I131T Mutation’s Effects on Van der Waals Forces and Solvation Energy in Congenital Hypothyroidism
DOI:
https://doi.org/10.47611/jsrhs.v12i4.5648Keywords:
Rosetta, I131T Mutation, Hypothyroidism, G protein coupled receptor, Van der Waals forcesAbstract
Garcia et al. (2017) unraveled the intricate mechanisms underlying the impact of the p.I131T mutation on the Thyrotropin Releasing Hormone Receptor (TRHR), a class A G-protein coupled receptor (GPCR). This mutation leads to Congenital Hypothyroidism in an 8-year-old patient with homozygosity and Hyperthyrotropinemia in heterozygous family members. The mutation substitutes a polar Thr for a non-polar Ile, disrupting the hydrophobic pocket within the TRHR-G-protein interface. While Molecular Dynamics (MD) simulations unveiled this interaction, the absence of experimental data on the activated TRH-TRHR-G protein complex hindered a comprehensive assessment. Addressing this gap, when Youwei Xu et al. (2022) recently presented the Cryo-EM structure of the activated complex, we employed Rosetta (Alford, et al., 2017) to optimize this structure and generated 100 starting structures; the five best ones were used as starting template structures to produce protein structures for both wild-type and mutant TRHR-TRH-G protein complexes. Our study not only validated Garcia et al.’s findings on reduced signal transduction but also pinpointed critical chemical interactions affected by the p.I131T mutation—specifically, Van der Waals forces and Solvation energy.
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References
Abelian, A., Dybek, M., Wallach, J., Gaye, B., & Adejare, A. (2021). Chapter 6 - Pharmaceutical Chemistry. In A. Adejare (Ed.), Remington (Twenty-third Edition) (pp. 105-128). Academic Press. ISBN 9780128200070. https://doi.org/10.1016/B978-0-12-820007-0.00006-4
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., Labonte, J. W., Pacella, M. S., Bonneau, R., Bradley, P., Dunbrack Jr., R. L., Das, R., Baker, D., Kuhlman, B., Kortemme, T., & Gray, J. J. (2017). The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design. Journal of Chemical Theory and Computation, 13(6), 3031-3048. http://doi.org/10.1021/acs.jctc.7b00125
Bonomi, M., Busnelli, M., Beck-Peccoz, P., Costanzo, D., Antonica, F., Dolci, C., Pilotta, A., Buzi, F., & Persani, L. (2009). A family with complete resistance to thyrotropin-releasing hormone. The New England journal of medicine, 360(7), 731–734. https://doi.org/10.1056/NEJMc0808557
Brown, B. P., Vu, O., Geanes, A. R., Kothiwale, S., Butkiewicz, M., Lowe, E. W., Mueller, R., Pape, R., Mendenhall, J., & Meiler, J. (2022). Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery. Frontiers in Pharmacology, 13, 833099. https://doi.org/10.3389/fphar.2022.833099
Collu, R., Tang, J., Castagné, J., Lagacé, G., Masson, N., Huot, C., Deal, C., Delvin, E., Faccenda, E., Eidne, K. A., & Van Vliet, G. (1997). A novel mechanism for isolated central hypothyroidism: inactivating mutations in the thyrotropin-releasing hormone receptor gene. The Journal of clinical endocrinology and metabolism, 82(5), 1561–1565. https://doi.org/10.1210/jcem.82.5.3918
DeVree, B. T., Mahoney, J. P., Vélez-Ruiz, G. A., Rasmussen, S. G., Kuszak, A. J., Edwald, E., Fung, J. J., Manglik, A., Masureel, M., Du, Y., Matt, R. A., Pardon, E., Steyaert, J., Kobilka, B. K., & Sunahara, R. K. (2016). Allosteric coupling from G protein to the agonist-binding pocket in GPCRs. Nature, 535(7610), 182–186. https://doi.org/10.1038/nature18324
