Predictions on impact of missense mutations on structure function relationship of PAX6 and its alternatively spliced isoform PAX6(5a)
Tóm tắt
Từ khóa
Tài liệu tham khảo
Ades, S.E., Sauer, R.T. 1994. Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50. Biochemistry 33, 9187–9194.
Alibes, A., Nadra, A.D., De, M.F., Bulyk, M.L., Serrano, L., Stricher, F. 2010. Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: The Pax6 example. Nucleic Acids Res 38, 7422–7431.
Azuma, N., Nishina, S., Yanagisawa, H., Okuyama, T., Yamada, M. 1996. PAX6 missense mutation in isolated foveal hypoplasia. Nat Genet 13, 141–142.
Azuma, N., Yamada, M. 1998. Missense mutation at the C terminus of the PAX6 gene in ocular anterior segment anomalies. Invest Ophthalmol Vis Sci 39, 828–830.
Birrane, G., Soni, A., Ladias, J.A. 2009. Structural basis for DNA recognition by the human PAX3 homeodomain. Biochemistry 48, 1148–1155.
Brown, A., McKie, M., van Heyningen, V., Prosser, J. 1998. The Human PAX6 Mutation Database. Nucleic Acids Res 26, 259–264.
Bruun, J.A., Thomassen, E.I., Kristiansen, K., Tylden, G., Holm, T., Mikkola, I., Bjorkoy, G., Johansen, T. 2005. The third helix of the homeodomain of paired class homeodomain proteins acts as a recognition helix both for DNA and protein interactions. Nucleic Acids Res 33, 2661–2675.
Callaerts, P., Halder, G., Gehring, W.J. 1997. PAX-6 in development and evolution. Annu Rev Neurosci 20, 483–532.
Chao, L.Y., Huff, V., Strong, L.C., Saunders, G.F. 2000. Mutation in the PAX6 gene in twenty patients with aniridia. Hum Mutat 15, 332–339.
Chao, L.Y., Mishra, R., Strong, L.C., Saunders, G.F. 2003. Missense mutations in the DNA-binding region and termination codon in PAX6. Hum Mutat 21, 138–145.
Chauhan, B.K., Yang, Y., Cveklova, K., Cvekl, A. 2004. Functional properties of natural human PAX6 and PAX6(5a) mutants. Invest Ophthalmol Vis Sci 45, 385–392.
Cheng, J., Baldi, P. 2007. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 8, 113.
Cheng, J., Randall, A., Baldi, P. 2006. Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62, 1125–1132.
Conte, I., Carrella, S., Avellino, R., Karali, M., Marco-Ferreres, R., Bovolenta, P., Banfi, S. 2010. miR-204 is required for lens and retinal development via Meis2 targeting. Proc Natl Acad Sci U S A 107, 15491–15496.
D’Elia, A.V., Puppin, C., Pellizzari, L., Pianta, A., Bregant, E., Lonigro, R., Tell, G., Fogolari, F., van Heyningen, V., Damante, G. 2006. Molecular analysis of a human PAX6 homeobox mutant. Eur J Hum Genet 14, 744–751.
Epstein, J., Cai, J., Glaser, T., Jepeal, L., Maas, R. 1994a. Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. J Biol Chem 269, 8355–8361.
Epstein, J.A., Glaser, T., Cai, J., Jepeal, L., Walton, D.S., Maas, R.L. 1994b. Two independent and interactive DNA-binding subdomains of the Pax6 paired domain are regulated by alternative splicing. Genes Dev 8, 2022–2034.
Favor, J., Peters, H., Hermann, T., Schmahl, W., Chatterjee, B., Neuhauser-Klaus, A., Sandulache, R. 2001. Molecular characterization of Pax6(2Neu) through Pax6(10Neu): An extension of the Pax6 allelic series and the identification of two possible hypomorph alleles in the mouse Mus musculus. Genetics 159, 1689–1700.
Glaser, T., Jepeal, L., Edwards, J.G., Young, S.R., Favor, J., Maas, R.L. 1994. PAX6 gene dosage effect in a family with congenital cataracts, aniridia, anophthalmia and central nervous system defects. Nat Genet 7, 463–471.
Glaser, T., Walton, D.S., Maas, R.L. 1992. Genomic structure, evolutionary conservation and aniridia mutations in the human PAX6 gene. Nat Genet 2, 232–239.
Hanson, I., Churchill, A., Love, J., Axton, R., Moore, T., Clarke, M., Meire, F., van Heyningen, V. 1999. Missense mutations in the most ancient residues of the PAX6 paired domain underlie a spectrum of human congenital eye malformations. Hum Mol Genet 8, 165–172.
McGuffin, L.J., Bryson, K., Jones, D.T. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405.
Mirzayans, F., Pearce, W.G., MacDonald, I.M., Walter, M.A. 1995. Mutation of the PAX6 gene in patients with autosomal dominant keratitis. Am J Hum Genet 57, 539–548.
Mishra, R., Gorlov, I.P., Chao, L.Y., Singh, S., Saunders, G.F. 2002. PAX6, paired domain influences sequence recognition by the homeodomain. J Biol Chem 277, 49488–49494.
Morrison, D., FitzPatrick, D., Hanson, I., Williamson, K., van Heyningen, V., Fleck, B., Jones, I., Chalmers, J., Campbell, H. 2002. National study of microphthalmia, anophthalmia, and coloboma (MAC) in Scotland: Investigation of genetic aetiology. J Med Genet 39, 16–22.
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. J Comput Chem 25, 1605–1612.
Sali, A., Potterton, L., Yuan, F., van Vlijmen, H., Karplus, M. 1995. Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318–326.
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L. 2005. The FoldX web server: an online force field. Nucleic Acids Res 33, W382–W388.
Singh, S., Chao, L.Y., Mishra, R., Davies, J., Saunders, G.F. 2001. Missense mutation at the C-terminus of PAX6 negatively modulates homeodomain function. Hum Mol Genet 10, 911–918.
Thaung, C., West, K., Clark, B.J., McKie. L., Morgan, J.E., Arnold, K., Nolan, P.M., Peters, J., Hunter, A.J., Brown, S.D., Jackson, I.J., Cross, S.H. 2002. Novel ENU-induced eye mutations in the mouse: Models for human eye disease. Hum Mol Genet 11, 755–767.
Tripathi, R., Mishra, R. 2010. Interaction of Pax6 with SPARC and p53 in brain of mice indicates smad3 dependent auto-regulation. J Mol Neurosci 41, 397–403.
Tripathi, R., Mishra, R. 2012. In-silico analysis of Pax6 interacting proteins indicates missing molecular link in development and disease. Int J Biol Life Sci 8, 150–156.
Tzoulaki, I., White, I.M., Hanson, I.M. 2005. PAX6 mutations: Genotype-phenotype correlations. BMC Genet 6, 27.
Wilson, D., Sheng, G., Lecuit, T., Dostatni, N., Desplan, C. 1993. Cooperative dimerization of paired class homeo domains on DNA. Genes Dev 7, 2120–2134.
Wilson, D.S., Sheng, G., Jun, S., Desplan, C. 1996. Conservation and diversification in homeodomain-DNA interactions: A comparative genetic analysis. Proc Natl Acad Sci USA 93, 6886–6891.
Xu, H.E., Rould, M.A., Xu, W., Epstein, J.A., Maas, R.L., Pabo, C.O. 1999. Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev 13, 1263–1275.