CIVIL ENGINEERING 365 ALL ABOUT CIVIL ENGINEERING

[ad_1]

  • 1.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 2.

    Köhrle, J. Iodothyronine deiodinases. In Methods in Enzymology (eds Sies, H. & Packer, L.) 125–167 (Academic Press, Cambridge, 2002).


    Google Scholar
     

  • 3.

    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).

    CAS 

    Google Scholar
     

  • 4.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 5.

    van der Spek, A. H., Fliers, E. & Boelen, A. The classic pathways of thyroid hormone metabolism. Mol. Cell. Endocrinol. 458, 29–38 (2017).

    PubMed 

    Google Scholar
     

  • 6.

    Bianco, A. C. & Kim, B. W. Deiodinases: implications of the local control of thyroid hormone action. J. Clin. Invest. 116, 2571–2579 (2006).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 7.

    Darras, V. M. & Herck, S. L. J. V. Iodothyronine deiodinase structure and function: from ascidians to humans. J. Endocrinol. 215, 189–206 (2012).

    CAS 
    PubMed 

    Google Scholar
     

  • 8.

    Luongo, C., Dentice, M. & Salvatore, D. Deiodinases and their intricate role in thyroid hormone homeostasis. Nat. Rev. Endocrinol. 15, 479–488 (2019).

    PubMed 

    Google Scholar
     

  • 9.

    Kuiper, G., Kester, M. H. A., Peeters, R. P. & Visser, T. J. Biochemical mechanisms of thyroid hormone deiodination. Thyroid 15, 787–798 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • 10.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 11.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 12.

    Jarque, S. & Piña, B. Deiodinases and thyroid metabolism disruption in teleost fish. Environ. Res. 135, 361–375 (2014).

    CAS 
    PubMed 

    Google Scholar
     

  • 13.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 14.

    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).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • 15.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 16.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 17.

    Fomenko, D. E. & Gladyshev, V. N. Identity and functions of CxxC-derived motifs. Biochemistry 42, 11214–11225 (2003).

    CAS 
    PubMed 

    Google Scholar
     

  • 18.

    Bayse, C. A. & Rafferty, E. R. Is halogen bonding the basis for iodothyronine deiodinase activity?. Inorg. Chem. 49, 5365–5367 (2010).

    CAS 
    PubMed 

    Google Scholar
     

  • 19.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 20.

    Manna, D. & Mugesh, G. A chemical model for the inner-ring deiodination of thyroxine by iodothyronine deiodinase. Angew. Chem. 122, 9432–9435 (2010).


    Google Scholar
     

  • 21.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 22.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 23.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 24.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 25.

    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).


    Google Scholar
     

  • 26.

    Marsan, E. S. & Bayse, C. A. A halogen bonding perspective on iodothyronine deiodinase activity. Molecules 25, 1328 (2020).

    CAS 
    PubMed Central 

    Google Scholar
     

  • 27.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 28.

    Fetrow, J. S. Omega loops: nonregular secondary structures significant in protein function and stability. FASEB J. 9, 708–717 (1995).

    CAS 
    PubMed 

    Google Scholar
     

  • 29.

    Pal, M. & Dasgupta, S. The nature of the turn in omega loops of proteins. Proteins Struct. Funct. Bioinform. 51, 591–606 (2003).

    CAS 

    Google Scholar
     

  • 30.

    Leszczynski, J. & Rose, G. Loops in globular proteins: a novel category of secondary structure. Science 234, 849–855 (1986).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • 31.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 32.

    Wriggers, W. et al. Automated event detection and activity monitoring in long molecular dynamics simulations. J. Chem. Theory Comput. 5, 2595–2605 (2009).

    CAS 
    PubMed 

    Google Scholar
     

  • 33.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 34.

    Gu, Y., Li, D.-W. & Brüschweiler, R. Decoding the mobility and time scales of protein loops. J. Chem. Theory Comput. 11, 1308–1314 (2015).

    CAS 
    PubMed 

    Google Scholar
     

  • 35.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 36.

    Schweizer, U. & Steegborn, C. New insights into the structure and mechanism of iodothyronine deiodinases. J. Mol. Endocrinol. 55, 37–52 (2015).


    Google Scholar
     

  • 37.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 38.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 39.

    Cavallo, G. et al. The halogen bond. Chem. Rev. 116, 2478–2601 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 40.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 41.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 42.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 43.

    Ghuman, J. et al. Structural basis of the drug-binding specificity of human serum albumin. J. Mol. Biol. 353, 38–52 (2005).

    CAS 
    PubMed 

    Google Scholar
     

  • 44.

    Köhrle, J. Local activation and inactivation of thyroid hormones: the deiodinase family. Mol. Cell. Endocrinol. 151, 103–119 (1999).

    PubMed 

    Google Scholar
     

  • 45.

    Berry, M. J. Identification of essential histidine residues in rat type I iodothyronine deiodinase. J. Biol. Chem. 267, 18055–18059 (1992).

    CAS 
    PubMed 

    Google Scholar
     

  • 46.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 47.

    Roy, G., Sarma, B. K., Phadnis, P. P. & Mugesh, G. Selenium-containing enzymes in mammals: chemical perspectives. J. Chem. Sci. 117, 287–303 (2005).

    CAS 

    Google Scholar
     

  • 48.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 49.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 50.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 51.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 52.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 53.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 54.

    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).

    CAS 
    PubMed 

    Google Scholar
     

  • 55.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 56.

    Sagar, G. D. V. et al. The thyroid hormone-inactivating deiodinase functions as a homodimer. Mol. Endocrinol. 22, 1382–1393 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 57.

    Lu, J. & Holmgren, A. Selenoproteins. J. Biol. Chem. 284, 723–727 (2009).

    CAS 
    PubMed 

    Google Scholar
     

  • 58.

    Bakan, A., Meireles, L. M. & Bahar, I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27, 1575–1577 (2011).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 59.

    Case, D. A. et al. AMBER 16. https://ambermd.org/ (2016).

  • 60.

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 61.

    DeLano, W.L. PyMol Molecular Graphics System. https://pymol.org/ (Schrodinger, Inc., 2015).

  • 62.

    Humphrey, W., Dalke, A. & Schulten, K. V. M. D. Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).

    CAS 
    PubMed 

    Google Scholar
     

  • 63.

    Wriggers, W. TimeScapes Analytics Package. https://timescapes.biomachina.org/ (2017).

  • [ad_2]

    Source link

    Leave a Reply

    Your email address will not be published. Required fields are marked *