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Research Articles

The pathogenic effect of SNPs on structure and function of human TLR4 using a computational approach

, ORCID Icon &
Pages 12387-12400 | Received 24 Sep 2022, Accepted 03 Jan 2023, Published online: 17 Jan 2023

References

  • Androutsakos, T., Bakasis, A. D., Pouliakis, A., Gazouli, M., Vallilas, C., & Hatzis, G. (2022). Single nucleotide polymorphisms of toll-like receptor 4 in Hepatocellular Carcinoma - A single-center study. International Journal of Molecular Sciences, 23(16), 9430. https://doi.org/10.3390/ijms23169430
  • Anwar, M. A., & Choi, S. (2017). Structure-activity relationship in TLR4 mutations: Atomistic molecular dynamics simulations and residue interaction network analysis. Scientific Reports, 7(1), 43807–43814. https://doi.org/10.1038/srep43807
  • Arbour, N. C., Lorenz, E., Schutte, B. C., Zabner, J., Kline, J. N., Jones, M., Frees, K., Watt, J. L., & Schwartz, D. A. (2000). TLR4 mutations are associated with endotoxin hyporesponsiveness in humans. Nature Genetics, 25(2), 187–191. https://doi.org/10.1038/76048
  • Arifuzzaman, M., Mitra, S., Das, R., Hamza, A., Absar, N., & Dash, R. (2020). In silico analysis of nonsynonymous single‐nucleotide polymorphisms (nsSNPs) of the SMPX gene. Annals of Human Genetics, 84(1), 54–71.
  • Bao, L., Zhou, M., & Cui, Y. (2005). nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms. Nucleic Acids Research, 33(Web Server issue), W480–W482. https://doi.org/10.1093/nar/gki372
  • Berendsen, H. J., Postma, J. V., Van Gunsteren, W. F., DiNola, A. R. H. J., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
  • Botos, I., Segal, D. M., & Davies, D. R. (2011). The structural biology of Toll-like receptors. Structure (London, England : 1993), 19(4), 447–459. https://doi.org/10.1016/j.str.2011.02.004
  • Capriotti, E., & Altman, R. B. (2011). Improving the prediction of disease-related variants using protein three-dimensional structure. BMC Bioinformatics, 12(S4), 1–11. https://doi.org/10.1186/1471-2105-12-S4-S3
  • Capriotti, E., Calabrese, R., & Casadio, R. (2006). Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics (Oxford, England), 22(22), 2729–2734. https://doi.org/10.1093/bioinformatics/btl423
  • Capriotti, E., Fariselli, P., & Casadio, R. (2005a). I-Mutant2.0: Predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Research, 33(Web Server issue), W306–W310. https://doi.org/10.1093/nar/gki375
  • Capriotti, E., Fariselli, P., Calabrese, R., & Casadio, R. (2005b). Predicting protein stability changes from sequences using support vector machines. Bioinformatics, 21(Suppl 2), ii54–ii58. https://doi.org/10.1093/bioinformatics/bti1109
  • Carter, D., Fox, C. B., Day, T. A., Guderian, J. A., Liang, H., Rolf, T., Vergara, J., Sagawa, Z. K., Ireton, G., Orr, M. T., Desbien, A., Duthie, M. S., Coler, R. N., & Reed, S. G. (2016). A structure‐function approach to optimizing TLR4 ligands for human vaccines. Clinical & Translational Immunology, 5(11), e108. https://doi.org/10.1038/cti.2016.63
  • Carter, H., Douville, C., Stenson, P. D., Cooper, D. N., & Karchin, R. (2013). Identifying Mendelian disease genes with the variant effect scoring tool. BMC Genomics. 14(S3), 1–16. https://doi.org/10.1186/1471-2164-14-S3-S3
  • Chasman, D., & Adams, R. M. (2001). Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation. Journal of Molecular Biology, 307(2), 683–706. https://doi.org/10.1006/jmbi.2001.4510
  • Choi, Y., & Chan, A. P. (2015). PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics (Oxford, England), 31(16), 2745–2747. https://doi.org/10.1093/bioinformatics/btv195
  • Dodé, C., Le Dû, N., Cuisset, L., Letourneur, F., Berthelot, J.-M., Vaudour, G., Meyrier, A., Watts, R. A., Scott, D. G. I., Nicholls, A., Granel, B., Frances, C., Garcier, F., Edery, P., Boulinguez, S., Domergues, J.-P., Delpech, M., & Grateau, G. (2002). New mutations of CIAS1 that are responsible for Muckle-Wells syndrome and familial cold urticaria: A novel mutation underlies both syndromes. American Journal of Human Genetics, 70(6), 1498–1506. https://doi.org/10.1086/340786
  • El-Zayat, S. R., Sibaii, H., & Mannaa, F. A. (2019). Toll-like receptors activation, signaling, and targeting: An overview. Bulletin of the National Research Centre, 43(1), 1–12. https://doi.org/10.1186/s42269-019-0227-2
  • Eswar, N., Eramian, D., Webb, B., Shen, M. Y., & Sali, A. (2008). Protein structure modeling with MODELLER. In Structural proteomics (pp. 145–159). Humana Press.
