calculated distances were in accord with those determined by comparison with a phosphatidylcholine calibration system having 2,2-dimethyloxazolidinyl-1-oxy spin-labels located at selected positions along the sn-2 fatty acyl chain. Since the distal nitroxide moiety of the maleimide spin-label (17 A from the bilayer surface) is 8 A from the sulfhydryl addition site, the two limiting distances of immersion of the reactive sulfhydryl within the bilayer are 9 and 25 A. The shorter distance is considered more compatible with facile access of the coenzyme to the active site of the enzyme.

Binding Sites↗
PubMed1987

Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics.

The solution conformation of potato carboxypeptidase inhibitor (CPI) has been investigated by 1H NMR spectroscopy. The spectrum is assigned in a sequential manner by using two-dimensional NMR techniques to identify through-bond and through-space (less than 5 A) connectivities. A set of 309 approximate interproton distance restraints is derived from the two-dimensional nuclear Overhauser enhancement spectra and used as the basis of a three-dimensional structure determination by a combination of metric matrix distance geometry and restrained molecular dynamics calculations. A total of 11 converged distance geometry structures were computed and refined by using restrained molecular dynamics. The average atomic root mean square (rms) difference between the final 11 structures and the mean structure obtained by averaging their coordinates is 1.4 +/- 0.3 A for residues 2-39 and 0.9 +/- 0.2 A for residues 5-37. The corresponding values for all atoms are 1.9 +/- 0.3 and 1.4 +/- 0.2 A, respectively. The larger values for residues 2-38 relative to those for residues 5-37 arise from the fact that the positions of the N- (residues 1-4) and C- (residues 38-39) terminal tails are rather poorly determined, whereas those of the core of the protein (residues 5-37) are well determined by the experimental interproton distance data. The computed structures are very close to the X-ray structure of CPI in its complex with carboxypeptidase, and the backbone atomic rms difference between the mean of the computed structures and the X-ray structure is only 1.2 A. Nevertheless, there are some real differences present which are evidenced by significant deviations between the experimental upper interproton distance limits and the corresponding interproton distances derived from the X-ray structure. These principally occur in two regions, residues 18-20 and residues 28-30, the latter comprising part of the region of secondary contacts between CPI and carboxypeptidase in the X-ray structure.

Carboxypeptidases↗
PubMed1989

Analysis of the relative contributions of the nuclear Overhauser interproton distance restraints and the empirical energy function in the calculation of oligonucleotide structures using restrained molecular dynamics.

The relative contributions of the interproton distance restraints derived from nuclear Overhauser enhancement measurements and of the empirical energy function in the determination of oligonucleotide structures by restrained molecular dynamics are investigated. The calculations are based on 102 intraresidue and 126 interresidue interproton distance restraints derived from short mixing time two-dimensional nuclear Overhauser enhancement data on the dodecamer 5'd(CGCGPATTCGCG)2 [Clore, G.M., Oschkinat, H., McLaughlin, L.W., Benseler, F., Scalfi Happ, C., Happ, E., & Gronenborn, A.M. (1988) Biochemistry 27, 4185-4197]. Eight interproton distance restraint lists were made up with errors ranging from -0.1/+0.2 to -1.2/+1.3 A for r less than 2.5 A and from -0.2/+0.3 to -1.3/+1.4 A for r greater than or equal to 2.5 A. These restraints were incorporated into the total energy function of the system in the form of square-well potentials with force constants set sufficiently high to ensure that the deviations between calculated distances and experimental restraints were very small (average interproton distance rms deviation of less than 0.06 A). For each data set, six calculations were carried out, three starting from classical A-DNA and three from classical B-DNA. The results show that structural changes occurring during the course of restrained molecular dynamics and the degree of structural convergence are determined by the interproton distance restraints. All the structures display similar small deviations from idealized geometry and have the same values for the nonbonding energy terms comprising van der Waals, electrostatic, and hydrogen-bonding components. Thus, the function of the empirical energy function is to maintain near perfect stereochemistry and nonbonded interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Magnetic Resonance Spectroscopy↗
PubMed1989

NMR distance measurements in DNA duplexes: sugars and bases have the same correlation times.

