Novel Feature for Catalytic Protein Residues Reflecting Interactions with Other Residues

Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10fold crossvalidation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structurefunction relationship

The biogeography of stream bacteria

Aim The extent to which bacterial communities exhibit biogeographic patterns in their distribution remains unclear. We examined the relative influence of factors including geographic distance, latitude, elevation and catchment land use on the distribution and taxon richness of stream bacterial communities across New Zealand. Location Bacterial communities were collected from biofilm growing on submerged rocks in 244 streams. Sample sites spanned a north–south gradient of over 970 km, an elevational gradient of c. 750 m and were collected from a variety of catchment types across New Zealand. Methods We used automated ribosomal intergenic spacer analysis, a DNA fingerprinting technique, to characterize the structure and taxon richness of each bacterial community. Key attributes relating to sample location, upstream catchment land use and a suite of additional environmental parameters were collected for every site using GIS procedures. Univariate correlations between measures of bacterial community structure and latitude, elevation and distance were examined. Variance partitioning was then used to assess the relative importance of purely spatial factors versus catchment land use and environmental attributes for determining bacterial community structure and taxon richness. Results Bacterial taxon richness was related to the geographic location of the sample site, being significantly greater at latitudes closer to the equator and reduced at higher elevations. We observed distance decay patterns in bacterial community similarity related to geographic distance and latitudinal distance, but not to elevational distance. Overall, however, bacterial community similarity and taxon richness was more closely related to variability in catchment land use than to climatic variability or geographic location. Main conclusion Our data suggest that stream biofilm communities across New Zealand are more influenced by catchment land use attributes than by dispersal limitation

Market liberalisation and drought in New Zealand: A case of ‘double exposure’ for dryland sheep farmers?

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