Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

References

• Alcón, P., Shakeel, S., Chen, Z. A., Rappsilber, J., Patel, K. J., & Passmore, L. A. (2020). FANCD2-FANCI is a clamp stabilized on DNA by monoubiquitination of FANCD2 during DNA repair. Nature Structural & Molecular Biology, 27(3), 240–248. https://doi.org/10.1038/s41594-020-0380-1
   PubMed Web of Science ®Google Scholar
• Arkinson, C., Chaugule, V. K., Toth, R., & Walden, H. (2021). Specificity for deubiquitination of momoubiquitinated FANCD2 is driven by the N-terminus of USP1. Life Science Alliance, 1(5), e201800162.
   Google Scholar
• Bhattacharjee, S., & Nandi, S. (2017). DNA damage response and cancer therapeutics through the lens of the Fanconi Anemia DNA repair pathway. Cell Communication Signal, 15, 41–50.
   PubMed Web of Science ®Google Scholar
• BIOVIA, Dassault Systèmes. (2018). [Discovery Studio], [DS 2018], Dassault Systèmes.
   Google Scholar
• Bremm, A., Freund, S. M. V., & Komander, D. (2010). Lys11-linked ubiquitin chains adopt compact conformations and are preferentially hydrolyzed by the deubiquitinase Cezanne. Nature Structural & Molecular Biology, 17(8), 939–947. https://doi.org/10.1038/nsmb.1873
   PubMed Web of Science ®Google Scholar
• Brooks, B. R., Brooks, C. L., Mackerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A. R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., … Karplus, M. (2009). CHARMM: The biomolecular simulation program. Journal of Computational Chemistry, 30(10), 1545–1615. https://doi.org/10.1002/jcc.21287
   PubMed Web of Science ®Google Scholar
• Castan Eda, C. A., Dixon, E. K., Walker, O., Chaturvedi, A., Nakasone, M. A., Curtis, J. E., Reed, M. R., Krueger, S., Cropp, T. A., & Fushman, D. (2016). Linkage via K27 bestows ubiquitin chains with unique properties among polyubiquitins. Structure, 24, 423–436. https://doi.org/10.1016/j.str.2016.01.007
   PubMed Web of Science ®Google Scholar
• Ceccaldi, R., Sarangi, P. A., & D’Andrea, D. (2016). The Fanconi anaemia pathway: New players and new functions. Nature Reviews Molecular Cell Biology, 17(6), 337–349. https://doi.org/10.1038/nrm.2016.48
   PubMed Web of Science ®Google Scholar
• Chaudhuri, A., Biswas, S., & Chakraborty, S. (2019). Exploring protein–protein intermolecular recognition between meprin-α and endogenous protease regulator cystatin C coupled with pharmacophore elucidation. Journal of Biomolecular Structure and Dynamics, 37(2), 440–453. https://doi.org/10.1080/07391102.2018.1429311
   PubMed Web of Science ®Google Scholar
• Chaugule, V. K., Arkinson, C., Toth, R., & Walden, H. (2019). Enzymatic preparation of monoubiquitinated FANCD2 and FANCI protein. Methods in Enzymology, 618, 73–104.
   PubMed Web of Science ®Google Scholar
• Cheatham, T. E., III, Miller, J. L., Fox, T., Darden, T. A., & Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle Mesh Ewald method leads to stable trajectories of DNA. Journal of the American Chemical Society, 117(14), 4193–4194. https://doi.org/10.1021/ja00119a045
   Web of Science ®Google Scholar
• Chen, R., Li, L., & Weng, Z. (2003). ZDOCK: An initial-stage protein-docking algorithm. Proteins, 52(1), 80–87. https://doi.org/10.1002/prot.10389
   PubMed Web of Science ®Google Scholar
• Chen, Z. J., Parent, L., & Maniatis, T. (1996). Site-specific phosphorylation of IκBα by a novel ubiquitination-dependent protein kinase activity. Cell, 84, 853–862. https://doi.org/10.1016/S0092-8674(00)81064-8
   PubMed Web of Science ®Google Scholar
• Cristobal, S., Zemla, A., Fischer, D., Rychlewski, L., & Elofsson, A. (2001). A study of quality measures for protein threading models. BMC Bioinformatics, 2, 5. https://doi.org/10.1186/1471-2105-2-5
   PubMed Web of Science ®Google Scholar
• Deakyne, J. S., & Mazin, A. V. (2011). Fanconi anemia: At the crossroads of DNA repair. Biochemistry, 76(1), 36–48. https://doi.org/10.1134/s0006297911010068
   PubMed Web of Science ®Google Scholar
• Duhovny, D., Nussinov, R., & Wolfson, H. J. (2002). Efficient unbound docking of rigid molecules. In R. Guigo & D. Gusfield (Eds.), Proceedings of the Fourth International Workshop on Algorithms in Bioinformatics. Springer-Verlag, September 17–21, 2002, Vol. 2452, pp. 185–200.