Dror, R. O., Pan, A. C., Arlow, D. H., Borhani, D. W., Maragakis, P., Shan, Y., Xu, H., & Shaw, D. E. (2011). Pathway and mechanism of drug binding to G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America, 108(32), 13118–13123. https://doi.org/10.1073/pnas.1104614108
Fleishman, S. J., Leaver-Fay, A., Corn, J. E., Strauch, E. M., Khare, S. D., Koga, N., Ashworth, J., Murphy, P., Richter, F., Lemmon, G., Meiler, J., & Baker, D. (2011). RosettaScripts: A scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE, 6(6), e20161. https://doi.org/10.1371/journal.pone.0020161
García, M., González de Buitrago, J., Jiménez-Rosés, M., Pardo, L., Hinkle, P. M., & Moreno, J. C. (2017). Central Hypothyroidism Due to a TRHR Mutation Causing Impaired Ligand Affinity and Transactivation of Gq. The Journal of Clinical Endocrinology and Metabolism, 102(7), 2433–2442. https://doi.org/10.1210/jc.2016-3977
Jumper, J et al. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583–589. https://doi.org/10.1038/s41586-021-03819-2
Koulouri, O., Nicholas, A. K., Schoenmakers, E., Mokrosinski, J., Lane, F., Cole, T., Kirk, J., Farooqi, I. S., Chatterjee, V. K., Gurnell, M., & Schoenmakers, N. (2016). A Novel Thyrotropin-Releasing Hormone Receptor Missense Mutation (P81R) in Central Congenital Hypothyroidism. The Journal of clinical endocrinology and metabolism, 101(3), 847–851. https://doi.org/10.1210/jc.2015-3916
Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), 105–132. https://doi.org/10.1016/0022-2836(82)90515-0
Leman, J. K., Weitzner, B. D., Lewis, S. M., et al. (2020). Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods, 17(7), 665–680. https://doi.org/10.1038/s41592-020-0848-2
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., Reiher, W. E., … 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
Mendenhall, J., Brown, B. P., Kothiwale, S., & Meiler, J. (2021). BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. Journal of Chemical Information and Modeling, 61(1), 189-201. https://pubs.acs.org/doi/10.1021/acs.jcim.0c01140
National Center for Biotechnology Information. (n.d.). Congenital Hypothyroidism. In GeneReviews®. Retrieved August 17, 2021, from https://www.ncbi.nlm.nih.gov/books/NBK558913/
Rastogi, M. V., & LaFranchi, S. H. (2010). Congenital hypothyroidism. Orphanet Journal of Rare Diseases, 5, 17. https://doi.org/10.1186/1750-1172-5-17
Schöneberg, T., & Liebscher, I. (2021). Mutations in G Protein-Coupled Receptors: Mechanisms, Pathophysiology and Potential Therapeutic Approaches. Pharmacological reviews, 73(1), 89–119. https://doi.org/10.1124/pharmrev.120.000011
Schroeder, A. C., & Privalsky, M. L. (2014). Thyroid hormones, T3 and T4, in the brain. Frontiers in Endocrinology, 5. https://doi.org/10.3389/fendo.2014.00040
Stoupa, A., Kariyawasam, D., Polak, M., & Carré, A. (2022). Genetics of congenital hypothyroidism: Modern concepts. Pediatric Investigation, 6, 123–134. https://doi.org/10.1002/ped4.12324
Uchida, K., & Suzuki, M. (2021). Congenital Hypothyroidism and Brain Development: Association With Other Psychiatric Disorders. Frontiers in Neuroscience, 15, 772382. https://doi.org/10.3389/fnins.2021.772382
Varadi, M., et al. (2022). AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research. https://doi.org/10.1093/nar/gkab1061
Xu, Y., Cai, H., You, C., He, X., Yuan, Q., Jiang, H., Cheng, X., Jiang, Y., & Xu, H. E. (2022). Structural insights into ligand binding and activation of the human thyrotropin-releasing hormone receptor. Cell Research, 32(9), 855–857. https://doi.org/10.1038/s41422-022-00641-x
Zamyatnin, A. A. (1972). Protein volume in solution. Progress in Biophysics and Molecular Biology, 24, 107-123. https://doi.org/10.1016/0079-6107(72)90005-3
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