Bianco, A. C., Salvatore, D., Gereben, B., Berry, M. J. & Larsen, P. R. Biochemistry, cellular and molecular biology, and physiological roles of the iodothyronine selenodeiodinases. Endocr. Rev. 23, 38–89 (2002).
Köhrle, J. Iodothyronine deiodinases. In Methods in Enzymology (eds Sies, H. & Packer, L.) 125–167 (Academic Press, Cambridge, 2002).
Mondal, S., Raja, K., Schweizer, U. & Mugesh, G. Chemistry and biology in the biosynthesis and action of thyroid hormones. Angew. Chem. Int. Ed. 55, 7606–7630 (2016).
Schweizer, U., Towell, H., Vit, A., Rodriguez-Ruiz, A. & Steegborn, C. Structural aspects of thyroid hormone binding to proteins and competitive interactions with natural and synthetic compounds. Mol. Cell. Endocrinol. 458, 57–67 (2017).
van der Spek, A. H., Fliers, E. & Boelen, A. The classic pathways of thyroid hormone metabolism. Mol. Cell. Endocrinol. 458, 29–38 (2017).
Bianco, A. C. & Kim, B. W. Deiodinases: implications of the local control of thyroid hormone action. J. Clin. Invest. 116, 2571–2579 (2006).
Darras, V. M. & Herck, S. L. J. V. Iodothyronine deiodinase structure and function: from ascidians to humans. J. Endocrinol. 215, 189–206 (2012).
Luongo, C., Dentice, M. & Salvatore, D. Deiodinases and their intricate role in thyroid hormone homeostasis. Nat. Rev. Endocrinol. 15, 479–488 (2019).
Kuiper, G., Kester, M. H. A., Peeters, R. P. & Visser, T. J. Biochemical mechanisms of thyroid hormone deiodination. Thyroid 15, 787–798 (2005).
Steegborn, C. & Schweizer, U. Structure and mechanism of iodothyronine deiodinases: what we know, what we don’t know, and what would be nice to know. Exp. Clin. Endocrinol. Diabetes. 128, 375–378 (2020).
Liu, X., Guo, Z., Sun, H., Li, W. & Sun, W. Comprehensive map and functional annotation of human pituitary and thyroid proteome. J. Proteome Res. 16, 2680–2691 (2017).
Jarque, S. & Piña, B. Deiodinases and thyroid metabolism disruption in teleost fish. Environ. Res. 135, 361–375 (2014).
Carpenter, E. P., Beis, K., Cameron, A. D. & Iwata, S. Overcoming the challenges of membrane protein crystallography. Curr. Opin. Struct. Biol. 18, 581–586 (2008).
Schweizer, U., Schlicker, C., Braun, D., Köhrle, J. & Steegborn, C. Crystal structure of mammalian selenocysteine-dependent iodothyronine deiodinase suggests a peroxiredoxin-like catalytic mechanism. Proc. Natl. Acad. Sci. 111, 10526–10531 (2014).
Callebaut, I. et al. The iodothyronine selenodeiodinases are thioredoxin-fold family proteins containing a glycoside hydrolase clan GH-A-like structure. J. Biol. Chem. 278, 36887–36896 (2003).
Berry, M., Kieffer, J., Harney, J. & Larsen, P. Selenocysteine confers the biochemical-properties characteristic of the type-I iodothyronine deiodinase. J. Biol. Chem. 266, 14155–14158 (1991).
Fomenko, D. E. & Gladyshev, V. N. Identity and functions of CxxC-derived motifs. Biochemistry 42, 11214–11225 (2003).
Bayse, C. A. & Rafferty, E. R. Is halogen bonding the basis for iodothyronine deiodinase activity?. Inorg. Chem. 49, 5365–5367 (2010).
Bayse, C. A. Halogen bonding from the bonding perspective with considerations for mechanisms of thyroid hormone activation and inhibition. New J. Chem. 42, 10623–10632 (2018).
