Structural and functional characterization of the MERIT40 to understand its role in DNA repair

References

• Bartek, J., & Lukas, J. (2007). DNA damage checkpoints: From initiation to recovery or adaptation. Current Opinion in Cell Biology, 19, 238–245.
   PubMed Web of Science ®Google Scholar
• Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72, 248–254.
   PubMed Web of Science ®Google Scholar
• Chen, J., Silver, D. P., Walpita, D., Cantor, S. B., Gazdar, A. F., Tomlinson, G., … Scully, R. (1998). Stable interaction between the products of the BRCA1 and BRCA2 tumor suppressor genes in mitotic and meiotic cells. Molecular Cell, 2, 317–328.
   PubMed Web of Science ®Google Scholar
• Corsepius, N. C., & Lorimer, G. H. (2013). Measuring how much work the chaperone GroEL can do. Proceedings of the National Academy of Sciences of the United States of America, 110, E2451–2459.
   PubMed Web of Science ®Google Scholar
• DeMars, R., & Held, K. R. (1972). The spontaneous azaguanine-resistant mutants of diploid human fibroblasts. Humangenetik, 16, 87–110.
   PubMedGoogle Scholar
• Eggertsen, G., Lind, P., & Sjoquist, J. (1981). Molecular characterization of the complement activating protein in the venom of the Indian cobra (Naja N. siamensis). Molecular Immunology, 18, 125–133.
   PubMed Web of Science ®Google Scholar
• Feeney, R. E. (1987). Chemical modification of proteins: Comments and perspectives. International Journal of Peptide and Protein Research, 29, 145–161.
   PubMedGoogle Scholar
• Feng, L., Huang, J., & Chen, J. (2009). MERIT40 facilitates BRCA1 localization and DNA damage repair. Genes & Development, 23, 719–728.
   PubMed Web of Science ®Google Scholar
• Fontana, A., de Laureto, P. P., Spolaore, B., & Frare, E. (2012). Identifying disordered regions in proteins by limited proteolysis. Methods in Molecular Biology, 896, 297–318.
   PubMedGoogle Scholar
• Fontana, A., Zambonin, M., Polverino de Laureto, P., De Filippis, V., Clementi, A., & Scaramella, E. (1997). Probing the conformational state of apomyoglobin by limited proteolysis. Journal of Molecular Biology, 266, 223–230.
   PubMed Web of Science ®Google Scholar
• Foulkes, W. D. (2004). BRCA1 functions as a breast stem cell regulator. Journal of Medical Genetics, 41, 1–5.
   PubMed Web of Science ®Google Scholar
• Fritzinger, D. C., Bredehorst, R., & Vogel, C. W. (1994). Molecular cloning and derived primary structure of cobra venom factor. Proceedings of the National Academy of Sciences of the United States of America, 91, 12775–12779.
   PubMed Web of Science ®Google Scholar
• Grimsley, G. R., & Pace, C. N. (2004). Spectrophotometric determination of protein concentration. Current Protocols in Protein Science, Unit 3. 1, 3.1.1-3.1.9.
   Google Scholar
• Haile, D. T., & Parvin, J. D. (1999). Activation of transcription in vitro by the BRCA1 carboxyl-terminal domain. Journal of Biological Chemistry, 274, 2113–2117.
   PubMed Web of Science ®Google Scholar
• Harper, J. W., & Elledge, S. J. (2007). The DNA damage response: Ten years after. Molecular Cell, 28, 739–745.
   PubMed Web of Science ®Google Scholar
• Havlis, J., Thomas, H., Sebela, M., & Shevchenko, A. (2003). Fast-response proteomics by accelerated in-gel digestion of proteins. Analytical Chemistry, 75, 1300–1306.
   PubMed Web of Science ®Google Scholar
• Hegyi, H., & Gerstein, M. (1999). The relationship between protein structure and function: A comprehensive survey with application to the yeast genome. Journal of Molecular Biology, 288, 147–164.
   PubMed Web of Science ®Google Scholar
• Hofmann, K., & Bucher, P. (1998). The PCI domain: A common theme in three multiprotein complexes. Trends in Biochemical Sciences, 23, 204–205.
   PubMed Web of Science ®Google Scholar
• Holm, L., & Rosenstrom, P. (2010). Dali server: Conservation mapping in 3D. Nucleic Acids Research, 38, W545–549.
   PubMed Web of Science ®Google Scholar
• Hu, Y., Scully, R., Sobhian, B., Xie, A., Shestakova, E., & Livingston, D. M. (2011). RAP80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci. Genes & Development, 25, 685–700.