To evaluate whether the sugar moieties of short DNA duplexes exhibit local motion of sufficient amplitude to affect interproton distance measurements, we have carried out a series of time-dependent NOESY experiments at increasingly shorter mixing times on dodecamer DNA duplexes. By use of the cytosine H5-H6 vector as a known distance in the bases and the geminal 2'H-2''H vector as a known distance in the sugars, the corresponding apparent cross-relaxation rates were sampled at various mixing times. While the ratio of the inverse sixth power of these two fixed distances is in the range 6-7, when the system is sampled at 100 ms the apparent initial rate of growth of the 2'H-2''H NOESY crosspeak is only 1.9-2.0 times faster than that of the H5-H6 crosspeak--in agreement with the results of Clore and Gronenborn [Clore, G. M., & Gronenborn, A. M. (1984) FEBS Lett. 172, 219; (1984) FEBS Lett. 175, 117] and of Gronenborn and Clore [Gronenborn, A. M., & Clore, G. M. (1985) Prog. NMR Spectrosc. 17, 1]. This observation was interpreted to indicate the existence of internal mobility with a 3-fold shorter correlation time for the sugar moieties in DNA and led to the use of this shorter correlation time to estimate sugar-sugar proton distances and many sugar-base proton distances in subsequent DNA structure determination. We have examined 2'H-2"H cross-relaxation and H5-H6 cross-relaxation at 100, 90, 60, 30, and 15 ms in dodecamer DNA duplexes.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2001

On the apparently anomalous distance dependence of charge-transfer rates in 9-amino-6-chloro-2-methoxyacridine-modified DNA.

From previous thermal and photoinduced charge-transfer reactions in duplex DNA there is accumulative evidence for an attenuation parameter beta of the distance dependence in the range 0.6-0.8 A(-1), with the exception of one specific system exhibiting beta = 1.5 A(-1) which is reinvestigated in this paper. Femtosecond to nanosecond time-resolved pump-probe spectroscopy has been used to follow photoinduced charge-shift dynamics in DNA duplexes containing a covalently appended, protonated 9-alkylamino-6-chloro-2-methoxyacridine chromophore. This acridine derivative (X+) resides in the DNA duplex at a specific abasic site, which is highly defined as reflected in the monoexponentiality of the kinetics. In the presence of only neighboring A:T base pairs, no charge transfer occurs within the excited-state lifetime (18 ns) of the chromophore. However, the presence of a guanine nucleobase as either a nearest neighbor or with one interspersed A:T base pair does result in fluorescence quenching. In the case of nearest neighbors, the intermediate radical state X* is formed within 4 ps and decays on the 30 ps time scale. Placing one A:T base pair between the X+ and guanine slows down the forward transfer rate by 3 orders of magnitude, corresponding to an apparent beta value of >2.0 A(-1). This dramatic decrease in the rate is due to a change in charge-transfer mechanism from a (nearly) activationless to a thermally activated regime in which the forward transfer is slower than the back transfer and the X* state is no longer observed. These observations indicate that the distance dependence of charge injection in the X+-labeled DNA duplex is not solely caused by a decrease in electronic couplings but also by a concomitant increase of the activation energy with increasing distance. This increase in activation energy may result from the loss of driving force due to excited-state relaxation competing with charge transfer, or reflect distance-dependent changes in the energetics, predominantly of the low-frequency reorganization energy in this charge-shift reaction, on purely electrostatic grounds. To test the hypothesis of distance-dependent activation energy, guanine has been replaced by 7-deazaguanine, its easier-to-oxidize purine analogue. In these duplexes, a similar change of charge-transfer mechanism is found. However, consistent with an a priori larger driving force this change occurs at a larger donor-acceptor separation than in the X+-guanine systems. Independent of the detailed contributions to the distance-dependent activation energy, this phenomenon illustrates the complex nature of experimental beta values.

Aminoacridines↗
PubMed2005

Explicit treatment of spin labels in modeling of distance constraints from dipolar EPR and DEER.

