References
- Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., Kondrashov, A. S., & Sunyaev, S. R. (2010). A method and server for predicting damaging missense mutations. Nature Methods, 7(4), 248–249. https://doi.org/10.1038/nmeth0410-248
- Alam, N. A., Olpin, S., Rowan, A., Kelsell, D., Leigh, I. M., Tomlinson, I. P., & Weaver, T. (2005). Missense mutations in fumarate hydratase in multiple cutaneous and uterine leiomyomatosis and renal cell cancer. The Journal of Molecular Diagnostics, 7(4), 437–443. https://doi.org/https://doi.org/10.1016/S1525-1578(10)60574-0
- Ashkenazy, H., Abadi, S., Martz, E., Chay, O., Mayrose, I., Pupko, T., & Ben-Tal, N. (2016). ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research, 44(W1), W344–W350. https://doi.org/10.1093/nar/gkw408
- Berendsen, H., Van Der Spoel, D., & Van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
- Bulku, A., Weaver, T. M., & Berkmen, M. B. (2018). Biochemical characterization of two clinically-relevant human fumarase variants defective for oligomerization. The Open Biochemistry Journal, 12(1), 1–15. https://doi.org/https://doi.org/10.2174/1874091X01812010001
- Capriotti, E., Calabrese, R., Fariselli, P., Martelli, P., Altman, R. B., & Casadio, R. (2013). WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genomics., 14(Suppl 3), S6. https://doi.org/10.1186/1471-2164-14-S3-S6
- Castro-Vega, L. J., Buffet, A., De Cubas, A. A., Cascón, A., Menara, M., Khalifa, E., … Gimenez-Roqueplo, A. P. (2014). Germline mutations in FH confer predisposition to malignant pheochromocytomas and paragangliomas. Human Molecular Genetics, 23(9), 2440–2446. https://doi.org/https://doi.org/10.1093/hmg/ddt639
- Choi, Y., & Chan, A. P. (2015). PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics, 31(16), 2745–2747. https://doi.org/10.1093/bioinformatics/btv195
- Doonan, S., Barra, D., & Bossa, F. (1984). Structural and genetic relationships between cytosolic and mitochondrial isoenzymes. The International Journal of Biochemistry, 16(12), 1193–1199. https://doi.org/https://doi.org/10.1016/0020-711X(84)90216-7
- Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
- Hospital, A., Goñi, J. R., Orozco, M., & Gelpí, J. L. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry, 8, 37–47.
- Isaacs, J. S., Jung, Y. J., Mole, D. R., Lee, S., Torres-Cabala, C., Chung, Y. L., … Neckers, L. (2005). HIF overexpression correlates with biallelic loss of fumarate hydratase in renal cancer: Novel role of fumarate in regulation of HIF stability. Cancer Cell, 8(2), 143–153. https://doi.org/https://doi.org/10.1016/j.ccr.2005.06.017
- Jiang, Y., Qian, X., Shen, J., Wang, Y., Li, X., Liu, R., … Lu, Z. (2015). Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation. Nature Cell Biology, 17(9), 1158–1168. https://doi.org/https://doi.org/10.1038/ncb3209
- Kayikci, M., Venkatakrishnan, A. J., Scott-Brown, J., Ravarani, C., Flock, T., & Babu, M. M. (2018). Visualization and analysis of non-covalent contacts using the protein contacts atlas. Nature Structural & Molecular Biology, 25(2), 185–194. https://doi.org/https://doi.org/10.1038/s41594-017-0019-z
- Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
- Leshets, M., Silas, Y., Lehming, N., & Pines, O. (2018). Fumarase: From the TCA cycle to DNA damage response and tumour suppression. Frontiers in Molecular Biosciences, 5, 68–77. https://doi.org/https://doi.org/10.3389/fmolb.2018.00068
- Mann, P. J., & Woolf, B. (1930). The action of salts on fumarase. I. .The Biochemical Journal, 24(2), 427–434. https://doi.org/https://doi.org/10.1042/bj0240427
- McCammon, J. A., Gelin, B. R., & Karplus, M. (1977). Dynamics of folded proteins. Nature, 267(5612), 585–590. https://doi.org/https://doi.org/10.1038/267585a0
- Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S., & Thomas, P. D. (2010). PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Research, 38(suppl_1), D204–D210. https://doi.org/10.1093/nar/gkp1019
- O’Hare, M. C., & Doonan, S. (1985). Purification and structural comparisons of the cytosolic and mitochondrial isoenzymes of fumarase from pig liver. Biochimica et Biophysica Acta (BBA) – Protein Structure and Molecular Enzymology, 827(2), 127–134.
