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PubMed1999

Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions.

The problem of protein tertiary structure prediction from primary sequence can be separated into two subproblems: generation of a library of possible folds and specification of a best fold given the library. A distance geometry procedure based on random pairwise metrization with good sampling properties was used to generate a library of 500 possible structures for each of 11 small helical proteins. The input to distance geometry consisted of sets of restraints to enforce predicted helical secondary structure and a generic range of 5 to 11 A between predicted contact residues on all pairs of helices. For each of the 11 targets, the resulting library contained structures with low RMSD versus the native structure. Near-native sampling was enhanced by at least three orders of magnitude compared to a random sampling of compact folds. All library members were scored with a combination of an all-atom distance-dependent function, a residue pair-potential, and a hydrophobicity function. In six of the 11 cases, the best-ranking fold was considered to be near native. Each library was also reduced to a final ab initio prediction via consensus distance geometry performed over the 50 best-ranking structures from the full set of 500. The consensus results were of generally higher quality, yielding six predictions within 6.5 A of the native fold. These favorable predictions corresponded to those for which the correlation between the RMSD and the scoring function were highest. The advantage of the reported methodology is its extreme simplicity and potential for including other types of structural restraints.

Protein Folding↗

PubMed2002

Direct conversion of EPR dipolar time evolution data to distance distributions.

Shallow electron spin echo envelope modulations due to dipole-dipole couplings between electron spins provide information on the radial distribution function of the spins in disordered systems while angular correlations between spin pairs are negligible. Under these conditions and in the absence of orientational selection, the dipolar time evolution data can be quantitatively simulated for arbitrary radial distribution functions by shell factorization, i.e., by performing the orientational average separately for thin spherical shells and multiplying the signals of all the shells. For distances below 5 nm, a linear superposition of the signals of the shells is sufficient. The dipolar time evolution data can be separated into this linear contribution and a nonlinear background. The linear contribution can then be converted directly to a radial distribution function. For a series of shape-persistent and flexible biradicals with end-to-end distances between 2 and 5 nm, shell factorization and direct conversion of the data are in good agreement with each other and with force-field computations of the end-to-end distances. The neglect of orientation selection does not cause significant distortions of the determined distance distributions.

Journal Article↗

PubMed1999

Total evidence, consensus, and bat phylogeny: A distance-based approach.

Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for combining trees, and (3) indifference to aspects of trees other than their topologies. We demonstrate a uniform, distance-based approach which allows for comparability among the results of character- and taxonomic-congruence studies, whether or not an identical suite of taxa has been included in all contributing data sets. Our results indicate that total-evidence and consensus trees differ little in topology if branch lengths are taken into account when combining two or more trees. In addition, when character-state data are converted to distances, our method permits their combination with information produced by techniques which generate distances directly. Moreover, treating all data sets or trees as distance matrices avoids the problem that different numbers of characters in contributing studies may confound the conclusions of a total-evidence or consensus analysis. Our protocol is illustrated with an example involving bats, in which the three component studies based on serology, DNA hybridization, and anatomy imply distinct phylogenies. However, the total-evidence and consensus trees support a fourth, somewhat different, topology resolved at all but one node and which conforms closely to the currently accepted higher category classification of Chiroptera.

Animals↗

PubMed1993

The tobamovirus capsid protein functions as a host-specific determinant of long-distance movement.

The tobamoviruses, tobacco mosaic virus (TMV) and Odontoglossum ringspot virus (ORSV), differ in the range of plant species that each can systemically infect. Both viruses systemically infect Nicotiana benthamiana similarly, but differ in the ability to systemically infect tobacco (N. tabacum). ORSV is confined to the inoculated leaves of N. tabacum, whereas TMV causes a rapid systemic infection. Genetic chimeras were created to identify viral genes involved in specific interactions in long-distance movement in N. tabacum. In N. tabacum, a chimera expressing the ORSV 30-kDa protein exhibited a reduced rate of cell-to-cell spread, similar to that of ORSV, and, also like ORSV, was deficient in systemic invasion, implying a relationship between the rates of cell-to-cell and long-distance movement. However, a TMV chimera expressing the ORSV capsid protein gene spread cell to cell similarly to TMV, but was deficient in long-distance movement and systemic infection. These data suggest that tobamovirus capsid protein(s) may be required to interact with host components in a specific manner to allow efficient long-distance movement, and the ORSV capsid protein did not function in this manner in tobacco plants.