  • Feterowski, C., Emmanuilidis, K., Miethke, T., Gerauer, K., Rump, M., Ulm, K., Holzmann, B., & Weighardt, H. (2003). Effects of functional Toll‐like receptor‐4 mutations on the immune response to human and experimental sepsis. Immunology, 109(3), 426–431. https://doi.org/10.1046/j.1365-2567.2003.01674.x
  • Garcia, M. M., Goicoechea, C., Molina-Álvarez, M., & Pascual, D. (2020). Toll-like receptor 4: A promising crossroads in the diagnosis and treatment of several pathologies. European Journal of Pharmacology, 874, 172975. https://doi.org/10.1016/j.ejphar.2020.172975
  • George Priya Doss, C., Nagasundaram, N., Chakraborty, C., Chen, L., & Zhu, H. (2013). Extrapolating the effect of deleterious nsSNPs in the binding adaptability of flavopiridol with CDK7 protein: A molecular dynamics approach. Human Genomics, 7(1), 1–15. https://doi.org/10.1186/1479-7364-7-10
  • Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
  • Ho, S. C., Goh, S. S., & Khoo, D. H. (2003). Association of Graves’ disease with intragenic polymorphism of the thyrotropin receptor gene in a cohort of Singapore patients of multi-ethnic origins. Thyroid, 13(6), 523–528. https://doi.org/10.1089/105072503322238773
  • Jabłońska, A., Studzińska, M., Szenborn, L., Wiśniewska-Ligier, M., Karlikowska-Skwarnik, M., Gęsicki, T., & Paradowska, E. (2020). TLR4 896A/G and TLR9 1174G/A polymorphisms are associated with the risk of infectious mononucleosis. Scientific Reports, 10(1), 1–11. https://doi.org/10.1038/s41598-020-70129-4
  • Jin, M. S., & Lee, J. O. (2008). Structures of the toll-like receptor family and its ligand complexes. Immunity, 29(2), 182–191. https://doi.org/10.1016/j.immuni.2008.07.007
  • Kabsch, W., & Sander, C. (1983). DSSP: Definition of secondary structure of proteins given a set of 3D coordinates. Biopolymers, 22(12), 2577–2637. https://doi.org/10.1002/bip.360221211
  • Kawata, M., & Nagashima, U. (2001). Particle mesh Ewald method for three-dimensional systems with two-dimensional periodicity. Chemical Physics Letters, 340(1-2), 165–172. https://doi.org/10.1016/S0009-2614(01)00393-1
  • Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, O., Nielsen, M., Petersen, B., & Marcatili, P. (2019). NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning. Proteins, 87(6), 520–527. https://doi.org/10.1002/prot.25674
  • Kucukkal, T. G., Petukh, M., Li, L., & Alexov, E. (2015). Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Current Opinion in Structural Biology, 32, 18–24. https://doi.org/10.1016/j.sbi.2015.01.003
  • Kutzner, C., Van Der Spoel, D., Fechner, M., Lindahl, E., Schmitt, U. W., De Groot, B. L., & Grubmüller, H. (2007). Speeding up parallel GROMACS on high‐latency networks. Journal of Computational Chemistry, 28(12), 2075–2084. https://doi.org/10.1002/jcc.20703
  • 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
  • Lobanov, M. Y., Bogatyreva, N. S., & Galzitskaya, O. V. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
  • Lu, C. C., Kuo, H. C., Wang, F. S., Jou, M. H., Lee, K. C., & Chuang, J. H. (2014). Upregulation of TLRs and IL-6 as a marker in human colorectal cancer. International Journal of Molecular Sciences, 16(1), 159–177. https://doi.org/10.3390/ijms16010159
  • Matsushima, N., Tachi, N., Kuroki, Y., Enkhbayar, P., Osaki, M., Kamiya, M., & Kretsinger, R. H. (2005). Structural analysis of leucine-rich-repeat variants in proteins associated with human diseases. Cellular and Molecular Life Sciences : CMLS, 62(23), 2771–2791. https://doi.org/10.1007/s00018-005-5187-z
  • Medzhitov, R., Preston-Hurlburt, P., & Janeway, C. A. (1997). A human homologue of the Drosophila toll protein signals activation of adaptive immunity. Nature, 388(6640), 394–397. https://doi.org/10.1038/41131
  • Mi, H., Ebert, D., Muruganujan, A., Mills, C., Albou, L. P., Mushayamaha, T., & Thomas, P. D. (2021). PANTHER version 16: A revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Research, 49(D1), D394–D403. https://doi.org/10.1093/nar/gkaa1106
  • Misch, E. A., & Hawn, T. R. (2008). Toll-like receptor polymorphisms and susceptibility to human disease. Clinical Science (London, England : 1979), 114(5), 347–360. https://doi.org/10.1042/CS20070214
  • Miyamoto, S., & Kollman, P. A. (1992). Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 13(8), 952–962. https://doi.org/10.1002/jcc.540130805
  • Nie, L., Cai, S. Y., Shao, J. Z., & Chen, J. (2018). Toll-like receptors, associated biological roles, and signaling networks in non-mammals. Frontiers in Immunology, 9, 1523. https://doi.org/10.3389/fimmu.2018.01523
