Exploring structurally conserved solvent sites in protein families

Protein-bound water molecules are important components of protein structure, and therefore, protein function and energetics. Although structural conservation of solvent has been studied in a few protein families, a lack of suitable computational tools has hindered more comprehensive analyses. Herein we present a semiautomated computational approach for identifying solvent sites that are conserved among proteins sharing a common three-dimensional structure. This method is tested on six protein families: (1) monodomain cytochrome c, (2) fatty-acid binding protein, (3) lactate/malate dehydrogenase, (4) parvalbumin, (5) phospholipase A2, and (6) serine protease. For each family, the method successfully identified previously known conserved solvent sites. Moreover, the method discovered 22 novel conserved solvent sites, some of which have higher degrees of conservation than the previously known sites. All six families studied had solvent sites with more than 90% conservation and these sites were invariably located in regions of the protein with very high sequence conservation. These results suggest that highly conserved solvent sites, by virtue of their proximity to conserved residues, should be considered as one of the defining three-dimensional structural characteristics of protein families and folds.     

<Emphasis Type="Italic">Methylophilaceae</Emphasis> and <Emphasis Type="Italic">Hyphomicrobium</Emphasis> as target taxonomic groups in monitoring the function of methanol-fed denitrification biofilters in municipal wastewater treatment plants

Molecular monitoring of bacterial communities can explain and predict the stability of bioprocesses in varying physicochemical conditions. To study methanol-fed denitrification biofilters of municipal wastewater treatment plants, bacterial communities of two full-scale biofilters were compared through fingerprinting and sequencing of the 16S rRNA genes. Additionally, 16S rRNA gene fingerprinting was used for 10-week temporal monitoring of the bacterial community in one of the biofilters. Combining the data with previous study results, the family Methylophilaceae and genus Hyphomicrobium were determined as suitable target groups for monitoring. An increase in the relative abundance of Hyphomicrobium-related biomarkers occurred simultaneously with increases in water flow, NO _x ^? load, and methanol addition, as well as a higher denitrification rate, although the dominating biomarkers linked to Methylophilaceae showed an opposite pattern. The results indicate that during increased loading, stability of the bioprocess is maintained by selection of more efficient denitrifier populations, and this progress can be analyzed using simple molecular fingerprinting.     

trkB-Receptor Activation Contributes to the Kainate-Induced Increase in BDNF mRNA Synthesis

1. The expression of brain-derived neurotrophic factor (BDNF) mRNA is induced by neuronal activity through increased intracellular calcium. As BDNF also increases intracellular calcium levels through trkB activation, we have examined here whether BDNF also regulates the synthesis of its own mRNA.2. Neurotrophin mRNA expression was induced with kainic acid administration in transgenic mice overexpressing the dominant-negative form of BDNF receptor trkB and wild-type littermates.3. Kainate strongly induced BDNF mRNA expression in both genotypes, but the upregulation was significantly lower in transgenic mice.4. These data suggest that the synthesis of BDNF mRNA is at least partly mediated by BDNF release and the activation of trkB receptors. The present findings further suggest that the BDNF signaling system in brain is regulated by positive feedback.