Current SDSL-EPR methods allow measurement of dipolar distances in the 8-70 A range; however, the use of extrinsic probes complicates the interpretation of these distances in modeling macromolecular structure and conformational changes. The data presented here show that interprobe distances correlate only weakly with Cbeta-Cbeta distances, especially for distances that are on the order of the spin label tether lengths. Explicitly incorporating the spin label into the modeling process increases the experiment/model correlation 4-fold and reduces the distance error from 6 A to 3 A.

Carbon↗
PubMed2006

Distance-dependent metal-enhanced fluorescence from Langmuir-Blodgett monolayers of alkyl-NBD derivatives on silver island films.

We described the effect of fluorophore distance from the silver island films (SIFs) on the metal-enhanced fluorescence (MEF) from two newly developed long-chain nitrobenzoxadiazole derivatives (NBD-C16 and NBD-C18). The well-established Langmuir-Blodgett technique is used to deposit the fluorophores at defined distances from the SIFs surface, and an inert amphiphilic stearic acid is used to control the distance. NBD probes deposited directly on the SIFs surface show the highest metal-enhanced fluorescence of approximately 32-fold, and both of the probes that were studied show a consistent decrease in metal-enhanced fluorescence when increasing the distance from the fluorophore to the SIFs surface. The lowest fluorescence enhancement of approximately 4-fold is observed for the probes located 90 nm from the SIFs surface. Additionally, we also have noticed the shortest fluorescence lifetimes for the NBD probes deposited directly onto the SIFs surface, and the lifetimes are consistently increased when increasing the distances between the fluorophore and SIFs surfaces. These contrasting spectral changes, enhanced fluorescence, and decreased fluorescence lifetimes are in accordance with an increase in the rate of radiative decay for fluorophores near the silver particles. The present study provides significant information on the effect of fluorophore distance on the metal-enhanced fluorescence phenomenon.

4-Chloro-7-nitrobenzofurazan↗
PubMed1998

Improved distance analysis in RNA using network-editing techniques for overcoming errors due to spin diffusion.

Multispin magnetization transfer, or spin diffusion, is a significant source of error in NOESY-derived distance measurements for the determination of nucleic acid solution structures. The BD-NOESY and CBD-NOESY experiments, which allow the measurement of interproton distances with greatly reduced contributions from spin diffusion, have been adapted to structural analysis in RNA oligonucleotides. The techniques are applied to a lead-dependent ribozyme (LZ2). We demonstrate the measurement of both aromatic proton-aromatic proton NOEs free of spin diffusion involving the intervening ribose moieties and aromatic proton-ribose proton NOEs free of the efficient cross-relaxation within the ribose ring. In LZ2, the accuracy and precision of the resulting distances are significantly improved. We also find that, by allowing the use of longer mixing times with greater sensitivity, the experimental attenuation of spin diffusion in RNA increases the distance range of interactions that can be analyzed. This effect permits measurement of important long-range distances in LZ2 that are not accessible with standard techniques. Thus, these techniques allow the simultaneous optimization of the number, accuracy, and precision of distance constraints used for RNA structure determinations.

Base Sequence↗
PubMed2004

Factors influencing social distance toward people with mental illness.

BACKGROUND: When identifying ways to reduce stigmatization because of mental illness it is crucial to understand contributing factors. Social distance-the willingness to engage in relationships of varying intimacy with a person--is an indicator of public attitudes toward persons with mental illness. METHODS: Multiple linear regression analysis of the results of a vignette-based opinion survey conducted on a representative population sample in Switzerland (n = 594). RESULTS: The level of social distance increases if situations imply 'social closeness.' The vignette describing a person with schizophrenia, attitudes to general aspects of mental health (lay helping, community psychiatry), emotions toward those affected, and the attitude toward consequences of mental illness (medical treatment, medication side effects, negative sanctions, e.g. withdrawal of the driver license) were found to predict social distance. Demographic factors such as age, gender, and the cultural background influence social distance. The explained variance (R2) is 44.8%. CONCLUSIONS: Social distance is a multifaceted concept influenced by, e.g., socio-economic and cultural factors, but also by the respondent's general attitude toward (mental) health issues. These results suggest that more knowledge about mental illnesses, especially schizophrenia, may increase social distance. The findings presented here may help to focus anti-stigma campaigns not only on transmission of knowledge, but on integrating different approaches.

