Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface

Background

A large number of studies have been carried out to obtain amino acid propensities for ??-helices and ??-sheets. The obtained propensities for ??-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the ??-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects ??-sheet propensity.

Results

We calculated amino acid propensities for ??-helices and ??-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that ??-helix propensities do not differ significantly by fold, but ??-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for ??-helix, but such is not the case for the ??-sheet propensities. We also found some fold dependence on amino acid frequency in ??-strands. Folds with a high Ser, Thr and Asn content at exposed sites in ??-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = ?0.90) and to have flat ??-sheets. At buried sites in ??-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = ?0.93). "All-??" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "??/??" proteins tend to have a higher content of Val, Ile and Leu.

Conclusions

The ??-helix propensities are similar for all folds and for exposed and buried residues. However, ??-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in ??-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding properties such as the twist of a ??-strand or association between two ?? sheets.     

Modelling of underwater light in freshwater lakes using survival and failure time analysis

1. This study presents a new approach to modelling subsurface irradiance using concepts from survival and failure time analysis. The model applies a modified Weibull distribution function to predict downwelling irradiance. Data sets from forty-seven Norwegian sites show extremely high coefficients of determination, up to 99.99%, when analysed by the Weibull model.
2. The uncritical use of a single k _d value to model underwater light conditions is likely to result in poor estimates of received irradiance. This error may amount to several hundred per cent. The practice of force-fitting linear least-squares regressions to log-transformed irradiance data inevitably leads to highly biased estimates of the true fraction of incident irradiance entering the water.
3. Wave effects causing fluctuations of subsurface irradiance are modelled with synthetic data and compared with field observations. Fluctuations of surface elevation by waves produce skewed frequency distributions of the underwater light field. The result of these effects, which are to reduce the accuracy of estimated model parameters, can be largely eliminated by carefully designing field procedures used for the acquisition of subsurface light data.     

WACHSTUMS-ÄNDERUNGEN IN DER ONTO-GENESE PALÄOZOISCHER AMMONOIDEEN

Ontogenetic allometries (heterauxesis according to Huxley) of about 50 Carboniferous goniatite species from Germany, Spain and USA have been studied by means of geometrical measurements of shell cross sections. They indicate changes of proportions during ontogeny between coiling spiral, umbilical spiral, and whorl width. The allometry constants change suddenly at defined stages. Thus the ontogenetic growth pattern is polyphase, each phase being determined by a different allometric formula.
Ontogenetische Allometrien wurden bei etwa 50 karbonischen Goniatiten-Arten aus Deutschland, Spanien und USA an Hand von Gehäuse-Querschnitten untersucht. Während der Ontogenese erfolgen mehrfach Proportionsverschie-bungen der äußeren Spirale, der Nabelspirale und der Windungsbreite, die sich durch scharfen Wechsel von Allometrie-Konstanten an definierten Stellen aus-drücken. Das Gehäusewachstum erfolgt somit in mehreren Phasen, die von unterschiedlichen Allometrieformeln bestimmt sind.     

Benthic insects in Swedish lake-outlet streams: patterns in species richness and assemblage structure

1. We studied how species richness of three hierarchical insect species groups, namely all benthic, lotic and filtering taxa, were related to a number of environmental variables in a data set from fifteen Swedish lake outlets. 2. In partial least-squares analyses, we found that size-related factors (stream width, discharge) and velocity-related factors (current velocity, substratum particle size) were positively associated, and productivity-related factors (chlorophyll a, seston energy, conductivity) negatively associated, with the species richness of the three groups. 3. The weak and negative relationship of richness with productivity largely negated theoretical predictions, whereas the species-environment results corroborated earlier findings from running water systems. 4. The most important factors associated with the species composition of the lake outlets studied included pH, lake area, discharge, channel width and detritus. 5. Of the filter feeders, most species of blackflies (Diptera: Simuliidae) showed a negative relationship with pH. 6. A nested subset analysis demonstrated that species-poor sites did not have a subset of species found at more species-rich sites in any of the three hierarchical groups.     

Seasonal Effects on Chlorophyll-Protein Complexes Isolated from P-inus silvestris

The seasonal changes in the relative distribution of P700 chlorophyll-protein complex a₁ and light harvesting chlorophyll-protein complex a/b were studied in a natural stand of Pinus silvestris. Similar measurements were made after artificial photobleaching of chlorophyll in pine seedlings or in isolated pine chloroplasts. The chlorophyll-protein complexes were solubilized by sodium dodecyl sulphate and separated by polyacrylamide gel electrophoresis. When autumn and winter destruction of chlorophyll occurs, the chlorophyll a antenna associated with P700 in photosystem 1 (P700-CPa₁) is relatively more affected than the light harvesting complex, which lacks a reaction centre. These results are further supported by low-temperature fluorescence emission properties of isolated chloroplasts presented in this work and elsewhere. The destruction of chlorophyll in stressing autumn and winter climates is most probably caused by photosensitized oxidation of chlorophyll.     

A paradox survival – report of a repaired syn vivo perforation in a nautiloid phragmocone

The nautiloid Trocholites depressus (Eichwald, 1840) from the Lasnamägi regional stage (Darrivillian, Middle Ordovician) of Vaike Pakri Island (North-West Estonia) is the only known ectocochleate cephalopod that survived and healed a perforation of the phragmocone. Two chambers of the specimen were broken during its lifetime. The injury is located on the venter of the conch directly above the peristomal opening of the body chamber. It is reconstructed that the peristomal mantle tissue carried out an initial sealing of the injured chambers. The complete calcified sealing and compensation of the irregular shell surface started late with the overgrowth of the septa of the preceding whorl. The position and diameter of the siphuncle were not disturbed by the regeneration showing that these characters allowed a low phenotypic variability. Despite the trauma in the midlife growth history of this specimen, it appears to have reached maturity.     

Predictable changes in trophic community structure along a spatial disturbance gradient in streams

1. We assessed insect and resource standing stocks along a spatial gradient of flood disturbance in 19 sub-alpine Swedish streams to test the prediction that change in trophic structure arises from the joint action of disturbance, which affect basal resources, and resource-control, which ties the response of the consumers to the response of the resources.
2. Trophic structure, quantified as scores of non-metric multidimensional scaling based on the biomass of insect trophic groups, changed predictably along the disturbance gradient. In early summer, predators and algae feeders decreased relative to suspension feeders with increasing disturbance; in autumn, algae feeders decreased relative to leaf feeders with increasing disturbance.
3. Across the disturbance gradient, the biomass of algae-, deposit- and leaf-feeders was principally controlled by the availability of the respective resource (algae, fine detritus and coarse detritus), while disturbance only had subsidiary effects on algae feeders in early summer.
4. Overall, patterns in trophic-group biomass along the disturbance gradient were more likely to reflect indirect effects of disturbance via impact on the resources, which reverberated to the consumers because of resource-control, rather than direct effects. In contrast with the view that stream communities are the result of stochastic colonization following disturbance events, in the study streams the trophic structure of insect assemblages is predictable and partly organized by resource-control across a broad range of disturbance conditions.