  • Núñez Miguel, R., Wong, J., Westoll, J. F., Brooks, H. J., O'Neill, L. A. J., Gay, N. J., Bryant, C. E., & Monie, T. P. (2007). A dimer of the Toll-like receptor 4 cytoplasmic domain provides a specific scaffold for the recruitment of signalling adaptor proteins. PloS One, 2(8), e788. https://doi.org/10.1371/journal.pone.0000788
  • Ohno, M., Endo, T., Ohta, K., Gunji, K., & Onaya, T. (1995). Point mutations in the thyrotropin receptor in human thyroid tumors. Thyroid, 5(2), 97–100. https://doi.org/10.1089/thy.1995.5.97
  • Ohto, U., Yamakawa, N., Akashi-Takamura, S., Miyake, K., & Shimizu, T. (2012). Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I. The Journal of Biological Chemistry, 287(48), 40611–40617. https://doi.org/10.1074/jbc.M112.404608
  • Oktay, E. O. (2022). Bioinformatics analysis of functional SNPs in human ASAH1 gene related to Farber disease. Russian Journal of Genetics, 58(1), 109–115. https://doi.org/10.1134/S1022795422010070
  • Pandurangan, A. P., Ochoa-Montaño, B., Ascher, D. B., & Blundell, T. L. (2017). SDM: A server for predicting effects of mutations on protein stability. Nucleic Acids Research, 45(W1), W229–W235. https://doi.org/10.1093/nar/gkx439
  • Park, B. S., & Lee, J. O. (2013). Recognition of lipopolysaccharide pattern by TLR4 complexes. Experimental & Molecular Medicine, 45(12), e66-e66. https://doi.org/10.1038/emm.2013.97
  • Park, B. S., Song, D. H., Kim, H. M., Choi, B. S., Lee, H., & Lee, J. O. (2009). The structural basis of lipopolysaccharide recognition by the TLR4–MD-2 complex. Nature, 458(7242), 1191–1195. https://doi.org/10.1038/nature07830
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • Parthiban, V., Gromiha, M. M., & Schomburg, D. (2006). CUPSAT: Prediction of protein stability upon point mutations. Nucleic Acids Research, 34(Web Server issue), W239–W242. https://doi.org/10.1093/nar/gkl190
  • Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., Mooney, S. D., & Radivojac, P. (2020). Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nature Communications, 11(1), 1–13. https://doi.org/10.1038/s41467-020-19669-x
  • Petukh, M., Kucukkal, T. G., & Alexov, E. (2015). On human disease‐causing amino acid variants: Statistical study of sequence and structural patterns. Human Mutation, 36(5), 524–534. https://doi.org/10.1002/humu.22770
  • Pires, D. E., Ascher, D. B., & Blundell, T. L. (2014a). DUET: A server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Research, 42(Web Server issue), W314–W319. https://doi.org/10.1093/nar/gku411
  • Pires, D. E., Ascher, D. B., & Blundell, T. L. (2014b). mCSM: Predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics (Oxford, England), 30(3), 335–342. https://doi.org/10.1093/bioinformatics/btt691
  • Priya Doss, C. G., Chakraborty, C., Chen, L., & Zhu, H. (2014). Integrating in silico prediction methods, molecular docking, and molecular dynamics simulation to predict the impact of ALK missense mutations in structural perspective. BioMed Research International, 2014, 895831. https://doi.org/10.1155/2014/895831
  • Ramensky, V., Bork, P., & Sunyaev, S. (2002). Human non‐synonymous SNPs: Server and survey. Nucleic Acids Research, 30(17), 3894–3900. https://doi.org/10.1093/nar/gkf493
  • Rämisch, S., Weininger, U., Martinsson, J., Akke, M., & André, I. (2014). Computational design of a leucine-rich repeat protein with a predefined geometry. Proceedings of the National Academy of Sciences of the United States of America, 111(50), 17875–17880. https://doi.org/10.1073/pnas.1413638111
  • Santhiya, P., Christian Bharathi, A., & Syed Ibrahim, B. (2020). The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study. Journal of Biomolecular Structure & Dynamics, 38(15), 4471–4482. https://doi.org/10.1080/07391102.2019.1682048
  • Sato, Y., Goto, Y., Narita, N., & Hoon, D. S. (2009). Cancer cells expressing toll-like receptors and the tumor microenvironment. Cancer Microenvironment, 2(S1), 205–214. https://doi.org/10.1007/s12307-009-0022-y
  • 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(Web Server issue), W452–W457. https://doi.org/10.1093/nar/gks539
  • Sneha, P., Kumar Thirumal, D., Tanwar, H., Siva, R., George Priya Doss, C., & Zayed, H. (2017). Structural analysis of G1691S variant in the Human Filamin B gene responsible for Larsen Syndrome: A comparative computational approach. Journal of Cellular Biochemistry, 118(7), 1900–1910. https://doi.org/10.1002/jcb.25920
  • The PyMOL Molecular Graphics System. (2021). Version 2.5.1 Schrödinger, LLC.
