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Practical methods for solid-state NMR distance measurements on large biomolecules: constant-time rotational resonance.

Simple modifications of the rotational resonance experiment substantially reduce the total experimental time needed to measure weak homonuclear dipolar couplings, a critical factor for achieving routine internuclear distance measurements in large biomolecular systems. These modifications also address several problems cited in the literature. Here we introduce a constant-time rotational resonance experiment that eliminates the need for control spectra to correct for effects from variable RF heating, particularly critical for accurate long-distance measurements. This reduces the total number of experiments needed by as much as a factor of 2. Other improvements incorporated include achieving selective inversion with a delay rather than a weak pulse (P. R. Costa et al., J. Am. Chem. Soc. 119, 10487-10493, 1997), which we observe results in the elimination of oscillations in peak intensities for short mixing time points. This reduces the total experiment time in two ways. First, there is no longer a need to average different "zero"-time points (S. O. Smith et al., Biochemistry 33, 6334-6341, 1994) to correct for intensity variations. Second, short-mixing-time lineshape differences observed in large membrane-bound proteins only appear with the weak-pulse inversion and not when using the delay inversion. Consistent lineshapes between short and long mixing times permit the use of a single spectrum for subtraction of natural abundance background signals from all labeled-protein time points. Elimination of these effects improves the accuracy and efficiency of rotational resonance internuclear distance measurements.

Magnetic Resonance Spectroscopy↗

Modulation of parietal activation by semantic distance in a number comparison task.

The time to compare two numbers shows additive effects of number notation and of semantic distance, suggesting that the comparison task can be decomposed into distinct stages of identification and semantic processing. Using event-related fMRI and high-density ERPs, we isolated cerebral areas where activation was influenced by input notation (verbal or Arabic notation). The bilateral extrastriate cortices and a left precentral region were more activated during verbal than during Arabic stimulation, while the right fusiform gyrus and a set of bilateral inferoparietal and frontal regions were more activated during Arabic than during verbal stimulation. We also identified areas that were influenced solely by the semantic content of the stimuli (numerical distance between numbers to be compared) independent of the input notation. Activation tightly correlated with numerical distance was observed mainly in a group of parietal areas distributed bilaterally along the intraparietal sulci and in the precuneus, as well as in the left middle temporal gyrus and posterior cingulate. Our results support the assumption of a central semantic representation of numerical quantity that relies on a common parietal network shared among notations.

Adult↗

Increased accuracy in analytical molecular distance estimation.

Analytical molecular distance estimates can be inaccurate and biased estimates of the total number of substitutions not only when the model of evolution they are based on is incorrect, but also when the method of estimating the total is too simple. This comes about because when there are different types of substitutions occurring simultaneously, it can become extremely difficult to estimate the number of the more quickly evolving type, and the variance of this larger number can overwhelm the total estimate. In this paper, in an extension of earlier work with a simple two-parameter model of evolution, more accurate analytical distances are derived for models appropriate to a variety of known DNA types using generalized least squares principles of noise reduction. It is shown that the new estimates can be applied to achieve more accurate results for site-to-site rate variation, regions with biased nucleotide frequencies, and synonymous sites in protein-coding regions. This study also includes a methodology to obtain accurate distance estimates for large numbers of sequence regions evolving in different manners.

Animals↗

Virion formation is required for the long-distance movement of red clover necrotic mosaic virus in movement protein transgenic plants.

The red clover necrotic mosaic dianthovirus (RCNMV) genome is split between two single-stranded RNA species. The polycistronic RNA-1 encodes the viral RNA polymerase and capsid protein (CP) and the monocistronic RNA-2 encodes the 35 kDa cell-to-cell movement protein (MP). Nicotiana benthamiana plants transformed with the RCNMV MP gene were generated. When inoculated onto the MP transgenic plants, cell-to-cell movement of RNA-1 occurred at a rate similar to wild-type virus. However, long-distance (leaf-to-leaf) movement of RNA-1 was not observed. Neither CP nor virions were detected in the inoculated leaves of the MP transgenic plants. When RNA-1 was coinoculated with RNA-2 mutants, which do not express a functional MP, onto MP transgenic plants, CP and virions were readily detected and a systemic infection resulted. These results demonstrate that both RNA-1 and RNA-2 are necessary for the accumulation of both CP and virions. Furthermore, CP accumulation was found to be required for long-distance movement of RCNMV. Therefore, these data provide evidence that CP, in the form of virions, is necessary for the long-distance movement of RCNMV.