   Google Scholar
• Eisenberg, R., Lüthy, J., & Bowie, U. (1977). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404.
   Google Scholar
• Fiser, A., Do, R. K., & Sali, A. (2000). Modeling of loops in protein structures. Protein Science, 9(9), 1753–1773. https://doi.org/10.1110/ps.9.9.1753
   PubMed Web of Science ®Google Scholar
• Freddie, R., & Salsbury, J. (2010). Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Current Opinion in Pharmacology, 10(6), 738–744.
   PubMed Web of Science ®Google Scholar
• Glickman, M. H., & Ciechanover, A. (2002). The ubiquitin-proteasome proteolytic pathway: Destruction for the sake of construction. Physiological Reviews, 82 (2), 373–428. https://doi.org/10.1152/physrev.00027.2001
   PubMed Web of Science ®Google Scholar
• Groban, E. S., Narayanan, A., & Jacobson, M. P. (2006). Conformational changes in protein loops and helices by post-translational phosphorylation. PLoS Computational Biology, 2(4), e32. https://doi.org/10.1371/journal.pcbi.0020032
   PubMed Web of Science ®Google Scholar
• Hagai, T., & Levy, Y. (2010). Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding. Proceedings of the National Academy of Sciences of the United States of America, 107(5), 2001–2006. https://doi.org/10.1073/pnas.0912335107
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
   Web of Science ®Google Scholar
• Joshi, N., Anniina, F., & Alan, D. D. (2019). The Fanconi Anemia pathway in the cancer. Annual Review Cancer Biology, 3, 457–478.
   PubMedGoogle Scholar
• Komander, D., Reyes-Turcu, F., Licchesi, J. D. F., Odenwaelder, P., Wilkinson, K. D., & Barford, D. (2009). Molecular discrimination of structurally equivalent Lys 63 linkedand linear polyubiquitin chain. EMBO Reports, 10, 466–473. https://doi.org/10.1038/embor.2009.55
   PubMed Web of Science ®Google Scholar
• Kristariyanto, Y. A., Arif, S., Rehman, A., Campbell, D. G., Morrice, N. A., Johnson, C., Toth, R., & Kulathu, Y. (2015). K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of K29 polyubiquitin. Molecular Cell, 58, 83–94. https://doi.org/10.1016/j.molcel.2015.01.041
   PubMed Web of Science ®Google Scholar
• Kristariyanto, Y. A., Choi, S. Y., Rehman, S. A. A., Ritorto, M. S., Campbell, D. G., Morrice, N. A., Toth, R., & Kulathu, Y. (2015). Assembly and structure of Lys33-linked polyubiquitin reveals distinct conformations. Biochemical Journal, 467 (2), 345–352. https://doi.org/10.1042/BJ20141502
   PubMedGoogle Scholar
• Laskowski, R. A., & Swaminathan, G. J. (2007). Comprehensive medicinal chemistry II. Elsevier Science.
   Google Scholar
• Levy, Y., Hanan, E., Soloman, B. & Becker, O. M. (2001). Helix-coil transition of PrP106-126: Molecular dynamic study. Proteins: Structures, Functions and Genetics, 45, 382–396. https://doi.org/10.1002/prot.1157
   PubMed Web of Science ®Google Scholar
• Li, L., Chen, R., & Weng, Z. (2003). RDOCK: Refinement of rigid-body protein docking predictions. Proteins, 53(3), 693–707. https://doi.org/10.1002/prot.10460
   PubMed Web of Science ®Google Scholar
• MacKay, C., Declais, A., Lundin, C., Agostinho, A., Deans, A. J., MacArtney, T. J., Hofmann, K., Gartner, A., West, S. C., Helleday, T., Lilley, D. M. J., & Rouse, J. (2010). Identification of KIAA1018/FAN1, a DNA repair nuclease recruited to DNA damage by monoubiquitinated FANCD2. Cell, 142, 65–76. https://doi.org/10.1016/j.cell.2010.06.021
   PubMed Web of Science ®Google Scholar
• Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Sali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual Review Biophysics Biomolecular Structure, 29, 291–325.
