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Research Article

Structural insight to human Retinoid X receptor alpha-Thyroid hormone receptor beta heterodimer by molecular modelling and MD-simulation studies: role of conserved water molecules

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Pages 9828-9839 | Received 01 Aug 2022, Accepted 08 Nov 2022, Published online: 21 Nov 2022

References

  • Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. https://doi.org/10.1002/prot.340170408
  • Anwar, F., Altayb, H. N., Al-Abbasi, F. A., Al-Malki, A. L., Kamal, M. A., & Kumar, V. (2021). Antiviral effects of probiotic metabolites on COVID-19. Journal of Biomolecular Structure and Dynamics, 39(11), 4175–4184. https://doi.org/10.1080/07391102.2020.1775123
  • Banerjee, A., Dasgupta, S., Mukhopadhyay, B. P., & Sekar, K. (2015). The putative role of some conserved water molecules in the structure and function of human transthyretin. Acta Crystallographica. Section D, Biological Crystallography, 71(11), 2248–2266. https://doi.org/10.1107/S1399004715016004
  • Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4(2), 187–217. https://doi.org/10.1002/jcc.540040211
  • Chandra, V., Wu, D., Li, S., Potluri, N., Kim, Y., & Rastinejad, F. (2017). The quaternary architecture of RARβ-RXRα heterodimer facilitates domain-domain signal transmission. Nature Communications, 8(1), 868. https://doi.org/10.1038/s41467-017-00981-y
  • Chen, Y., & Young, M. A. (2010). Structure of a thyroid hormone receptor DNA-binding domain homodimer bound to an inverted palindrome DNA response element. Molecular Endocrinology (Baltimore, Md.), 24(8), 1650–1664. https://doi.org/10.1210/me.2010-0129
  • Chillemi, G., D'Annessa, I., Fiorani, P., Losasso, C., Benedetti, P., & Desideri, A. (2008). Thr729 in human topoisomerase I modulates anti-cancer drug resistance by altering protein domain communications as suggested by molecular dynamics simulations. Nucleic Acids Research, 36(17), 5645–5651. https://doi.org/10.1093/nar/gkn558
  • Couch, G. S., Hendrix, D. K., & Ferrin, T. E. (2006). Nucleic acid visualization with UCSF Chimera. Nucleic Acids Research, 34(4), e29. https://doi.org/10.1093/nar/gnj031
  • Dasgupta, S., Mukherjee, S., Mukhopadhyay, B. P., Banerjee, A., & Mishra, D. K. (2018). Recognition dynamics of dopamine to human Monoamine oxidase B: Role of Leu171/Gln206 and conserved water molecules in the active site cavity. Journal of Biomolecular Structure & Dynamics, 36(6), 1439–1462. https://doi.org/10.1080/07391102.2017.1325405
  • Germain, P., Altucci, L., Bourguet, W., Rochette-Egly, C., & Gronemeyer, H. (2003). Nuclear receptor superfamily: Principles of signaling. Pure and Applied Chemistry, 75(11–12), 1619–1664. https://doi.org/10.1351/pac200375111619
  • Germain, P., Staels, B., Dacquet, C., Spedding, M., & Laudet, V. (2006). Overview of nomenclature of nuclear receptors. Pharmacological Reviews, 58(4), 685–704. ( https://doi.org/10.1124/pr.58.4.2
  • Grant, B. J., Rodrigues, A. P. C., ElSawy, K. M., McCammon, J. A., & Caves, L. S. D. (2006). Bio3d: An R package for the comparative analysis of protein structures. Bioinformatics, 22(21), 2695–2696. https://doi.org/10.1093/bioinformatics/btl461
  • Gullingsrud, J., Kosztin, D., & Schulten, K. (2001). Structural determinants of MscL gating studied by molecular dynamics simulations. Biophysical Journal, 80(5), 2074–2081.(01)76181-4 https://doi.org/10.1016/S0006-3495
  • Harvey, M. J., & De Fabritiis, G. (2009). An implementation of the smooth particle mesh Ewald method on GPU hardware. Journal of Chemical Theory and Computation, 5(9), 2371–2377. https://doi.org/10.1021/ct900275y
  • Hörlein, A. J., Näär, A. M., Heinzel, T., Torchia, J., Gloss, B., Kurokawa, R., Ryan, A., Kamei, Y., Söderström, M., Glass, C. K., & Rosenfeld, M. G. (1995). Ligand-independent repression by the thyroid hormone receptor mediated by a nuclear receptor co-repressor. Nature, 377(6548), 397–404. https://doi.org/10.1038/377397a0
  • Huang, J., & MacKerell, A. D. (2013). CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Johansson, M. U., Zoete, V., Michielin, O., & Guex, N. (2012). Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics, 13(1), 173. https://doi.org/10.1186/1471-2105-13-173
  • Jonkman, J. G., Wijsbeek, J., Hollenbeek, S., de Boer, S. H., de Zeeuw, R. A., Van Bork, L. E., & Orie, N. G. (1975). Determination of low cencentrations of the quaternary ammonium compound thiazinamium methylsulphate in plasma and urine. The Journal of Pharmacy and Pharmacology, 27(11), 849–854. https://doi.org/10.1016/0021-9991(77)90098-5