Adolescent↗
PubMed1986

Depth perception as a function of motion parallax and absolute-distance information.

The results of three experiments demonstrated that the visual system calibrates motion parallax according to absolute-distance information in processing depth. The parallax was created by yoking the relative movement of random dots displayed on a cathode-ray tube to the movements of the head. In Experiment 1, at viewing distances of 40 cm and 80 cm, observers reported the apparent depth produced by motion parallax equivalent to a binocular disparity of 0.47 degree. The mean apparent depth at 80 cm was 2.6 times larger than at 40 cm. In Experiment 2, again at viewing distances of 40 cm and 80 cm, observers adjusted the extent of parallax so that the apparent depth was 7.0 cm. The mean extent of parallax at 80 cm was 31% of that at 40 cm. In Experiment 3, distances ranged from 40 cm to 320 cm, and a wide range of parallax was used. As distance and parallax increased, the perception of a rigid three-dimensional surface was accompanied by rocking motion; perception of depth was replaced by perception of motion in some trials at 320 cm. Moreover, the mean apparent depths were proportional to the viewing distance at 40 cm and 80 cm but not at 160 cm and 320 cm.

Cues↗
PubMed2001

Honeybee dances communicate distances measured by optic flow.

In honeybees, employed foragers recruit unemployed hive mates to food sources by dances from which a human observer can read the distance and direction of the food source. When foragers collect food in a short, narrow tunnel, they dance as if the food source were much farther away. Dancers gauge distance by retinal image flow on the way to their destination. Their visually driven odometer misreads distance because the close tunnel walls increase optic flow. We examined how hive mates interpret these dances. Here we show that recruited bees search outside in the direction of the tunnel at exaggerated distances and not inside the tunnel where the foragers come from. Thus, dances must convey information about the direction of the food source and the total amount of image motion en route to the food source, but they do not convey information about absolute distances. We also found that perceived distances on various outdoor routes from the same hive could be considerably different. Navigational errors are avoided as recruits and dancers tend to fly in the same direction. Reported racial differences in honeybee dances could have arisen merely from differences in the environments in which these bees flew.

Animal Communication↗
PubMed2005

Do polymorphic loci require large sample sizes to estimate genetic distances?

The coefficient of variation of estimates of three genetic distances (standard genetic distance of Nei, chord distance, FST) was examined with computer simulation to determine if large samples (per population) are necessary to precisely estimate genetic distances at loci with high levels of polymorphism. These simulations showed that loci with high mutation rates produce estimates of genetic distance with lower coefficients of variation than loci with lower mutation rates--without requiring larger sample sizes from each population. In addition, the rate at which increasing sample sizes decreases the coefficient of variation of estimates of genetic distances was shown to be approximately determined by the value of FST between the populations being sampled. When FST was greater than 0.05, sampling fewer than 20 individuals (per population) should be sufficient. When FST was less than 0.01, sampling 100 individuals (per population) or more will be useful.

Alleles↗
PubMed1996

Three-dimensional ultrasound: accuracy of distance and volume measurements.

The aim of this study was to evaluate the accuracy of three-dimensional ultrasound distance and volume measurements using a commercially available three-dimensional ultrasound scanner. Sixty-two distance measurements were performed twice on an ultrasound tissue-mimicking phantom located in a water bath. Three-dimensional ultrasound distance measurements were compared to the actual distance. Volume measurements were made in a water bath with 21 balloons of various shapes ranging in volume from 20 ml to 490 ml. Three-dimensional ultrasound volume measurements were compared to actual balloon volumes and to conventional two-dimensional ultrasound volume calculations. The mean absolute error in three-dimensional ultrasound distance measurements was 1.0 +/- 0.8% (range, -2.3 to +1.9%) in the plane of acquisition and 1.0 +/- 0.6% (range, -2.0 to -0.2%) for planes with other orientations. Three-dimensional ultrasound volume measurements showed a mean absolute error of 6.4 +/- 4.4% (range, -6.0% to +15.5%), which was considerably better than two-dimensional ultrasound volume estimates having a mean absolute error of 12.6 +/- 8.7% (range, -27.5% to +39.2%). Volume measurements using two-dimensional ultrasound methods were much less accurate than three-dimensional ultrasound methods for irregularly shaped objects. In conclusion, our data show that three-dimensional ultrasound measurements of distance and volume are sufficiently accurate to use clinically.

