Structural and biophysical properties of h-FANCI ARM repeat protein

References

• Abraham, M. J., & Gready, J. E. (2011). Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5. Journal of Computational Chemistry, 32, 2031–2040.10.1002/jcc.v32.9
   PubMed Web of Science ®Google Scholar
• Alter, B. P., Greene, M. H., Velazquez, I., & Rosenberg, P. S. (2003). Cancer in Fanconi anemia. Blood, 101, 2072.10.1182/blood-2002-11-3597
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17, 412–425.10.1002/(ISSN)1097-0134
   PubMed Web of Science ®Google Scholar
• Andrade, M. A., Petosa, C., O’Donoghue, S. I., Muller, C. W., & Bork, P. (2001). Comparison of ARM and HEAT protein repeats. Journal of Molecular Biology, 309, 1–18.10.1006/jmbi.2001.4624
   PubMed Web of Science ®Google Scholar
• Aravind, L., Anantharaman, V., Balaji, S., Babu, M. M., & Iyer, L. M. (2005). The many faces of the helix-turn-helix domain: Transcription regulation and beyond. FEMS Microbiology Reviews, 29, 231–262.10.1016/j.fmrre.2004.12.008
   PubMed Web of Science ®Google Scholar
• Bahar, I., Erman, B., Jernigan, R. L., Atilgan, A. R., & Covell, D. G. (1999). Collective motions in HIV-1 reverse transcriptase: Examination of flexibility and enzyme function. Journal of Molecular Biology, 285, 1023–1037.10.1006/jmbi.1998.2371
   PubMed Web of Science ®Google Scholar
• Brennan, R. G., & Matthews, B. W. (1989). The helix-turn-helix DNA binding motif. The Journal of Biological Chemistry, 264, 1903–1906.
   PubMed Web of Science ®Google Scholar
• Butturini, A., Gale, R. P., Verlander, P. C., Adler-Brecher, B., Gillio, A. P., & Auerbach, A. D. (1994). Hematologic abnormalities in Fanconi anemia: An international Fanconi anemia registry study. Blood, 84, 1650–1655.
   PubMed Web of Science ®Google Scholar
• Castella, M., Jacquemont, C., Thompson, E. L., Yeo, J. E., Cheung, R. S., Huang, J. W., … Taniguchi, T. (2015). FANCI regulates recruitment of the FA core complex at sites of DNA damage independently of FANCD2. PLoS Genetics, 11, e1005563.10.1371/journal.pgen.1005563
   PubMed Web of Science ®Google Scholar
• Choudhary, R. K., Vikrant, Siddiqui, Q. M., Thapa, P. S., Raikundalia, S., Gadewal, N., … Varma, A. K. (2015). Multimodal approach to explore the pathogenicity of BARD1, ARG 658 CYS, and ILE 738 VAL mutants. Journal of Biomolecular Structure and Dynamics, 34, 1–12.
   PubMed Web of Science ®Google Scholar
• Coates, J. C. (2003). Armadillo repeat proteins: Beyond the animal kingdom. Trends in Cell Biology, 13, 463–471.10.1016/S0962-8924(03)00167-3
   PubMed Web of Science ®Google Scholar
• Cohen, M. M., Simpson, S. J., Honig, G. R., Maurer, H. S., Nicklas, J. W., & Martin, A. O. (1982). The identification of fanconi anemia genotypes by clastogenic stress. The American Journal of Human Genetics, 34, 794–810.
   PubMed Web of Science ®Google Scholar
• Crist, R. C., Roth, J. J., Baran, A. A., McEntee, B. J., Siracusa, L. D., & Buchberg, A. M. (2010). The armadillo repeat domain of Apc suppresses intestinal tumorigenesis. Mammalian Genome, 21, 450–457.10.1007/s00335-010-9288-0
   PubMed Web of Science ®Google Scholar
• de Vries, S. J., van Dijk, M., & Bonvin, A. M. (2010). The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883–897.10.1038/nprot.2010.32
   PubMed Web of Science ®Google Scholar
• Dorsman, J. C., Levitus, M., Rockx, D., Rooimans, M. A., Oostra, A. B., Haitjema, A., … Joenje, H. (2007). Identification of the Fanconi anemia complementation group I gene, FANCI. Cellular Oncology, 29, 211–218.
