Impact of residue accessible surface area on the prediction of protein secondary structures

<p>Abstract</p> <p>Background</p> <p>The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibility (RSA) might be an effective factor for increasing the accuracy of protein secondary structure prediction. Previous studies have either used a single constant threshold to classify residues into discrete classes (buries vs. exposed), or used the real-value predicted RSAs in their prediction method.</p> <p>Results</p> <p>We studied the effect of applying different RSA threshold types (namely, fixed thresholds vs. residue-dependent thresholds) on a variety of secondary structure prediction methods. With the consideration of DSSP-assigned RSA values we realized that improvement in the accuracy of prediction strictly depends on the selected threshold(s). Furthermore, we showed that choosing a single threshold for all amino acids is not the best possible parameter. We therefore used residue-dependent thresholds and most of residues showed improvement in prediction. Next, we tried to consider predicted RSA values, since in the real-world problem, protein sequence is the only available information. We first predicted the RSA classes by RVP-net program and then used these data in our method. Using this approach, improvement in prediction was also obtained.</p> <p>Conclusion</p> <p>The success of applying the RSA information on different secondary structure prediction methods suggest that prediction accuracy can be improved independent of prediction approaches. Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods.</p

TRANSCRIPTIONAL TIMERS REGULATING MITOSIS IN EARLY DROSOPHILA EMBRYOS

The development of an embryo requires a precise spatiotemporal regulation of cellular processes. We use transcriptional regulation of cdc25string and mitotic domains during Drosophila gastrulation as a model to demonstrate how a precise temporal pattern is established. Using a genetic screen, we demonstrate that the same spatial regulators of cdc25string transcription encode its temporal activation and identify buttonhead and empty spiracles as the major activators of cdc25string expression in mitotic domain 2. The effect of these activators is balanced through repression by hairy, sloppy paired 1 and huckebein. We show that a 500 bp enhancer element serves as an integrator to set the temporal pattern in mitotic domain 2 by measuring the levels of two activators buttonhead and empty-spiracles. Ectopic expression of these activators can override the intrinsic temporal pattern through the same enhancer element. Within the mitotic domain, temporal precision of mitosis is robust and is unaffected by changing dosage of rate-limiting transcriptional factors. Precision can however be disrupted by altering the levels of the two activators or two repressors. We propose that the additive and balanced action of activators and repressors is a general strategy for precise temporal regulation of cellular transitions during development

Transcriptional Timers Regulating Mitosis in Early Drosophila Embryos

The development of an embryo requires precise spatiotemporal regulation of cellular processes. During Drosophila gastrulation, a precise temporal pattern of cell division is encoded through transcriptional regulation of cdc25string in 25 distinct mitotic domains. Using a genetic screen, we demonstrate that the same transcription factors that regulate the spatial pattern of cdc25string transcription encode its temporal activation. We identify buttonhead and empty spiracles as the major activators of cdc25string expression in mitotic domain 2. The effect of these activators is balanced through repression by hairy, sloppy paired 1, and huckebein. Within the mitotic domain, temporal precision of mitosis is robust and unaffected by changing dosage of rate-limiting transcriptional factors. However, precision can be disrupted by altering the levels of the two activators or two repressors. We propose that the additive and balanced action of activators and repressors is a general strategy for precise temporal regulation of cellular transitions during development