Base Sequence↗

PubMed2001

Long-distance movement and replication maintenance functions correlate with silencing suppression activity of potyviral HC-Pro.

The tobacco etch potyviral protein, HC-Pro, is a multifunctional proteinase required for long-distance movement in plants and maintenance of genome replication at the single-cell level. It also functions in a counterdefensive capacity as a suppressor of posttranscriptional gene silencing (PTGS). To determine whether the requirements for HC-Pro during long distance movement and replication maintenance are due to the silencing suppressor function of the protein, a series of HC-Pro alanine scanning and other site-directed mutants were analyzed. Using a transient silencing suppression assay in Agrobacterium-injected leaf tissue, several suppression-defective mutants were identified. Each of six HC-Pro mutations, which were shown previously to confer long-distance movement and replication maintenance defects, conferred PTGS suppression defects. Interestingly, the genes encoding these defective HC-Pro derivatives were themselves susceptible targets of PTGS, resulting in low levels of mRNA and protein accumulation. Mutations that inactivated the proteinase domain active site had no effect on PTGS suppression function. The results are consistent with the hypothesis that the role of HC-Pro in long-distance movement and genome replication depends on PTGS suppression function and that this function is independent of HC-Pro proteolytic activity.

Alanine↗

PubMed1993

Unitary distance of ATP-induced actin-myosin sliding studied with an in vitro force-movement assay system.

We studied the unitary distance of ATP-induced actin-myosin sliding using an in vitro force-movement assay system consisting of a myosin-coated glass microneedle and well organized actin filament arrays (actin cables) in the internodal cell of an alga Nitellopsis obtusa. The number of myosin heads interacting with actin cables was reduced to about 100, as judged from the isometric force of about 100 pN attained in the presence of 2 mM ATP. When the amount of iontophoretically applied ATP was reduced by decreasing the amount of charge passed through the ATP electrode from 80 to 2 nC, the distance of the ATP-induced actin-myosin sliding decreased almost linearly from about 100 to about 10 nm, no detectable sliding being observed with further reduction of charge through the electrode. The sliding distances with small amounts of ATP (7-16 nC) distributed around integral multiples of 10 nm, suggesting the unitary distance of actin-myosin sliding of about 10 nm.

Actins↗

PubMed1993

A unified approach to study hypervariable polymorphisms: statistical considerations of determining relatedness and population distances.

Relatedness between individuals as well as evolutionary relationships between populations can be studied by comparing genotypic similarities between individuals. When hypervariable loci are used to describe genotypes, it is shown that both of these problems can be approached with a unified theory based on allele sharing between individuals. The distributions of the number of shared alleles between individuals indicate their kin relationships. Extending this, we obtain statistics for genetic distances between populations based on average number of alleles shared between individuals within and between two different populations. Traditional statistical inferential procedure can be used to establish specific kinship relationships between individuals. We derive estimates of the number of hypervariable loci needed for a specified reliability of such an inference. Evolutionary dynamics of genetic distance statistics based on allele sharing is also studied. It shows that such measures of genetic distances remain linear with the time of divergence for a period comparable to that of the gene frequency-based measures of genetic distances. Statistical properties of measures based on allele sharing establish that for using such summary statistics it is not necessary to know the full characteristics of all loci used. It is enough to know the degree of heterozygosity per locus and the number of loci. Therefore, in principle, this approach can also be used for DNA fingerprinting data in the studies of relatedness between individuals as well as between populations. The possible compromising features of multilocus DNA fingerprinting data are also discussed.