   PubMed Web of Science ®Google Scholar
• Huen, M. S., & Chen, J. (2008). The DNA damage response pathways: At the crossroad of protein modifications. Cell Research, 18, 8–16.
   PubMed Web of Science ®Google Scholar
• Huen, M. S., Grant, R., Manke, I., Minn, K., Yu, X., Yaffe, M. B., & Chen, J. (2007). RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly. Cell, 131, 901–914.
   PubMed Web of Science ®Google Scholar
• Jimenez, C. R., Huang, L., Qiu, Y., & Burlingame, A. L. (2001). In-gel digestion of proteins for MALDI-MS fingerprint mapping. Current protocols in protein science, Unit 16. 14, 1604–1614.
   Google Scholar
• Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research, 32, W526–531.
   PubMed Web of Science ®Google Scholar
• Kim, H., Huang, J., & Chen, J. (2007). CCDC98 is a BRCA1-BRCT domain-binding protein involved in the DNA damage response. Nature Structural & Molecular Biology, 14, 710–715.
   PubMed Web of Science ®Google Scholar
• Kolas, N. K., Chapman, J. R., Nakada, S., Ylanko, J., Chahwan, R., Sweeney, F. D., … Durocher, D. (2007). Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science, 318, 1637–1640.
   PubMed Web of Science ®Google Scholar
• Lobley, A., Whitmore, L., & Wallace, B. A. (2002). DICHROWEB: An interactive website for the analysis of protein secondary structure from circular dichroism spectra. Bioinformatics, 18, 211–212.
   PubMed Web of Science ®Google Scholar
• Mailand, N., Bekker-Jensen, S., Faustrup, H., Melander, F., Bartek, J., Lukas, C., & Lukas, J. (2007). RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins. Cell, 131, 887–900.
   PubMed Web of Science ®Google Scholar
• Martin, S. G., Laroche, T., Suka, N., Grunstein, M., & Gasser, S. M. (1999). Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell, 97, 621–633.
   PubMed Web of Science ®Google Scholar
• Miki, Y., Swensen, J., Shattuck-Eidens, D., Futreal, P. A., Harshman, K., Tavtigian, S., Liu, Q., Cochran, C., Bennett, L. M., Ding, W., … Bogden, R. (1994). A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science, 266, 66–71.
   PubMed Web of Science ®Google Scholar
• Mills, K. D., Sinclair, D. A., & Guarente, L. (1999). MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks. Cell, 97, 609–620.
   PubMed Web of Science ®Google Scholar
• Monteiro, A. N., August, A., & Hanafusa, H. (1996). Evidence for a transcriptional activation function of BRCA1 C-terminal region. Proceedings of the National Academy of Sciences of the United States of America, 93, 13595–13599.
   PubMed Web of Science ®Google Scholar
• Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12, 345–364.
   PubMed Web of Science ®Google Scholar
• Muniz, V. A., Srinivasan, S., Boswell, S. A., Meinhold, D. W., Childs, T., Osuna, R., & Colon, W. (2011). The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS. Protein Science, 20, 302–312.
   PubMed Web of Science ®Google Scholar
• Nikkila, J., Coleman, K. A., Morrissey, D., Pylkas, K., Erkko, H., Messick, T. E., … Greenberg, R. A. (2009). Familial breast cancer screening reveals an alteration in the RAP80 UIM domain that impairs DNA damage response function. Oncogene, 28, 1843–1852.
   PubMed Web of Science ®Google Scholar
• Noble, J. E., & Bailey, M. J. (2009). Quantitation of protein. Methods in Enzymology, 463, 73–95.
   PubMed Web of Science ®Google Scholar
• Pace, C. N. (1986). Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods in Enzymology, 131, 266–280.
   PubMedGoogle Scholar
• Pace, C. N., & Shaw, K. L. (2000). Linear extrapolation method of analyzing solvent denaturation curves. Proteins Supplements, 4, 1–7.
   PubMedGoogle Scholar
• Pace, C. N., Shirley, B. A., McNutt, M., & Gajiwala, K. (1996). Forces contributing to the conformational stability of proteins. FASEB Journal, 10, 75–83.
   PubMed Web of Science ®Google Scholar
• Paull, T. T., Rogakou, E. P., Yamazaki, V., Kirchgessner, C. U., Gellert, M., & Bonner, W. M. (2000). A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Current Biology, 10, 886–895.