Diagnostic Imaging↗
PubMed1997

Growth of the fetal nose width and nostril distance in normal pregnancies.

The study was planned to obtain the dimensions of the fetal nose width and nostril distance during normal pregnancy as a basis for further studies and for identification of deviations in growth. The study group included 302 healthy pregnant women at 14-40 weeks' gestation. Routine biometric measurements were obtained from all the participants, including biparietal diameter, head and abdominal circumferences, measurements of the long bones and dimensions of the fetal nose width and nostril distance. The nose width and nostril distance were also calculated for each gestational age. A linear growth relationship was observed between nose width and gestational age (r = 0.88; p < 0.0001; y = 0.27 + 0.57 x gestational age), biparietal diameter (r = 0.92; p < 0.0001; y = 0.41 + 0.23 x biparietal diameter), head circumference (r = 0.91; p < 0.00001; y = 0.85 + 0.63 x head circumference), femoral length (r = 0.91; p < 0.0001; y = 3.18 + 0.26 x femoral length) and humeral length (r = 0.73; p < 0.0001; y = 1.94 + 0.11 humeral length). A linear growth function was also observed between nostril distance and gestational age (r = 0.54; p < 0.00001; y = 2.77 + 0.15 x gestational age), biparietal diameter (r = 0.71; p < 0.00001; y = 1.83 + 0.08 x biparietal diameter), head circumference (r = 0.70; p < 0.00001; y = 1.99 + 0.2 x head circumference), femoral length (r = 0.75; p < 0.00001; y = 2.49 + 0.09 x femoral length) and humeral length (r = 0.91; p < 0.00001; y = 1.89 + 0.32 x humeral length). A linear growth relationship was found between nose width and nostril distance (r = 0.71; p < 0.00001; y = 1.81 + 0.31 x nose width). These results provide normative data of the fetal nose width and nostril distance in various dimensions and across gestational age. In addition, the data offer the potential for prenatal diagnosis of nose and nostril abnormalities.

Female↗
PubMed2003

The effects of wearing corrective lenses for presbyopia on distance vision.

The possibility of patient behaviour concerning the wearing of reading spectacles influencing the magnitude and rate of change in distance vision has been hypothesised but not fully examined. This study examined the changes in distance vision over time of 674 presbyopic patients between the ages of 44 and 69 who came to their eye professional needing reading spectacles. Prior to this study, these patients had never worn spectacles. The majority of patients opted for full-eye (complete) reading spectacles and 150 patients selected bifocals. It was found that patients wearing complete reading spectacles eventually adapted to wearing their reading spectacles for intermediate or distance work. Through X2, it was found that there were significant differences in the reduction of distance visual acuity between groups based on the amount of time spent wearing reading spectacles for intermediate or distance work. The greater the number of hours spent wearing reading spectacles and viewing beyond their focal point, the greater the change in distance visual acuity. It also appeared to affect the degree of change in their prescription. Age was not significantly related.

Accommodation, Ocular↗
PubMed1989

Iron status of women distance runners, sprinters, and control women.

Fasting blood samples from 11 women distance runners, 12 sprinters, and 11 moderately active women were examined to determine iron status. Dietary iron intake and bioavailability were analyzed from 3-day food diaries. Both distance runners and sprinters had lower hematocrits and haptoglobins than moderately active women. Distance runners had significantly lower ferritin (15.8 micrograms/l) than sprinters (32.8 micrograms/l), but moderately active women's ferritin (26.1 micrograms/l) was not significantly different than in the other groups. Five distance runners, two sprinters, and one moderately active woman had ferritins below 12 micrograms/l, which suggests iron depletion. Differences in hemoglobin, plasma iron, transferrin, and food iron intake were not significant among the three groups. Absorbable iron and heme iron intake were significantly lower for the distance runners and control women than the sprinters. The results suggest that low ferritin is more common among women who train for distance events than for sprints. This difference may by due to differences in bioavailability of food iron intake.

Adult↗