Alleles↗

PubMed1996

Solution structure of a Lewis(x) analogue by off-resonance 1H NMR spectroscopy without use of an internal distance reference.

A recent 1H NMR method has been applied to the determination of the solution structure and internal dynamics of a synthetic mixed C/O trisaccharide related to sialyl Lewis(x). Varying the rf field offset in ROESY-type experiments enabled the measurement of longitudinal and transverse dipolar cross-relaxation rates with high accuracy. Assuming that for each proton pair the motion could be represented by a single exponential autocorrelation function, it was possible to derive geometrical parameters (r) and dynamic parameters (tau(cp)). With this assumption, 224 cross-relaxation rates have been transformed into 30 interproton distance constraints and 30 dipolar correlation times. The distance constraints have been used in a simulated-annealing procedure. This trisaccharide exhibits a structure close to the O-glycosidic analogue, but its flexibility seems highly reduced. On the basis of the determined structure and dynamics, it is shown that no conformational exchange occurs, the molecule existing in the form of a unique family in aqueous solution. In order to assess the quality of the resulting structures and to validate this new experimental procedure of distance extraction, we finally compare these solution structures to the ones obtained using three different sets of distances deduced from three choices of internal reference. It appears that this procedure allows the determination of the most precise and accurate solution.

Gangliosides↗

PubMed1990

Significance of the contribution of aerobic and anaerobic components to several distance running performances in female athletes.

To assess the most important determinant for successful distance running (800 m, 1500 m and 3000 m events) in female athletes, measurements of several anaerobic indices were made (peak power, mean power) using the Wingate anaerobic test (WAnT), and aerobic indices such as oxygen uptake (VO2) or running velocity (v) at lactate threshold (LT), VO2 or v at onset of blood lactate accumulation (OBLA), running economy (RE), and maximal oxygen uptake were determined using the incremental treadmill test. The RE was represented by a VO2 value measured at 240 m.min-1 of a standard treadmill velocity. A stepwise multiple regression analysis (SAS stepwise procedure) combined the best features of forward inclusion and backward elimination to determine the most important factors in predicting the performance of running these distances as dependent variables. The stepwise procedure showed that the blood lactate variables such as LT and/or OBLA are highly correlated with, and contributed to predicting performance running 800 m-3000 m, whereas the anaerobic component was related only to running 800 m. In conclusion, blood lactate variables account for a large part of the variation in distance running performance in female as in male runners. The component of the anaerobic system which can be measured by the WAnT was shown to contribute to performance in running 800 m, but not in longer distances.

Adult↗

PubMed1981

[The fixateur-externe-osteosynthesis without osseous support (external distance-osteosynthesis) in the lower limbs. Biomechanic, surgical and osteoplastic basic principles (author's transl)].

The stability of external distance osteosynthesis for complete tibia and femur defects rests solely on the rigidity of the external support. The rigidity of the external support is an function of the mechanical data of its individual elements, of the hold between the bone and the other system, as well as of the individually optimized construction form. The response of an osseous contact area which is not resistant to compression when external osteosynthesis is applied is mechanically similar to the response to distance osteosynthesis in the presence of a defect. The basic application rules for distance osteosynthesis of the lower limbs are given. The symmetric frame fixator applied in a three-dimensional arrangement is indicated for tibia defects. External distance osteosynthesis of femur defects can only be recommended when plate osteosynthesis alone or plate osteosynthesis in conjunction with a bracket fixator are out of the question. The various application forms for external osteosynthesis of femur defects are described and their indication with respect to knee function given. Although none of the construction forms for defects in the tibia and especially in the femur can eliminate mechanical interfragmental movement of the main fragments, their clinical use has been successfully established; however, surgical and osteoplastic measures must ensure more and more biological stability with time. The necessary surgical techniques and procedures are described. Whereas even extensive defects of the femur can be bridged exclusively with autologous cancellous bone, varied measures are required for the lower leg, depending on the various individual conditions. Should the direct bridging of the main tibia fragments not be appropriate, fibular-tibial synostosis is necessary. The various options for such fibular-tibial osteoplasty which may be required, depending on the individual case, are described.