   PubMed Web of Science ®Google Scholar
• Rajagopalan, K., Mooney, S. M., Parekh, N., Getzenberg, R. H., & Kulkarni, P. (2011). A majority of the cancer/testis antigens are intrinsically disordered proteins. Journal of Cellular Biochemistry, 112, 3256–3267.
   PubMed Web of Science ®Google Scholar
• Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95–99.
   PubMed Web of Science ®Google Scholar
• Ramachandran, G. N., & Sasisekharan, V. (1968). Conformation of polypeptides and proteins. Advances in Protein Chemistry, 23, 283–438.
   PubMedGoogle Scholar
• Rogakou, E. P., Boon, C., Redon, C., & Bonner, W. M. (1999). Megabase chromatin domains involved in DNA double-strand breaks in vivo. Journal of Cell Biology, 146, 905–916.
   PubMed Web of Science ®Google Scholar
• Sael, L., Chitale, M., & Kihara, D. (2012). Structure- and sequence-based function prediction for non-homologous proteins. Journal of Structural and Functional Genomics, 13, 111–123.
   PubMedGoogle Scholar
• Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research, 33, W363–367.
   PubMed Web of Science ®Google Scholar
• Scully, R., Chen, J., Ochs, R. L., Keegan, K., Hoekstra, M., Feunteun, J., & Livingston, D. M. (1997). Dynamic changes of BRCA1 subnuclear location and phosphorylation state are initiated by DNA damage. Cell, 90, 425–435.
   PubMed Web of Science ®Google Scholar
• Scully, R., Ganesan, S., Vlasakova, K., Chen, J., Socolovsky, M., & Livingston, D. M. (1999). Genetic analysis of BRCA1 function in a defined tumor cell line. Molecular Cell, 4, 1093–1099.
   PubMed Web of Science ®Google Scholar
• Shao, G., Patterson-Fortin, J., Messick, T. E., Feng, D., Shanbhag, N., Wang, Y., & Greenberg, R. A. (2009). MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks. Genes & Development, 23, 740–754.
   PubMed Web of Science ®Google Scholar
• Shiotani, B., & Zou, L. (2009). ATR signaling at a glance. Journal of Cell Science, 122, 301–304.
   PubMed Web of Science ®Google Scholar
• Solyom, S., Patterson-Fortin, J., Pylkas, K., Greenberg, R. A., & Winqvist, R. (2010). Mutation screening of the MERIT40 gene encoding a novel BRCA1 and RAP80 interacting protein in breast cancer families. Breast Cancer Research and Treatment, 120, 165–168.
   PubMed Web of Science ®Google Scholar
• Sreerama, N., Venyaminov, S. Y., & Woody, R. W. (2000). Estimation of protein secondary structure from circular dichroism spectra: Inclusion of denatured proteins with native proteins in the analysis. Analytical Biochemistry, 287, 243–251.
   PubMed Web of Science ®Google Scholar
• Stephens, P. J., McKenna, C. E., McKenna, M. C., Nguyen, H. T., & Devlin, F. (1981). Circular dichroism and magnetic circular dichroism of reduced molybdenum-iron protein of Azotobacter vinelandii nitrogenase. Biochemistry, 20, 2857–2864.
   PubMed Web of Science ®Google Scholar
• Uversky, V. N., & Dunker, A. K. (2010). Understanding protein non-folding. Biochimica et Biophysica Acta, 1804, 1231–1264.
   PubMed Web of Science ®Google Scholar
• Uversky, V. N., Oldfield, C. J., & Dunker, A. K. (2008). Intrinsically disordered proteins in human diseases: Introducing the D2 concept. Annual Review of Biophysics, 37, 215–246.
   PubMed Web of Science ®Google Scholar
• Venkitaraman, A. R. (1999). Breast cancer genes and DNA repair. Science, 286, 1100–1102.
   PubMed Web of Science ®Google Scholar
• Venkitaraman, A. R. (2002). Cancer susceptibility and the functions of BRCA1 and BRCA2. Cell, 108, 171–182.
   PubMed Web of Science ®Google Scholar
• Vikrant Kumar, R., Yadav, L. R., Nakhwa, P., Waghmare, S. K., Goyal, P., & Varma, A. K. (2013). Structural and functional implication of RAP80 DeltaGlu81 mutation. PLoS One, 8, e72707.
   PubMed Web of Science ®Google Scholar
• Vogel, C. W., & Fritzinger, D. C. (2010). Cobra venom factor: Structure, function, and humanization for therapeutic complement depletion. Toxicon, 56, 1198–1222.
