CASP6 Knockout Cell Lysate

Huntington's disease (HD) is caused by a mutation in the huntingtin (htt) gene encoding an expansion of glutamine repeats at the N terminus of the Htt protein. Proteolysis of Htt has been identified as a critical pathological event in HD models. In particular, it has been postulated that proteolysis of Htt at the putative caspase-6 cleavage site (at amino acid Asp-586) plays a critical role in disease progression and pathogenesis. However, whether caspase-6 is indeed the essential enzyme that cleaves Htt at this site in vivo has not been determined. To evaluate, we crossed the BACHD mouse model with a caspase-6 knock-out mouse (Casp6(-/-)). Western blot and immunocytochemistry confirmed the lack of caspase-6 protein in Casp6(-/-) mice, regardless of HD genotype. We predicted the Casp6(-/-) mouse would have reduced levels of caspase-6 Htt fragments and increased levels of full-length Htt protein. In contrast, we found a significant reduction of full-length mutant Htt (mHtt) and fragments in the striatum of BACHD Casp6(-/-) mice. Importantly, we detected the presence of Htt fragments consistent with cleavage at amino acid Asp-586 of Htt in the BACHD Casp6(-/-) mouse, indicating that caspase-6 activity cannot fully account for the generation of the Htt 586 fragment in vivo. Our data are not consistent with the hypothesis that caspase-6 activity is critical in generating a potentially toxic 586 aa Htt fragment in vivo. However, our studies do suggest a role for caspase-6 activity in clearance pathways for mHtt protein.

Background: Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure. Although improvements have occurred over the last years, the problem of accurately predicting residue contact maps from primary sequences is still largely unsolved. Among the reasons for this are the unbalanced nature of the problem (with far fewer examples of contacts than non-contacts), the formidable challenge of capturing long-range interactions in the maps, the intrinsic difficulty of mapping one-dimensional input sequences into two-dimensional output maps. In order to alleviate these problems and achieve improved contact map predictions, in this paper we split the task into two stages: the prediction of a map's principal eigenvector (PE) from the primary sequence; the reconstruction of the contact map from the PE and primary sequence. Predicting the PE from the primary sequence consists in mapping a vector into a vector. This task is less complex than mapping vectors directly into two-dimensional matrices since the size of the problem is drastically reduced and so is the scale length of interactions that need to be learned. Results: We develop architectures composed of ensembles of two-layered bidirectional recurrent neural networks to classify the components of the PE in 2, 3 and 4 classes from protein primary sequence, predicted secondary structure, and hydrophobicity interaction scales. Our predictor, tested on a non redundant set of 2171 proteins, achieves classification performances of up to 72.6%, 16% above a base-line statistical predictor. We design a system for the prediction of contact maps from the predicted PE. Our results show that predicting maps through the PE yields sizeable gains especially for long-range contacts which are particularly critical for accurate protein 3D reconstruction. The final predictor's accuracy on a non-redundant set of 327 targets is 35.4% and 19.8% for minimum contact separations of 12 and 24, respectively, when the top length/5 contacts are selected. On the 11 CASP6 Novel Fold targets we achieve similar accuracies (36.5% and 19.7%). This favourably compares with the best automated predictors at CASP6. Conclusion: Our final system for contact map prediction achieves state-of-the-art performances, and may provide valuable constraints for improved ab initio prediction of protein structures. A suite of predictors of structural features, including the PE, and PE-based contact maps, is available at http://distill.ucd.ie.