Biomechanical Phenomena↗

PubMed1981

Lognormal distribution of intercapillary distance in normal and hypertrophic rat heart as estimated by the method of concentric circles: its effect on tissue oxygenation.

The inhomogeneity of the capillary net in the cardiac muscle was estimated using our morphometric measurements in normal and hypertrophic rats hearts. As entry data we used the distribution of tissue at different distances from the nearest capillary as measured by the method of concentric circles and the mean intercapillary distance independently calculated from the capillary density. The derived distribution of intercapillary distances was approximated by lognormal distribution in which the spread can be characterized by a single parameter, namely the log standard deviation. The effect of the log standard deviation on tissue oxygenation was evaluated in normal and hypertrophic hearts, at normoxia and at hypoxia. The mean tissue PO2 and the percentage of anoxic tissue at the venous end of the tissue cylinder were calculated using Krogh's model. Two boundary situations were considered: A) the end-capillary PO2 was assumed to be equal in all capillaries due to compensatory adjustment in blood flow; B) the same flow in all capillaries was assumed resulting in varying end-capillary PO2. The real situation is expected to be between situations A and B. Increased variability of intercapillary distance proved to impair considerably the tissue oxygenation, especially when the results were expressed as a percentage of anoxic tissue. The percentage of anoxic tissue turned out to be a better index of tissue oxygenation than the mean PO2 particularly at hypoxia. The results suggest the presence of at least a partial adjustment of blood flow with respect to the width of tissue cylinder. Without such adjustment, a large part of tissue would become anoxic already in normal hearts at normoxia and this would be further aggravated by hypertrophy and/or hypoxia.

Animals↗

PubMed1992

Training-overtraining: influence of a defined increase in training volume vs training intensity on performance, catecholamines and some metabolic parameters in experienced middle- and long-distance runners.

The influence of an increase in training volume (ITV; February 1989) vs intensity (ITI; February 1990) on performance, catecholamines, energy metabolism and serum lipids was examined in two studies on eight, and nine experienced middle- or long-distance runners; seven participated in both studies. During ITV, mean training volume was doubled from 85.9 km.week-1 (pretrial phase) to 174.6 km within 3 weeks. Some 96%-98% of the training was performed at 67 (SD 8)% of maximal performance. During ITI, speed-endurance, high-speed and interval runs increased within 3 weeks from 9 km.week-1 (pretrial phase) to 22.7 km.week-1 and the total training distance from 61.6 to 84.7 km.week-1. The ITV resulted in stagnation of running velocity at 4 mmol lactate concentration and a decrease in total running distance in the increment test. Heart rate, energy metabolic parameters, nocturnal urinary catecholamine excretion, low density, very low density lipoprotein-cholesterol and triglyceride concentrations decreased significantly; the exercise-related catecholamine plasma concentrations increased at an identical exercise intensity. The ITI produced an improvement in running velocity at 4 mmol lactate concentration and in total running distance in the increment test; heart rate, energy metabolic parameters, nocturnal catecholamine excretion, and serum lipids remained nearly constant, and the exercise-related plasma catecholamine concentrations decreased at an identical exercise intensity. The ITV-related changes in metabolism and catecholamines may have indicated an exhaustion syndrome in the majority of the athletes examined but this hypothesis has to be proven by future experimental studies.

Adult↗

PubMed1992

[Effect of carbohydrate intake during a long distance run on work capacity and metabolism].