Capsid↗

Mutations in viral movement protein alter systemic infection and identify an intercellular barrier to entry into the phloem long-distance transport system.

Viral systemic infection of a plant host involves two processes, cell-to-cell movement and long-distance transport. Molecular determinants associated with these two processes were probed by investigating the effects that alanine scanning mutations in the movement protein (MP) of red clover necrotic mosaic virus (RCNMV) had on viral infection in the plant hosts Nicotiana edwardsonii, Vigna unguiculata (cowpea), and the experimental plant Nicotiana benthamiana. Plants were inoculated with RCNMV expressing wild-type and mutant forms of the MP. Immunocytochemical studies at the light and electron microscope levels were performed on these plants, using a polyclonal antibody raised against the RCNMV capsid protein to identify the cells/tissues that RCNMV could infect. These experiments demonstrated that one cellular boundary at which the RCNMV MP functions to facilitate entry into the phloem long-distance transport system is located at the interfaces between the bundle sheath and phloem parenchyma cells and the companion cell-sieve element complex. Interestingly, in Nicotiana tabacum, a host that only allows a local infection, RCNMV cell-to-cell movement was found to be blocked at this same intercellular boundary. Four mutants that were able to systemically infect N. benthamiana were partially or completely defective for systemic infection of N. edwardsonii and cowpea, which indicated that these MP mutants exhibited host-specific defects. Thus, the roles of the RCNMV MP in cell-to-cell movement and in long-distance transport appear to be genetically distinct. These results are discussed in terms of the mechanism by which RCN MV enters the phloem to establish a systemic infection.

Biological Transport↗

Host-specific cell-to-cell and long-distance movements of cucumber mosaic virus are facilitated by the movement protein of groundnut rosette virus.

The cucumovirus, cucumber mosaic virus (CMV), requires both the 3a movement protein (MP) and the capsid protein (CP) for cell-to-cell movement. Replacement of the MP of CMV with the MP of the umbravirus, groundnut rosette virus (GRV), which does not encode a CP, resulted in a hybrid virus, CMV(ORF4), which could move cell to cell in Nicotiana tabacum and long distance in N. benthamiana. After replacement of the CMV CP in CMV(ORF4) with the gene encoding the green fluorescent protein (GFP), the hybrid virus, CMV(ORF4.GFP), expressing both the GRV MP and the GFP, could move cell to cell but not systemically in either Nicotiana species. Immunoelectron microscopic analysis of cells infected by the hybrid viruses showed different cellular barriers in the vasculature preventing long-distance movement of CMV(ORF4) in N. tabacum and CMV(ORF4.GFP) in N. benthamiana. Thus the GRV MP, which shows limited sequence similarity to the CMV MP, was able to support CP-independent cell-to-cell movement of the hybrid virus, but CP was still required for long-distance movement and entry of particular vascular cells required functions encoded by different proteins.

Capsid↗

Investigating the extension of pairwise distance pharmacophore measures to triplet-based descriptors.

Distances between key functional groups have been used for some time as molecular descriptors in 3D database screening and clustering calculations. More recently, a number of groups have explored triplets of molecular centers to describe key ligand features in terms of the properties of triangles. Three-body distances are attractive, since they retain more information than pairwise representations. In most applications, the triangular descriptors have been used to detail molecular shape, using all the constituent atoms or molecular surface points as descriptor centers. As a consequence, the database keying times were such that only single conformers could be considered during molecular descriptor calculations. In this paper we reduce the points used in the molecular description down to the key functional centers, as applied in 3D pharmacophore database searches. Molecular triplets can then be calculated which describe the relative dispositions of differing functional groups, made up from multiple molecular conformations of a given molecule. The new triplet descriptors are compared with classical pairwise distance measures using a variety of pharmacophores, and their potential in database screening, clustering and pharmacophore identification is discussed.