   PubMedGoogle Scholar
• McCammon, J. A., Gelin, B. R., & Karplus, M. (1980). Dynamics of folded proteins. Nature, 267, 585–590. https://doi.org/10.1038/267585a0
   Google Scholar
• Mondal, S., Mondal, T. K., Mandal, M., & Sinha, C. (2015). Structural characterization of new Schiff bases of sulfamethoxazole and sulfathiazole, their antibacterial activity and docking computation with DHPS protein structure. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 150, 268–279. https://doi.org/10.1016/j.saa.2015.05.049
   PubMed Web of Science ®Google Scholar
• Mondal, S., Mondal, T. K., Rajesh, Y., Mandal, M., & Sinha, C. (2018). Copper (II)-sulfonamide Schiff base complexes: Structure, biological activity and theoretical interpretation. Polyhedron, 151, 344–354. https://doi.org/10.1016/j.poly.2018.05.037
   Web of Science ®Google Scholar
• Mukhopadhyay, D., & Riezman, H. (2007). Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science, 315 (5809), 201–205. https://doi.org/10.1126/science.1127085
   PubMed Web of Science ®Google Scholar
• Pagadala, N. S., Syed, K., & Tuszynski, J. (2017). Software for molecular docking: A review. Biophysical Reviews, 9(2), 91–102. https://doi.org/10.1007/s12551-016-0247-1
   PubMedGoogle Scholar
• Pierce, B., & Weng, Z. (2007). ZRANK: Reranking protein docking predictions with an optimized energy function. Proteins, 67(4), 1078–1086. https://doi.org/10.1002/prot.21373
   PubMed Web of Science ®Google Scholar
• Rodríguez, A., & D’Andrea, A. (2017). Fanconi anemia pathway. Current Biology, 27, R986–R988. https://doi.org/10.1016/j.cub.2017.07.043
   PubMed Web of Science ®Google Scholar
• Roy, A., Kucukural, A. K., & Zang, Y. (2010). I-TASSER: A unified platform for automated protein structure and function preduction. Natural Protocol, 5, 725–738. https://doi.org/10.1038/nprot.2010.5
   PubMed Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical-integration of Cartesian equations of motion of a system with constraints – Molecular-dynamics of N-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Moecular Biology, 234, 779–815. https://doi.org/10.1006/jmbi.1993.1626
   PubMed Web of Science ®Google 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–W367. https://doi.org/10.1093/nar/gki481
   PubMed Web of Science ®Google Scholar
• Schnell, J. D., & Hicke, L. (2003). Non-traditional functions of ubiquitin and ubiquitin-binding proteins. The Journal of Biological Chemistry, 278 (38), 35857–35860. https://doi.org/10.1074/jbc.R300018200
   PubMed Web of Science ®Google Scholar
• Trempe, J. F., Brown, N. R., Noble, M. E. M., & Endicott, J. A. (2010). A new crystal form of Lys48-linked diubiquitin. Structural Communications, 66(9), 994–998. https://doi.org/10.1107/S1744309110027600
   Google Scholar
• Ulrich, H. D., & Walden, H. (2010). Ubiquitin signalling in DNA replication and repair. Nature Reviews Molecular Cell Biology, 11(7), 479–489. https://doi.org/10.1038/nrm2921
   PubMed Web of Science ®Google Scholar
• Virdee, S., Duy, Y. Y., Nguyen, P., Komander, D., & Chin, J. W. (2010). Engineered diubiquitin synthesis reveals Lys29-isopeptide specificity of an OTU deubiquitinase. Nature Chemical Biology, 6(10), 750–757. https://doi.org/10.1038/nchembio.426
   PubMed Web of Science ®Google Scholar
• Walden, H., & Deans, A. J. (2014). The Fanconi anemia DNA repair pathway: Structural and functional insights into a complex disorder. Annual Review of Biophysics, 43, 257–278. https://doi.org/10.1146/annurev-biophys-051013-022737
   PubMed Web of Science ®Google Scholar
• Wang, R., Wang, S., Dhar, A., Peralta, C., & Pavletich, N. P. (2020). DNA clamp functionfuntion of the monoubiquitinated Fanconi anemis ID complex. Nature, 580, 278–282. https://doi.org/10.1038/s41586-020-2110-6
   PubMed Web of Science ®Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using modeller. Current Protocols in Bioinformatics, 54, 5.6.1–5.6.37. https://doi.org/10.1002/cpbi.3
   PubMedGoogle Scholar
• Wiltgen, M. (2019). Encyclopedia of bioinformatics and computational biology. Elsevier.
   Google Scholar
• Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12, 7–8. https://doi.org/10.1038/nmeth.3213
   PubMed Web of Science ®Google Scholar
• Yang, J., & Zang, Y. (2015). I_TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43, W174–W181. https://doi.org/10.1093/nar/gkv342
   PubMed Web of Science ®Google Scholar
• Zhang, J., Li, W. F., Wang, J., Qin, M., Wu, L., Yan, Z. Q., Zuo, G. H., & Wang, W. (2009). Protein folding simulations: From coarse-grained Model to all-atom model. IUBMB Life, 61, 627–643. https://doi.org/10.1002/iub.223
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Zhou, X., & Huang, P. (2007). Fanconi anemia and ubiquitination. Journal of Genetics and Genomics, 34(7), 573–580. https://doi.org/10.1016/S1673-8527(07)60065-4
   PubMedGoogle Scholar