The present study addressed the effects of carbohydrate consumption during endurance exercise on performance, energy turnover, and metabolism. Well-trained endurance runners consumed a beverage with (cho[+]) or without (cho[-]) carbohydrates during a long-distance run (46.6 km). The respiratory quotient (RQ), plasma levels of carbohydrate and fat metabolites, and of hormones (insulin, glucagon) were measured before, several times during, and after the run. The mean running speed for the entire distance was 13.6 and 13.4 km/h with the cho[+] and cho[-] beverage, respectively. The decrease in speed that was observed towards the end of the run was somewhat more pronounced with consumption of the cho[-] beverage. The RQ decreased during the run almost linearly. This decrease was independent of the consumed beverage. The changes in plasma levels of lactate, free fatty acids (FFA), glycerol, D-3-hydroxybutyrate (DHB), glucagon and insulin that occurred during the run were not affected by intake of the cho[+] beverage. However, intake of the cho[+] beverage prevented the decrease in plasma glucose observed towards the end of the run under control conditions, and eliminated the steep postexercise increase in plasma DHB. The intake of the cho[+] beverage also caused a rapid decrease in plasma levels of FFA and glucagon after the run, and slightly increased plasma insulin. The results demonstrate that ingestion of a carbohydrate-containing beverage during a long-distance run affects metabolism only during the final phase of the run and during the subsequent recovery period. Moreover, carbohydrate consumption improves performance only during the final phase of a long-distance run.

3-Hydroxybutyric Acid↗

PubMed1998

Distances between the cochlea and adjacent structures related to cochlear implant surgery.

A sound knowledge of the topographic anatomy of the cochlea, especially of the distances between it and the adjacent structures, is essential for otosurgery in general, and in surgical procedures for cochlear implantation in particular. One hundred temporal bones of humans aged from one month to 71 years, of either sex, taken from both body sides (but not bilaterally) were studied by dissection under the operating microscope and exposing the cochlea and its neighbourhood. The minimal distances were measured between the cochlear turns and the internal carotid artery, the bulb of the jugular vein, the facial nerve and the floor of the internal acoustic meatus. It was found that in children aged up to 4 years most of the measured distances were significantly smaller than in older individuals. Only the minimal distance between the basal turn of the cochlea and the floor of the internal acoustic meatus was shorter in small children without statistical significance.

Adolescent↗

PubMed1996

Estimation of the physical distance between major genomic markers in the Werner syndrome locus (8p11.2-12) by dual-color fish analysis.

The gene responsible for Werner syndrome (WS) is considered to be located between D8S131 and D8S87 in the 8p11.2-12 region that includes the closest marker D8S339 (Goto et al. (1992) Nature 355: 735-738). In this experiment, the order of major markers in this region was determined and the physical distances between them were estimated by dual-color fluorescence in situ hybridization (FISH) using P1, PAC and cosmid clone DNAs as probes. The fine overall order of telomere-D8S131-D8S339-GSR-PP2A beta-D8S283-D8S87-centromere was determined for the first time. The distance from D8S131 to D8S87 was estimated to be 1,634 kb. To our surprise, the distance between D8S131 and D8S87 is much shorter than previously estimated by recombination analysis, 8.3 cM equivalent to 8.3 Mb in physical distance. These information provide the basis for the positional cloning of WS gene and the identification of its mutation.

DNA↗

PubMed1992

Proliferative activity of colonic mucosa at different distances from primary adenocarcinoma as determined by the presence of statin: a nonproliferation-specific nuclear protein.