Manna, D. & Mugesh, G. A chemical model for the inner-ring deiodination of thyroxine by iodothyronine deiodinase. Angew. Chem. 122, 9432–9435 (2010).
Manna, D. & Mugesh, G. Regioselective deiodination of thyroxine by iodothyronine deiodinase mimics: an unusual mechanistic pathway involving cooperative chalcogen and halogen bonding. J. Am. Chem. Soc. 134, 4269–4279 (2012).
Cesario, D. et al. The role of the halogen bond in iodothyronine deiodinase: dependence on chalcogen substitution in naphthyl-based mimetics. J. Comput. Chem. 40, 944–951 (2019).
Visser, T. J., Kaptein, E., Terpstra, O. T. & Krenning, E. P. Deiodination of thyroid hormone by human liver. J. Clin. Endocrinol. Metab. 67, 17–24 (1988).
Marsan, E. S. & Bayse, C. A. Halogen-bonding interactions of polybrominated diphenyl ethers and thyroid hormone derivatives: a potential mechanism for the inhibition of iodothyronine deiodinase. Chem. Eur. J. 23, 6625–6633 (2017).
Marsan, E. S. & Bayse, C. A. Halogen bonding interactions of polychlorinated biphenyls and the potential for thyroid disruption. Chem. Eur. J. 26, 5200–5207 (2020).
Marsan, E. S. & Bayse, C. A. A halogen bonding perspective on iodothyronine deiodinase activity. Molecules 25, 1328 (2020).
Manna, D., Mondal, S. & Mugesh, G. Halogen bonding controls the regioselectivity of the deiodination of thyroid hormones and their sulfate analogues. Chem. Eur. J. 21, 2409–2416 (2015).
Fetrow, J. S. Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J. 9, 708–717 (1995).
Pal, M. & Dasgupta, S. The nature of the turn in omega loops of proteins. Proteins Struct. Funct. Bioinform. 51, 591–606 (2003).
Leszczynski, J. & Rose, G. Loops in globular proteins: a novel category of secondary structure. Science 234, 849–855 (1986).
Wako, H. & Endo, S. Normal mode analysis as a method to derive protein dynamics information from the protein data bank. Biophys. Rev. 9, 877–893 (2017).
Wriggers, W. et al. Automated event detection and activity monitoring in long molecular dynamics simulations. J. Chem. Theory Comput. 5, 2595–2605 (2009).
Kovacs, J. A. & Wriggers, W. Spatial heat maps from fast information matching of fast and slow degrees of freedom: application to molecular dynamics simulations. J. Phys. Chem. B 120, 8473–8484 (2016).
Gu, Y., Li, D.-W. & Brüschweiler, R. Decoding the mobility and time scales of protein loops. J. Chem. Theory Comput. 11, 1308–1314 (2015).
Gu, Y., Li, D.-W. & Brüschweiler, R. Statistical database analysis of the role of loop dynamics for protein–protein complex formation and allostery. Bioinformatics 33, 1814–1819 (2017).
Schweizer, U. & Steegborn, C. New insights into the structure and mechanism of iodothyronine deiodinases. J. Mol. Endocrinol. 55, 37–52 (2015).
Bui, J. M., Tai, K. & McCammon, J. A. Acetylcholinesterase: enhanced fluctuations and alternative routes to the active site in the complex with fasciculin-2. J. Am. Chem. Soc. 126, 7198–7205 (2004).
Jorgensen, W. L. & Schyman, P. Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents. J. Chem. Theory Comput. 8, 3895–3901 (2012).
Cavallo, G. et al. The halogen bond. Chem. Rev. 116, 2478–2601 (2016).
Wilcken, R., Zimmermann, M. O., Lange, A., Joerger, A. C. & Boeckler, F. M. Principles and applications of halogen bonding in medicinal chemistry and chemical biology. J. Med. Chem. 56, 1363–1388 (2013).