  • Kalé, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K., & Schulten, K. (1999). NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151(1), 283–312. https://doi.org/10.1006/jcph.1999.6201
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
  • Le Maire, A., Teyssier, C., Balaguer, P., Bourguet, W., & Germain, P. (2019). Regulation of RXR-RAR heterodimers by RXR- and RAR-specific ligands and their combinations. Cells, 8(11), 1392., https://doi.org/10.3390/cells8111392
  • MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., … Karplus, M. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins †. The Journal of Physical Chemistry B, 102(18), 3586–3616. https://doi.org/10.1021/jp973084f
  • Madan Babu, M., Kumar Singh, S., & Balaram, P. (2002). A C–H⋯O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins. Journal of Molecular Biology, 322(4), 871–880. https://doi.org/10.1016/S0022-2836(02)00715-5
  • Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
  • Mesentean, S., Fischer, S., & Smith, J. C. (2006). Analyzing large-scale structural change in proteins: Comparison of principal component projection and Sammon mapping. Proteins: Structure, Function, and Bioinformatics, 64(1), 210–218. https://doi.org/10.1002/prot.20981
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Mukherjee, S., Dasgupta, S., Adhikari, U., & Panja, S. S. (2021). Molecular modeling and molecular dynamics simulation studies on thyroid hormone receptor from Rattus norvegicus: Role of conserved water molecules. Journal of Molecular Modeling, 27(5), 126. https://doi.org/10.1007/s00894-021-04740-1
  • Oñate, S. A., Tsai, S. Y., Tsai, M. J., & O'Malley, B. W. (1995). Sequence and characterization of a coactivator for the steroid hormone receptor superfamily. Science (New York, N.Y.), 270(5240), 1354–1357. https://doi.org/10.1126/science.270.5240.1354
  • Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera? A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
  • Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/10.1002/jcc.20289
  • Šali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779–815. https://doi.org/10.1006/jmbi.1993.1626
  • Sandler, B., Webb, P., Apriletti, J. W., Huber, B. R., Togashi, M., Lima, S. T. C., Juric, S., Nilsson, S., Wagner, R., Fletterick, R. J., & Baxter, J. D. (2004). Thyroxine-thyroid hormone receptor interactions. The Journal of Biological Chemistry, 279(53), 55801–55808. https://doi.org/10.1074/jbc.M410124200
  • Sever, R., & Glass, C. K. (2013). Signaling by nuclear receptors. Cold Spring Harbor Perspectives in Biology, 5(3), a016709. https://doi.org/10.1101/cshperspect.a016709
  • St-Arnaud, R., Jones, G., & Glorieux, F. H. (2016). Genetic defects in vitamin D metabolism and action. In J. Larry Jameson, Leslie J De Groot, David M. de Kretser, Linda C. Giudice, Ashley B. Grossman, Shlomo Melmed, John T. Potts, Gordon C. Weir (Eds.), Endocrinology: Adult and pediatric 7th ed (pp. 1160–1172). Elsevier. https://doi.org/10.1016/B978-0-323-18907-1.00067-6
  • Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), NA–NA. https://doi.org/10.1002/jcc.21334
  • Tuszynska, I., Magnus, M., Jonak, K., Dawson, W., & Bujnicki, J. M. (2015). NPDock: A web server for protein–nucleic acid docking. Nucleic Acids Research, 43(W1), W425–W430. https://doi.org/10.1093/nar/gkv493
  • Ufimtsev, I. S., & Martinez, T. J. (2009). Quantum chemistry on graphical processing units. 3. Analytical energy gradients, geometry optimization, and first principles molecular dynamics. Journal of Chemical Theory and Computation, 5(10), 2619–2628. https://doi.org/10.1021/ct9003004
  • Upadhyay, S. K. (2014). Dynamics of Gal80p in the Gal80p–Gal3p complex differ significantly from the dynamics in the Gal80p–Gal1p complex: Implications for the higher specificity of Gal3p. Molecular bioSystems, 10(12), 3120–3129. https://doi.org/10.1039/C4MB00371C
  • Weikum, E. R., Liu, X., & Ortlund, E. A. (2018). The nuclear receptor superfamily: A structural perspective. Protein Science : A Publication of the Protein Society, 27(11), 1876–1892. https://doi.org/10.1002/pro.3496
  • Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. Journal of the American Chemical Society, 106(3), 765–784. https://doi.org/10.1021/ja00315a051

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