The field change is one hypothesis concerning the development of colorectal carcinoma. Removal of a carcinoma without its entire surrounding altered mucosa may result in the development of a recurrence. S44, a monoclonal antibody directed against statin, a nuclear protein expressed in nonproliferating cells in either a quiescent or senescent state, was used to determine the rate of cell growth in colorectal mucosa at different distances from carcinomas. The specimens of 18 patients undergoing resection of a colorectal carcinoma were immediately opened after operation, and strips of mucosa were taken at distances of 1 cm, 5 cm, and 10 cm from the carcinoma. For each location, 10 longitudinally oriented crypts were evaluated for statin-positive cells identified by the presence of a dark brown peroxidase-conjugated antibody reaction product. The average percentage of statin-positive cells per crypt was significantly lower at a 1-cm distance from the carcinoma compared with the mucosa located 5 and 10 cm from the carcinoma (20.89 +/- 4.33 at 1 cm, 32.41 +/- 5.27 at 5 cm, and 34.23 +/- 6.45 at 10 cm). None of the calculated parameters showed any significant difference between the 5-cm and 10-cm locations. The fact that the proliferation rate of the mucosal cells returns to the normal level at 5 cm from the margin of the carcinoma suggests that cells located within this distance still retain proliferative potential even though they are morphologically indistinguishable from their normal counterparts. We conclude that failure to remove this transitional, potentially proliferative mucosa may result in subsequent development of anastomotic or perianastomotic recurrences.

Antibodies, Monoclonal↗

PubMed1987

Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics.

Operator metrics are explicitly designed to measure evolutionary distances from nucleic acid sequences when substitution rates differ greatly among the organisms being compared, or when substitutions have been extensive. Unlike lengths calculated by the distance matrix and parsimony methods, in which substitutions in one branch of a tree can alter the measured length of another branch, lengths determined by operator metrics are not affected by substitutions outside the branch. In the method, lengths (operator metrics) corresponding to each of the branches of an unrooted tree are calculated. The metric length of a branch reconstructs the number of (transversion) differences between sequences at a tip and a node (or between nodes) of a tree. The theory is general and is fundamentally independent of differences in substitution rates among the organisms being compared. Mathematically, the independence has been obtained because the metrics are eigenvectors of fundamental equations which describe the evolution of all unrooted trees. Even under conditions when both the distance matrix method or a simple parismony length method are shown to indicate lengths that are an order of magnitude too large or too small, the operator metrics are accurate. Examples, using data calculated with evolutionary rates and branchings designed to confuse the measurement of branch lengths and to camouflage the topology of the true tree, demonstrate the validity of operator metrics. The method is robust. Operator metric distances are easy to calculate, can be extended to any number of taxa, and provide a statistical estimate of their variances. The utility of the method is demonstrated by using it to analyze the origins and evolution of chloroplasts, mitochondria, and eubacteria.

Base Sequence↗

PubMed1996

Variation in the ratio of physical to genetic distance in intervals adjacent to the Mla locus on barley chromosome 1H.

Variants of the pulsed-field gel electrophoresis technique were used in conjunction with two-dimensional DNA gel electrophoresis (2-DDGE) to determine the ratio of physical to genetic distance in two genetically defined intervals on barley chromosome 1H.2-DDGE analysis demonstrated that two loci that define a 0.3 cM interval, as determined by hybridization with BCD249, reside on a single 450-kb MluI fragment. This result indicates a maximum ratio of physical to genetic distance in this interval of 1500 kb/cM as compared to 3.7-4.2 Mb/cM for the barley genome as a whole. High molecular weight (HMW) DNA restricted with NotI and probed sequentially with MWG068 and BCD249 yield diffuse bands at approximately 2.8 Mb and 3.0 Mb in the C.I. 16151 and C.I. 16155 parental lines, respectively. These results suggest the maximum ratio of physical to genetic distance in the interval defined by these probes is 7.8 Mb/cM. Unique HMW DNA restriction fragment length polymorphisms (RFLP) were attributed to the presence of recombination breakpoints. Data from the recombination breakpoint analysis were used to estimate a ratio of physical to genetic distance of 2.5 Mb/cM in the Xbcd249.2-Xmwg068 interval and 0.465 Mb/cM in the Xbcd249.1-Xbcd249.2 interval. Both physical linkage and recombination breakpoint analysis indicate the Xbcd249.1-Xbcd249.2 interval is approximately five-fold smaller, physically, than the Xbcd249.2-Xmwg068 interval.

Bacterial Proteins↗