Sirimulla, S., Bailey, J. B., Vegesna, R. & Narayan, M. Halogen interactions in protein–ligand complexes: implications of halogen bonding for rational drug design. J. Chem. Inf. Model. 53, 2781–2791 (2013).
Berry, R. E. et al. Axial ligand complexes of the Rhodnius nitrophorins: reduction potentials, binding constants, EPR spectra, and structures of the 4-iodopyrazole and imidazole complexes of NP4. JBIC J. Biol. Inorg. Chem. 9, 135–144 (2004).
Ghuman, J. et al. Structural basis of the drug-binding specificity of human serum albumin. J. Mol. Biol. 353, 38–52 (2005).
Köhrle, J. Local activation and inactivation of thyroid hormones: the deiodinase family. Mol. Cell. Endocrinol. 151, 103–119 (1999).
Berry, M. J. Identification of essential histidine residues in rat type I iodothyronine deiodinase. J. Biol. Chem. 267, 18055–18059 (1992).
Nascimento, A. S. et al. Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function. J. Mol. Biol. 360, 586–598 (2006).
Roy, G., Sarma, B. K., Phadnis, P. P. & Mugesh, G. Selenium-containing enzymes in mammals: chemical perspectives. J. Chem. Sci. 117, 287–303 (2005).
Koh, C. S. et al. Crystal structures of a poplar thioredoxin peroxidase that exhibits the structure of glutathione peroxidases: insights into redox-driven conformational changes. J. Mol. Biol. 370, 512–529 (2007).
Hall, A., Parsonage, D., Poole, L. B. & Karplus, P. A. Structural evidence that peroxiredoxin catalytic power is based on transition-state stabilization. J. Mol. Biol. 402, 194–209 (2010).
Edeling, M. A., Guddat, L. W., Fabianek, R. A., Thöny-Meyer, L. & Martin, J. L. Structure of CcmG/DsbE at 1.14 Å resolution: high-fidelity reducing activity in an indiscriminately oxidizing environment. Structure 10, 973–979 (2002).
Copley, S. D., Novak, W. R. P. & Babbitt, P. C. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry 43, 13981–13995 (2004).
Ferguson, A. D. et al. NMR structures of the selenoproteins Sep15 and SelM reveal redox activity of a new thioredoxin-like family. J. Biol. Chem. 281, 3536–3543 (2006).
Arrojo e Drigo, R., Fonseca, T. L., Werneck-de-Castro, J. P. S. & Bianco, A. C. Role of the type 2 iodothyronine deiodinase (D2) in the control of thyroid hormone signaling. Biochim. Biophys. Acta BBA 1830, 3956–3964 (2013).
Gereben, B., Goncalves, C., Harney, J. W., Larsen, P. R. & Bianco, A. C. Selective proteolysis of human type 2 deiodinase: a novel ubiquitin-proteasomal mediated mechanism for regulation of hormone activation. Mol. Endocrinol. 14, 1697–1708 (2000).
Anandakrishnan, R., Aguilar, B. & Onufriev, A. V. H++ 30: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40, W537–W541 (2012).
Sagar, G. D. V. et al. The thyroid hormone-inactivating deiodinase functions as a homodimer. Mol. Endocrinol. 22, 1382–1393 (2008).
Lu, J. & Holmgren, A. Selenoproteins. J. Biol. Chem. 284, 723–727 (2009).
Bakan, A., Meireles, L. M. & Bahar, I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27, 1575–1577 (2011).
Case, D. A. et al. AMBER 16. https://ambermd.org/ (2016).
Trott, O. & Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010).
DeLano, W.L. PyMol Molecular Graphics System. https://pymol.org/ (Schrodinger, Inc., 2015).
Humphrey, W., Dalke, A. & Schulten, K. V. M. D. Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Wriggers, W. TimeScapes Analytics Package. https://timescapes.biomachina.org/ (2017).