Databases, Factual↗

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances.

This paper reports a comparison of several methods for measuring the degree of similarity between pairs of 3-D chemical structures that are represented by inter-atomic distance matrices. The methods that have been tested use the distance information in very different ways and have very different computational requirements. Experiments with 10 small datasets, for which both structural and biological activity data are available, suggest that the most cost-effective technique is based on a mapping procedure that tries to match pairs of atoms, one from each of the molecules that are being compared, that have neighbouring atoms at approximately the same distances.

Computer Simulation↗

Genetic distance and species formation in evolving populations.

We compare the behavior of the genetic distance between individuals in evolving populations for three stochastic models. In the first model reproduction is asexual and the distribution of genetic distances reflects the genealogical tree of the population. This distribution fluctuates greatly in time, even for very large populations. In the second model reproduction is sexual with random mating allowed between any pair of individuals. In this case, the population becomes homogeneous and the genetic distance between pairs of individuals has small fluctuations which vanish in the limit of an infinitely large population. In the third model reproduction is still sexual but instead of random mating, mating only occurs between individuals which are genetically similar to each other. In that case, the population splits spontaneously into species which are in reproductive isolation from one another and one observes a steady state with a continual appearance and extinction of species in the population. We discuss this model in relation to the biological theory of speciation and isolating mechanisms. We also point out similarities between these three models of evolving populations and the theory of disordered systems in physics.

Biological Evolution↗

Do NOE distances contain enough information to assess the relative populations of multi-conformer structures?

The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.

Allergens↗

Extensive distance geometry calculations with different NOE calibrations: new criteria for structure selection applied to Sandostatin and BPTI.

To generate structures efficiently, a version of the distance geometry program DIANA for a parallel computer was developed, new objective criteria for the selection of NMR solution structures are presented, and the influence of using different calibrations of NOE intensities on the final structures are described. The methods are applied to the structure determination of Sandostatin, a disulfide-bridged octapeptide, and to model calculations of BPTI. On an Alliant FX2800 computer using 10 processors in parallel, the calculations were done 9.2 times faster than with a single processor. Up to 7000 Sandostatin structures were calculated with distance and angular constraints. The procedure for selecting acceptable structures is based on the maximum values of pairwise RMSDs between structures. Suitable target function cut-offs are defined independent of the number of starting structures. The method allowed for an objective comparison of three groups of Sandostatin structures that were calculated from different sets of upper distance constraints which were derived from the same NOE intensity data using three empirical calibration curves. The number of converged structures and the target function values differed significantly among the three groups, but the structures were qualitatively and quantitatively very similar. The conformation is well determined in the cyclic region Cys2-Cys7 and adopts a beta-turn centered at D-Trp4-Lys5. The criteria for structure selection were further tested with BPTI. Results obtained from sets of structures calculated with and without using the REDAC strategy are consistent and suggest that the structure selection method is objective and generally applicable.

Amino Acid Sequence↗

Fluorimetric distance determination by resonance energy transfer. Ribosome-bound transfer RNA.

Using the technique of singlet-singlet (Förster-type) resonance energy transfer, we have determined five distances in the programmed ribosome, either with the P site or with both the A and the P sites occupied. Two of the distances are new and two agree with earlier measurements; the fifth showed disagreement in detail with earlier results of others, but a consistent general trend. The distances substantiate a current model for the location of ribosomally bound tRNA, except in regard of the position of the 3' end of P-site tRNA, which seems according to our results to lie too far away from the 3' terminus of the 16 S RNA to be accommodated in the model. We present new evidence for the hypothesis that anomalously charged tRNA does not bind to the cognately programmed A site in the same way as does tRNA charged with an amino acid. Occupation of the A site restricts mobility of the 3' end of tRNA in the P site.

Energy Transfer↗

Linkage disequilibrium analyses and restriction mapping of four RFLPs at the pro alpha 2(I) collagen locus: lack of correlation between linkage disequilibrium and physical distance.

