References
- Albrecht, M., Golatta, M., Wullner, U., & Lengauer, T. (2004). Structural and functional analysis of ataxin-2 and ataxin-3. European Journal of Biochemistry, 271(15), 3155–3170. https://doi.org/https://doi.org/10.1111/j.1432-1033.2004.04245.x
- Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological), 57(1), 289–300.
- Ellisdon, A. M., & Bottomley, S. P. (2004). The role of protein misfolding in the pathogenesis of human diseases. IUBMB Life, 56(3), 119–123. https://doi.org/https://doi.org/10.1080/15216540410001674003
- Galzitskaya, O. V., & Lobanov, M. Y. (2018). Proteome-scale understanding of relationship between homo-repeat enrichments and protein aggregation properties. PLoS One, 13(11), e0206941. https://doi.org/https://doi.org/10.1371/journal.pone.0206941
- Ge, H., Zhou, D., Tong, S., Gao, Y., Teng, M., & Niu, L. (2008). Crystal structure and possible dimerization of the single RRM of human PABPN1. Proteins, 71(3), 1539–1545. https://doi.org/https://doi.org/10.1002/prot.21973
- Jahn, T. R., & Radford, S. E. (2008). Folding versus aggregation: Polypeptide conformations on competing pathways. Archives of Biochemistry and Biophysics, 469(1), 100–117. https://doi.org/https://doi.org/10.1016/j.abb.2007.05.015
- Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12), 2577–2637. https://doi.org/https://doi.org/10.1002/bip.360221211
- Källberg, M., Wang, H., Wang, S., Peng, J., Wang, Z., Lu, H., & Xu, J. (2012). Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 7(8), 1511–1522. https://doi.org/https://doi.org/10.1038/nprot.2012.085
- Kim, M. (2014). Pathogenic polyglutamine expansion length correlates with polarity of the flanking sequences. Molecular Neurodegeneration, 9(1), 45. https://doi.org/https://doi.org/10.1186/1750-1326-9-45
- Kim, M. W., Chelliah, Y., Kim, S. W., Otwinowski, Z., & Bezprozvanny, I. (2009). Secondary structure of Huntingtin amino-terminal region. Structure (London, England: 1993), 17(9), 1205–1212. https://doi.org/https://doi.org/10.1016/j.str.2009.08.002
- Lobanov, M. Y., Klus, P., Sokolovsky, I. V., Tartaglia, G. G., & Galzitskaya, O. V. (2016). Non-random distribution of homo-repeats: Links with biological functions and human diseases. Scientific Reports, 6, 26941. https://doi.org/https://doi.org/10.1038/srep26941
- Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/https://doi.org/10.1002/jcc.20084
- Rhys, N. H., & Dougan, L. (2013). The emerging role of hydrogen bond interactions in polyglutamine structure, stability and association. Soft Matter, 9(8), 2359–2364. https://doi.org/https://doi.org/10.1039/C2SM27565A
- Ross, C. A., Poirier, M. A., Wanker, E. E., & Amzel, M. (2003). Polyglutamine fibrillogenesis: The pathway unfolds. Proceedings of the National Academy of Sciences of the United States of America, 100(1), 1–3. https://doi.org/https://doi.org/10.1073/pnas.0237018100
- Schaefer, M. H., Wanker, E. E., & Andrade-Navarro, M. A. (2012). Evolution and function of CAG/polyglutamine repeats in protein-protein interaction networks. Nucleic Acids Research, 40(10), 4273–4287. https://doi.org/https://doi.org/10.1093/nar/gks011
- Shoubridge, C., & Polyalanine, G. J. (2012). Tract disorders and neurocognitive phenotypes (pp. 185–203). Springer.
- Tobelmann, M. D., & Murphy, R. M. (2011). Location trumps length: Polyglutamine-mediated changes in folding and aggregation of a host protein. Biophysical Journal, 100(11), 2773–2782. https://doi.org/https://doi.org/10.1016/j.bpj.2011.04.028
- Toll-Riera, M., Radó-Trilla, N., Martys, F., & Alba, M. M. (2012). Role of low-complexity sequences in the formation of novel protein coding sequences. Molecular Biology and Evolution, 29(3), 883–886. https://doi.org/https://doi.org/10.1093/molbev/msr263
- Usdin, K. (2008). The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases. Genome Research, 18(7), 1011–1019. https://doi.org/https://doi.org/10.1101/gr.070409.107
- Welch, B. L. (1947). The generalisation of student's problems when several different population variances are involved. Biometrika, 34(1–2), 28–35. https://doi.org/https://doi.org/10.1093/biomet/34.1-2.28
- Wen, J., Scoles, D. R., & Facelli, J. C. (2014). Structure prediction of polyglutamine disease proteins: Comparison of methods. BMC Bioinformatics, 15(Suppl. 7), S11.https://doi.org/https://doi.org/10.1186/1471-2105-15-S7-S11
- Wen, J., Scoles, D. R., & Facelli, J. C. (2017a). Effects of the enlargement of polyglutamine segments on the structure and folding of ataxin-2 and ataxin-3 proteins. Journal of Biomolecular Structure & Dynamics, 35(3), 504–519. https://doi.org/https://doi.org/10.1080/07391102.2016.1152199
- Wen, J., Scoles, D. R., & Facelli, J. C. (2017b). Molecular dynamics analysis of the aggregation propensity of polyglutamine segments. PLoS One, 12(5), e0178333.https://doi.org/https://doi.org/10.1371/journal.pone.0178333
- Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O'Donovan, C., Redaschi, N., & Suzek, B. (2006). The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Research, 34, D187–D191. https://doi.org/https://doi.org/10.1093/nar/gkj161
- Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/https://doi.org/10.1038/nmeth.3213
- Zhang, Y., Larsen, C. A., Stadler, H. S., & Ames, J. B. (2011). Structural basis for sequence specific DNA binding and protein dimerization of HOXA13. PLoS One, 6(8), e23069.https://doi.org/https://doi.org/10.1371/journal.pone.0023069