  • Thirumal Kumar, D., George Priya Doss, C., Sneha, P., Tayubi, I. A., Siva, R., Chakraborty, C., & Magesh, R. (2017). Influence of V54M mutation in giant muscle protein titin: A computational screening and molecular dynamics approach. Journal of Biomolecular Structure & Dynamics, 35(5), 917–928. https://doi.org/10.1080/07391102.2016.1166456
  • Tonacchera, M., Perri, A., De Marco, G., Agretti, P., Banco, M. E., Di Cosmo, C., Grasso, L., Vitti, P., Chiovato, L., & Pinchera, A. (2004). Low prevalence of thyrotropin receptor mutations in a large series of subjects with sporadic and familial nonautoimmune subclinical hypothyroidism. The Journal of Clinical Endocrinology and Metabolism, 89(11), 5787–5793. https://doi.org/10.1210/jc.2004-1243
  • Tulic, M. K., Hurrelbrink, R. J., Prêle, C. M., Laing, I. A., Upham, J. W., Le Souef, P., Sly, P. D., & Holt, P. G. (2007). TLR4 polymorphisms mediate impaired responses to respiratory syncytial virus and lipopolysaccharide. Journal of Immunology (Baltimore, Md. : 1950), 179(1), 132–140. https://doi.org/10.4049/jimmunol.179.1.132
  • Turner, P. J. (2005). XMGRACE, Version 5.1. 19. Center for Coastal and Land-Margin Research. Oregon Graduate Institute of Science and Technology, 2.
  • Vaure, C., & Liu, Y. (2014). A comparative review of toll-like receptor 4 expression and functionality in different animal species. Frontiers in Immunology, 5, 316. https://doi.org/10.3389/fimmu.2014.00316
  • Venkata Subbiah, H., Ramesh Babu, P., & Subbiah, U. (2020). In silico analysis of non-synonymous single nucleotide polymorphisms of human DEFB1 gene. Egyptian Journal of Medical Human Genetics, 21(1), 1–9. https://doi.org/10.1186/s43042-020-00110-3
  • Venselaar, H., Te Beek, T. A., Kuipers, R. K., Hekkelman, M. L., & Vriend, G. (2010). Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics, 11(1), 1–10. https://doi.org/10.1186/1471-2105-11-548
  • Wang, Z., & Moult, J. (2003). Three‐dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor Vβ domain. Proteins, 53(3), 748–757. https://doi.org/10.1002/prot.10522
  • Zhang, K., Zhou, B., Wang, Y., Rao, L., & Zhang, L. (2013). The TLR4 gene polymorphisms and susceptibility to cancer: A systematic review and meta-analysis. European Journal of Cancer (Oxford, England : 1990), 49(4), 946–954. https://doi.org/10.1016/j.ejca.2012.09.022
  • Zimprich, A., Biskup, S., Leitner, P., Lichtner, P., Farrer, M., Lincoln, S., Kachergus, J., Hulihan, M., Uitti, R. J., Calne, D. B., Stoessl, A. J., Pfeiffer, R. F., Patenge, N., Carbajal, I. C., Vieregge, P., Asmus, F., Müller-Myhsok, B., Dickson, D. W., Meitinger, T., … Gasser, T. (2004). Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron, 44(4), 601–607. https://doi.org/10.1016/j.neuron.2004.11.005

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