Restriction fragment length polymorphisms (RRLPs) located at short distances may demonstrate linkage disequilibrium. Under the assumption that the distances between the loci of the RFLPs are inversely related to the linkage disequilibria, gene order may be deduced. However, if the assumption is invalid, the results may be incorrect. We have studied four different DNA polymorphisms at the COLIA2 locus in 180 unrelated Norwegian individuals. Observed frequencies (presence/absence) for the different polymorphic sites were as follows: site A (EcoRI) 0.30/0.70, site B (MspI) 0.83/0.16, site C (StuI) 0.86/0.14, and site D (RsaI) 0.66/0.34. Of 16 possible haplotypes 12 were demonstrated, and 2 additional were deduced to be present. Restriction mapping of the four polymorphic sites gave the following order of the sites from the 5' to the 3' of the gene: A-D-B-C. Linkage disequilibrium was not found between the sites A and D; strong disequilibrium was found between sites A and C, and B and C; and less strong, between A and B, B and D, and C and D. Analysis of linkage disequilibrium coefficients between all pairs of loci demonstrated that there is no consistent relationship between linkage disequilibrium and physical distance (tau = -0.07). These results suggest that for a small region of the genome, factors such as deviating mutation rate and gene conversion may add significantly to rearrangements by recombination. Thus, a deduced gene order from linkage disequilibrium data has to be regarded with great caution.

Chromosome Mapping↗

Specificity of physiological adaptation to endurance training in distance runners and competitive walkers.

The present study was designed to evaluate the specificity of physiological adaptation to extra endurance training in five female competitive walkers and six female distance runners. The mean velocity (v) during training, corresponding to 4 mM blood lactate [onset of blood lactate accumulation (OBLA)] during treadmill incremental exercise (training v was 2.86 m.s-1, SD 0.21 in walkers and 4.02 m.s-1, SD 0.11 in runners) was added to their normal training programme and was performed for 20 min, 6 days a week for 8 weeks, and was called extra training. An additional six female distance runners performed only their normal training programme every day for about 120 min at an exercise intensity equivalent to their lactate threshold (LT) (i.e. a running v of about 3.33 m.s-1). After the extra training, there were statistically significant increases in blood lactate variables (i.e. oxygen uptake (VO2) at LT, v at LT, VO2 at OBLA, v at OBLA; P less than 0.05), and running v for 3,000 m (P less than 0.01) in the running training group. In the walking training group, there were significant increases in blood lactate variables (i.e., v at LT, v at OBLA; P less than 0.05), and walking economy. In contrast, there were no significant changes in lactate variables, running v and economy in the group of runners which carried out only the normal training programme. It is suggested that the changes in blood lactate variables such as LT and OBLA played a role in improving v of both the distance runners and the competitive walkers.(ABSTRACT TRUNCATED AT 250 WORDS)

Adaptation, Physiological↗

Comparison of sympatho-adrenergic regulation at rest and of the adrenoceptor system in swimmers, long-distance runners, weight lifters, wrestlers and untrained men.

The effects of different physical training regimes on the plasma catecholamine values at rest and the density and responsiveness of adrenergic receptors at rest were investigated. The changes during well-defined training periods of swimmers, long-distance runners, weight lifters and wrestlers were compared with untrained male volunteers. The training of swimmers and long-distance runners, building up endurance, resulted in a significantly lower basal plasma norepinephrine (NE) concentration and a significantly or possibly lower ratio NE:EPI (epinephrine). Both values indicated reduced sympathetic activity and resulted also in a significantly lower beta-receptor density and a higher alpha 2-receptor sensitivity compared with the other groups investigated. However, swimming-specific characteristics provoked labile hypertensive blood pressure regulation with an unchanged heart rate in swimmers. Static training of weight lifters, building up power, also led to a lower NE concentration compared with untrained subjects, whereas beta-receptor density was unchanged and alpha 2-receptor density and sensitivity were decreased. Elevated blood pressure values were observed in weight lifters and swimmers due to a reduced baroreceptor sensitivity. The dynamic training of wrestlers affected only basal heart rate and alpha 2-receptor sensitivity, both of which were decreased. Different kinds of physical training caused various adaptations of the basal activity of the autonomic nervous system in which adrenergic receptors also became adapted. In this context, the stronger adrenergic circulatory component of overall sympathetic activity at rest in swimmers and long-distance runners resulted in lower beta-receptor density, and the reduced noradrenergic component sensitized alpha 2-receptors.