   PubMed Web of Science ®Google Scholar
• Vogel, C. W., Smith, C. A., & Muller-Eberhard, H. J. (1984). Cobra venom factor: Structural homology with the third component of human complement. The Journal of Immunology, 133, 3235–3241.
   PubMed Web of Science ®Google Scholar
• Walters, J., Milam, S. L., & Clark, A. C. (2009). Practical approaches to protein folding and assembly: Spectroscopic strategies in thermodynamics and kinetics. Methods in Enzymology, 455, 1–39.
   PubMed Web of Science ®Google Scholar
• Wang, B., & Elledge, S. J. (2007). Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage. Proceedings of the National Academy of Sciences of the United States of America, 104, 20759–20763.
   PubMed Web of Science ®Google Scholar
• Wang, B., Hurov, K., Hofmann, K., & Elledge, S. J. (2009). NBA1, a new player in the Brca1 A complex, is required for DNA damage resistance and checkpoint control. Genes & Development, 23, 729–739.
   PubMed Web of Science ®Google Scholar
• Wang, B., Matsuoka, S., Ballif, B. A., Zhang, D., Smogorzewska, A., Gygi, S. P., & Elledge, S. J. (2007). Abraxas and RAP80 form a BRCA1 protein complex required for the DNA damage response. Science, 316, 1194–1198.
   PubMed Web of Science ®Google Scholar
• Whitmore, L., & Wallace, B. A. (2004). DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data. Nucleic Acids Research, 32, W668–673.
   PubMed Web of Science ®Google Scholar
• Whitmore, L., & Wallace, B. A. (2008). Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases. Biopolymers, 89, 392–400.
   PubMed Web of Science ®Google Scholar
• Williams, R. S., & Glover, J. N. (2003). Structural consequences of a cancer-causing BRCA1-BRCT missense mutation. Journal of Biological Chemistry, 278, 2630–2635.
   PubMed Web of Science ®Google Scholar
• Wootton, S. K., & Yoo, D. (2003). Homo-oligomerization of the porcine reproductive and respiratory syndrome virus nucleocapsid protein and the role of disulfide linkages. Journal of Virology, 77, 4546–4557.
   PubMed Web of Science ®Google Scholar
• Wrzeszczynski, K. O., & Rost, B. (2009). Cell cycle kinases predicted from conserved biophysical properties. Proteins, 74, 655–668.
   PubMed Web of Science ®Google Scholar
• Xu, X., Weaver, Z., Linke, S. P., Li, C., Gotay, J., Wang, X. W., … Deng, C. X. (1999). Centrosome amplification and a defective G2-M cell cycle checkpoint induce genetic instability in BRCA1 exon 11 isoform-deficient cells. Molecular Cell, 3, 389–395.
   PubMed Web of Science ®Google Scholar
• Yadav, S., & Ahmad, F. (2000). A new method for the determination of stability parameters of proteins from their heat-induced denaturation curves. Analytical Biochemistry, 283, 207–213.
   PubMed Web of Science ®Google Scholar
• Yan, J., & Jetten, A. M. (2008). RAP80 and RNF8, key players in the recruitment of repair proteins to DNA damage sites. Cancer Letters, 271, 179–190.
   PubMed Web of Science ®Google Scholar
• Yan, Z., Kim, Y. S., & Jetten, A. M. (2002). RAP80, a novel nuclear protein that interacts with the retinoid-related testis-associated receptor. Journal of Biological Chemistry, 277, 32379–32388.
   PubMed Web of Science ®Google Scholar
• Zerovnik, E. (2011). Oligomerization preceding amyloid fibril formation: A process in common to intrinsically disordered and globular proteins. Network, 22, 154–161.
   PubMed Web of Science ®Google Scholar
• Zhang, C., Vasmatzis, G., Cornette, J. L., & DeLisi, C. (1997). Determination of atomic desolvation energies from the structures of crystallized proteins. Journal of Molecular Biology, 267, 707–726.
   PubMed Web of Science ®Google Scholar
• Zhang, X., & Simon, R. (2005). Estimating the number of rate limiting genomic changes for human breast cancer. Breast Cancer Research and Treatment, 91, 121–124.
   PubMed Web of Science ®Google Scholar
• Zhou, B. B., & Elledge, S. J. (2000). The DNA damage response: Putting checkpoints in perspective. Nature, 408, 433–439.
   PubMed Web of Science ®Google Scholar