   PubMed Web of Science ®Google Scholar
• Fiser, A., & Sali, A. (2003). ModLoop: Automated modeling of loops in protein structures. Bioinformatics, 19, 2500–2501.10.1093/bioinformatics/btg362
   PubMed Web of Science ®Google 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, 223–230.10.1006/jmbi.1996.0787
   PubMed Web of Science ®Google Scholar
• Grant, B. J., Rodrigues, A. P., ElSawy, K. M., McCammon, J. A., & Caves, L. S. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22, 2695–2696.10.1093/bioinformatics/btl461
   PubMed Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Kabsch, W., & Sander, C. (1983). Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577–2637.10.1002/(ISSN)1097-0282
   PubMed Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105, 6474–6487.10.1021/jp003919d
   Web of Science ®Google Scholar
• Kim, D. E., Chivian, D., & Baker, D. (2004). Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research, 32, W526–W531.10.1093/nar/gkh468
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51, 2778–2786.10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Longerich, S., San Filippo, J., Liu, D., & Sung, P. (2009). FANCI binds branched DNA and is monoubiquitinated by UBE2T-FANCL. Journal of Biological Chemistry, 284, 23182–23186.10.1074/jbc.C109.038075
   PubMed Web of Science ®Google Scholar
• Louis-Jeune, C., Andrade-Navarro, M. A., & Perez-Iratxeta, C. (2012). Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins: Structure, Function, and Bioinformatics, 80, 374–381.10.1002/prot.v80.2
   PubMed Web of Science ®Google Scholar
• Luscombe, N. M., & Thornton, J. M. (2002). Protein–DNA interactions: Amino acid conservation and the effects of mutations on binding specificity. Journal of Molecular Biology, 320, 991–1009.10.1016/S0022-2836(02)00571-5
   PubMed Web of Science ®Google Scholar
• McCabe, K. M., Olson, S. B., & Moses, R. E. (2009). DNA interstrand crosslink repair in mammalian cells. Journal of Cellular Physiology, 220, 569–573.10.1002/jcp.v220:3
   PubMed Web of Science ®Google Scholar
• Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y., & Matthews, B. W. (1982). The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature, 298, 718–723.10.1038/298718a0
   PubMed Web of Science ®Google Scholar
• Pace, C. N., & Scholtz, J. M. (1998). A helix propensity scale based on experimental studies of peptides and proteins. Biophysical Journal, 75, 422–427.10.1016/S0006-3495(98)77529-0
   PubMed Web of Science ®Google Scholar
• Rajpurohit, Y. S., & Misra, H. S. (2013). Structure-function study of deinococcal serine/threonine protein kinase implicates its kinase activity and DNA repair protein phosphorylation roles in radioresistance of Deinococcus radiodurans. The International Journal of Biochemistry & Cell Biology, 45, 2541–2552.10.1016/j.biocel.2013.08.011
   PubMed Web of Science ®Google Scholar
• Religa, T. L., Johnson, C. M., Vu, D. M., Brewer, S. H., Dyer, R. B., & Fersht, A. R. (2007). The helix–turn–helix motif as an ultrafast independently folding domain: The pathway of folding of Engrailed homeodomain. Proceedings of the National Academy of Sciences, 104, 9272–9277.10.1073/pnas.0703434104
   PubMed Web of Science ®Google Scholar
• Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341.10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Smogorzewska, A., Matsuoka, S., Vinciguerra, P., McDonald 3rd, E. R., Hurov, K. E., Luo, J., … Elledge, S. J. (2007). Identification of the FANCI Protein, a monoubiquitinated FANCD2 paralog required for DNA repair. Cell, 129, 289–301.10.1016/j.cell.2007.03.009
   PubMed Web of Science ®Google Scholar
• Tsytlonok, M., Craig, P. O., Sivertsson, E., Serquera, D., Perrett, S., Best, R. B., … Itzhaki, L. S. (2013). Complex energy landscape of a giant repeat protein. Structure, 21, 1954–1965.10.1016/j.str.2013.08.028
   PubMed Web of Science ®Google Scholar
• Wang, W. (2007). Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. Nature Reviews Genetics, 8, 735–748.10.1038/nrg2159
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, W407–W410.10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yuan, F., El Hokayem, J., Zhou, W., & Zhang, Y. (2009). FANCI protein binds to DNA and interacts with FANCD2 to recognize branched structures. Journal of Biological Chemistry, 284, 24443–24452.10.1074/jbc.M109.016006
   PubMed Web of Science ®Google Scholar