Adenylyl Cyclases↗

Muscle cell leakage due to long distance training.

Abnormal myoglobinemia (above 77 microgram/l) and free hemoglobin in plasma were found in 16 runners and in nine non runners immediately following distance running. The same abnormalities were found iun six elite rowers following rowing. In parallel with the rise in myoglobin and free hemoglobin a rise was found in serum concentrations of cellular enzymes (LDH, CK, ASAT, alkaline phosphatase) and of various metabolites. We found no proteinuria nor casts in the urine. Non runners had a higher rise in serum myoglobin than runners. Competitive running caused a rise in the serum concentration of the heart specific fraction of creatine kinase in seven of the nine (healthy) elite runners. The abnormal findings are only explainable on the basis of leakage of proteins from muscle cells to the circulation in otherwise healthy, well trained persons. Myoglobinemia and a transient rhabdomyolysis is a common phenomenon in long distance running, but evidently also occurs in distance rowing. Three months of running training prevented most of the muscle damage from relaxed jogging in the nine previous non runners. Neither the observed myoglobinemia nor the hemoglobinemia resulted in any significant loss of iron in the urine.

Adult↗

Genetic distance in fungus genus Fusarium measured by comparative computer analysis of DNA thermal denaturation profiles.

High resolution thermal denaturation profiles of different members of fungus genus Fusarium were compared with respect to the shape of their DNA melting curves. Quantitative comparison of the shape (areas under differential curves) of all thermal denaturation profiles was made. Thermal denaturation profiles can be used to derive the quantitative parameter, genetic distance, defined by Soumpasis (12). Based on such data of genetic distance a dendrogram and a genetic distance tree was constructed.

Computers↗

Sustained noradrenaline sulphate response in long-distance runners and untrained subjects up to 2 h after exhausting exercise.

We investigated the response of plasma and platelet:free catecholamine ([CA]) and sulphated catecholamine ([CA-S]) concentrations after an incremental treadmill test to exhaustion and during recovery. In triathletes (n = 9) plasma and platelet [CA] and [CA-S] were measured before, immediately after and 0.5 and 24 h after exercise. In long-distance runners (n = 9) and in controls (n = 10) plasma [CA] and [CA-S] were determined 2 h instead of 24 h after exercise. Platelet [CA] and [CA-S] remained unchanged throughout the study. Plasma [CA] increased after exercise in all groups (P < 0.05) and returned to pre-exercise values within 0.5 h of recovery. Plasma sulphoconjugated noradrenaline concentration ([NA-S]) was elevated after exercise in the triathletes, long-distance runners and in controls [9.96 (SEM 0.84) nmol.l-1, 11.8 (SEM 1.19) nmol.l-1, 9.53 (SEM 1.10) nmol.l-1, respectively; P < 0.05] compared with resting values [7.13 (SEM 1.04) nmol.l-1, 6.19 (SEM 0.56) nmol.l-1, 6.76 (SEM 0.67) nmol.l-1, respectively] and remained elevated after 0.5 h of recovery [9.94 (SEM 1.14) nmol.l-1, 10.96 (SEM 0.80) nmol.l-1, 8.95 (SEM 0.99) nmol.l-1, respectively; P < 0.05]. In the long-distance runners and controls plasma [NA-S] remained elevated during 2 h of recovery [9.96 (SEM 0.76) nmol.l-1, 9.03 (SEM 0.88) nmol.l-1, respectively]. These results would indicate that plasma [NA-S] increases after sympathetic nervous system activation by an exhausting incremental exercise test and remain elevated up to 2 h after exercise.

Adult↗

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