Analysis of superfamily specific profile-profile recognition accuracy

Background  

Annotation of sequences that share little similarity to sequences of known function remains a major obstacle in genome annotation. Some of the best methods of detecting remote relationships between protein sequences are based on matching sequence profiles. We analyse the superfamily specific performance of sequence profile-profile matching. Our benchmark consists of a set of 16 protein superfamilies that are highly diverse at the sequence level. We relate the performance to the number of sequences in the profiles, the profile diversity and the extent of structural conservation in the superfamily.     

MARCKS is a natively unfolded protein with an inaccessible actin-binding site: evidence for long-range intramolecular interactions

Myristoylated alanine-rich C kinase substrate (MARCKS) is an unfolded protein that contains well characterized actin-binding sites within the phosphorylation site domain (PSD), yet paradoxically, we now find that intact MARCKS does not bind to actin. Intact MARCKS also does not bind as well to calmodulin as does the PSD alone. Myristoylation at the N terminus alters how calmodulin binds to MARCKS, implying that, despite its unfolded state, the distant N terminus influences binding events at the PSD. We show that the free PSD binds with site specificity to MARCKS, suggesting that long-range intramolecular interactions within MARCKS are also possible. Because of the unusual primary sequence of MARCKS with an overall isoelectric point of 4.2 yet a very basic PSD (overall charge of +13), we speculated that ionic interactions between oppositely charged domains of MARCKS were responsible for long-range interactions within MARCKS that sterically influence binding events at the PSD and that explain the observed differences between properties of the PSD and MARCKS. Consistent with this hypothesis, chemical modifications of MARCKS that neutralize negatively charged residues outside of the PSD allow the PSD to bind to actin and increase the affinity of MARCKS for calmodulin. Similarly, both myristoylation of MARCKS and cleavage of MARCKS by calpain are shown to increase the availability of the PSD so as to activate its actin-binding activity. Because abundant evidence supports the conclusion that MARCKS is an important protein in regulating actin dynamics, our data imply that post-translational modifications of MARCKS are necessary and sufficient to regulate actin-binding activity.     

Effects of the fungicides mancozed and dithianon on mortality and reproduction of the predatory miteAmblyseius andersoni

Laboratory studies using commercial formulations of mancozeb and dithianon at concentrations equivalent to recommended field rates of 200 and 80 g/hl, respectively, were conducted to evaluate toxic effects of these fungicides on the predatory miteAmblyseius andersoni Chant. In short-term tests where females were placed on apple-leaf disks and sprayed with mancozeb, no mortality of adults was observed; however, there was a 34% decrease in fecundity, a 7.1% decrease in egg hatch, and mortality of larvae and protonymphs was 6.7%. In long-term tests, a significant reduction in fecundity was also observed. A decrease in hatch that was dependent on age at time of treatment was found when eggs were treated directly with mancozeb. No effects on mite mortality or reproduction were observed in short-term tests with dithianon. These results suggest that dithianon might be considered as a potential alternative to mancozeb for scab control.