- Patel, M., Day, B. J., Crapo, J. D., Fridovich, I., & McNamara, J. O. (1996). Requirement for superoxide in excitotoxic cell death. Neuron, 16(2), 345–355. https://doi.org/https://doi.org/10.1016/S0896-6273(00)80052-5
- Picaud, S., Kavanagh, K. L., Yue, W. W., Lee, W. H., Muller-Knapp, S., Gileadi, O., Sacchettini, J., & Oppermann, U. (2011). Structural basis of fumarate hydratase deficiency. Journal of Inherited Metabolic Disease, 34(3), 671–676. https://doi.org/https://doi.org/10.1007/s10545-011-9294-8
- Pollard, P. J., Brière, J. J., Alam, N. A., Barwell, J., Barclay, E., Wortham, N. C., Hunt, T., Mitchell, M., Olpin, S., Moat, S. J., Hargreaves, I. P., Heales, S. J., Chung, Y. L., Griffiths, J. R., Dalgleish, A., McGrath, J. A., Gleeson, M. J., Hodgson, S. V., Poulsom, R., Rustin, P., & Tomlinson, I. P. M. (2005). Accumulation of Krebs cycle intermediates and over-expression of HIF1alpha in tumours which result from germline FH and SDH mutations. Human Molecular Genetics, 14(15), 2231–2239. https://doi.org/https://doi.org/10.1093/hmg/ddi227
- Schmidt, C., Sciacovelli, M., & Frezza, C. (2020). Fumarate hydratase in cancer: A multifaceted tumour suppressor. Seminars in Cell & Developmental Biology, 98, 15–25. https://doi.org/https://doi.org/10.1016/j.semcdb.2019.05.002
- 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
- Sharma, S., Ding, F., & Dokholyan, N. V. (2007). Multiscale modeling of nucleosome dynamics. Biophysical Journal, 92(5), 1457–1470. https://doi.org/https://doi.org/10.1529/biophysj.106.094805
- Sim, N.-L., Kumar, P., Hu, J., Henikoff, S., Schneider, G., & Ng, P. C. (2012). SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Research, 40(W1), W452–W457. https://doi.org/10.1093/nar/gks539
- Subasri, S., Chaudhary, S. K., Sekar, K., Kesherwani, M., & Velmurugan, D. (2017). Molecular docking and molecular dynamics simulations of fumarate hydratase and its mutant H235N complexed with pyromellitic acid and citrate. Journal of Bioinformatics and Computational Biology, 15(6), 1750026. https://doi.org/https://doi.org/10.1142/S0219720017500263
- Teipel, J. W., & Hill, R. L. (1968). The number of substrate- and inhibitor-binding sites of fumarase. The Journal of Biological Chemistry, 243(21), 5679–5683.
- Tomlinson, I. P., Alam, N. A., Rowan, A. J., Barclay, E., Jaeger, E. E., Kelsell, D, … Multiple Leiomyoma Consortium 20. (2002). Germline mutations in FH predispose to dominantly inherited uterine fibroids, skin leiomyomata and papillary renal cell cancer. Nature Genetics, 30(4), 406–410.
- Trpkov, K., Hes, O., Agaimy, A., Bonert, M., Martinek, P., Magi-Galluzzi, C., … Gill, A. J. (2016). Fumarate Hydratase-deficient renal cell carcinoma is strongly correlated with fumarate hydratase mutation and hereditary leiomyomatosis and renal cell carcinoma syndrome. The American Journal of Surgical Pathology, 40(7), 865–875.
- Weaver, T., & Banaszak, L. (1996). Crystallographic studies of the catalytic and a second site in fumarase C from Escherichia coli. Biochemistry, 35(44), 13955–13965. https://doi.org/https://doi.org/10.1021/bi9614702
- Webb, B., & Sali, A. (2016). Comparative Protein Structure Modeling Using MODELLER. Current Protocols in Bioinformatics, 54(1). https://doi.org/10.1002/cpbi.3
- Woods, S. A., Schwartzbach, S. D., & Guest, J. R. (1988). Two biochemically distinct classes of fumarase in Escherichia coli. Biochimica et Biophysica Acta (Bba) – Protein Structure and Molecular Enzymology, 954(1), 14–26. https://doi.org/https://doi.org/10.1016/0167-4838(88)90050-7
- Wu, M., & Tzagoloff, A. (1987). Mitochondrial and cytoplasmic fumarases in Saccharomyces cerevisiae are encoded by a single nuclear gene FUM1. The Journal of Biological Chemistry, 262(25), 12275–12282.
- Yogev, O., Yogev, O., Singer, E., Shaulian, E., Goldberg, M., Fox, T. D., & Pines, O. (2010). Fumarase: A mitochondrial metabolic enzyme and a cytosolic/nuclear component of the DNA damage response. PLoS Biology, 8(3), e1000328. https://doi.org/https://doi.org/10.1371/journal.pbio.1000328