References
- Arkhipov, A., Shan, Y., Kim, E. T., & Shaw, D. E. (2014). Membrane interaction of bound ligands contributes to the negative binding cooperativity of the EGF receptor. PLoS Computational Biology, 10(7), e1003742. https://doi.org/https://doi.org/10.1371/journal.pcbi.1003742
- Azimzadeh Irani, M. (2018). Correlation between experimentally indicated and atomistically simulated roles of EGFR N-glycosylation. Molecular Simulation, 44, 743–748.
- Azimzadeh Irani, M., & Ejtehadi, M. R. (2019). GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation. Glycobiology, 29(11), 803–812. https://doi.org/https://doi.org/10.1093/glycob/cwz055
- Azimzadeh Irani, M., Kannan, S., & Verma, C. (2017). Role of N-glycosylation in EGFR ectodomain ligand binding. Proteins, 85(8), 1529–1549. https://doi.org/https://doi.org/10.1002/prot.25314
- Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
- Bulek, K., Swaidani, S., Qin, J., Lu, Y., Gulen, M. F., Herjan, T., Min, B., Kastelein, R. A., Aronica, M., Kosz-Vnenchak, M., & Li, X. (2009). The essential role of single Ig IL-1 receptor-related molecule/Toll IL-1R8 in regulation of Th2 immune response. Journal of Immunology, 182(5), 2601–2609. https://doi.org/https://doi.org/10.4049/jimmunol.0802729
- Colotta, F., Re, F., Muzio, M., Bertini, R., Polentarutti, N., Sironi, M., Giri, J. G., Dower, S. K., Sims, J. E., & Mantovani, A. (1993). Interleukin-1 type II receptor: A decoy target for IL-1 that is regulated by IL-4. Science, 261(5120), 472–475. https://doi.org/https://doi.org/10.1126/science.8332913
- Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., III, Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghoreishi, D., Gilson, M. K., Gohlke, H., Goetz, A. W., Greene, D., Harris, R., Homeyer, N., Izadi, S., Kovalenko, A., Kurtzman, T., Lee, T. S., LeGrand, S., … Kollman, P. A. (2018). AMBER 2018. University of California.
- de Oliveira, C. A. F., Grant, B. J., Zhou, M., & McCammon, J. A. (2011). Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation. PLoS Computational Biology, 7(10), e1002178. https://doi.org/https://doi.org/10.1371/journal.pcbi.1002178
- Dinarello, C. A. (2018a). Overview of the IL-1 family in innate inflammation and acquired immunity. Immunological Reviews, 281(1), 8–27. https://doi.org/https://doi.org/10.1111/imr.12621
- Dinarello, C. A. (2018b). Introduction to the interleukin-1 family of cytokines and receptors: Drivers of innate inflammation and acquired immunity. Immunological Reviews, 281(1), 5–7. https://doi.org/https://doi.org/10.1111/imr.12624
- Dinarello, C. A. (2019a). Interleukin-1 mediated autoinflammation from heart disease to cancer. In Textbook of autoinflammation (pp. 711-725). Springer.
- Dinarello, C. A. (2019b). The IL-1 family of cytokines and receptors in rheumatic diseases. Nature Reviews. Rheumatology, 15(10), 612–632. https://doi.org/https://doi.org/10.1038/s41584-019-0277-8
- Durrant, J. D., & McCammon, J. A. (2011). HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis. Journal of Molecular Graphics & Modelling, 31, 5–9. https://doi.org/https://doi.org/10.1016/j.jmgm.2011.07.008
- Fields, J. K., Günther, S., & Sundberg, E. J. (2019). Structural basis of IL-1 family cytokine signaling. Frontiers in Immunology, 10, 1412 https://doi.org/https://doi.org/10.3389/fimmu.2019.01412
- Freeze, H. H., & Aebi, M. (2005). Altered glycan structures: The molecular basis of congenital disorders of glycosylation. Current Opinion in Structural Biology, 15(5), 490–498. https://doi.org/https://doi.org/10.1016/j.sbi.2005.08.010
- Fuentes, G., Scaltriti, M., Baselga, J., & Verma, C. S. (2011). Synergy between trastuzumab and pertuzumab for human epidermal growth factor 2 (Her2) from colocalization: An in silicobased mechanism. Breast Cancer Research, 13(3), R54. https://doi.org/https://doi.org/10.1186/bcr2888
- Garlanda, C., Dinarello, C. A., & Mantovani, A. (2013). The interleukin-1 family: Back to the future. Immunity, 39(6), 1003–1018. https://doi.org/https://doi.org/10.1016/j.immuni.2013.11.010
- Garlanda, C., Riva, F., Bonavita, E., Gentile, S., & Mantovani, A. (2013). Decoys and regulatory “receptors” of the IL-1/Toll-like receptor Superfamily. Frontiers in Immunology, 4, 180. https://doi.org/https://doi.org/10.3389/fimmu.2013.00180
- Ge, J., Remesh, S. G., Hammel, M., Pan, S., Mahan, A. D., Wang, S., & Wang, X. (2019). Functional relevance of interleukin-1 receptor inter-domain flexibility for cytokine binding and signaling. Structure, 27(8), 1296–1307.e5. https://doi.org/https://doi.org/10.1016/j.str.2019.05.011
- Ge, Y., Huang, M., & Yao, Y-m. (2019). Recent advances in the biology of IL-1 family cytokines and their potential roles in development of sepsis. Cytokine & Growth Factor Reviews, 45, 24–34. https://doi.org/https://doi.org/10.1016/j.cytogfr.2018.12.004
- Grant, B. J., Gorfe, A. A., & McCammon, J. A. (2009). Ras conformational switching: Simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Computational Biology, 5(3), e1000325. https://doi.org/https://doi.org/10.1371/journal.pcbi.1000325
- Günther, S., Deredge, D., Bowers, A. L., Luchini, A., Bonsor, D. A., Beadenkopf, R., Liotta, L., Wintrode, P. L., & Sundberg, E. J. (2017). IL-1 family cytokines use distinct molecular mechanisms to signal through their shared co-receptor. Immunity, 47(3), 510–523.e4. https://doi.org/https://doi.org/10.1016/j.immuni.2017.08.004
- Hamelberg, D., de Oliveira, C. A. F., & McCammon, J. A. (2007). Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. The Journal of Chemical Physics, 127(15), 155102. https://doi.org/https://doi.org/10.1063/1.2789432
- Hamelberg, D., Mongan, J., & McCammon, J. A. (2004). Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. The Journal of Chemical Physics, 120(24), 11919–11929. https://doi.org/https://doi.org/10.1063/1.1755656
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD – Visual Molecular Dynamics. Journal of Molecular Graphics, 14(1), 33–38.
- Joao, H. C., & Dwek, R. A. (1993). Effects of glycosylation on protein structure and dynamics in ribonuclease B and some of its individual glycoforms. European Journal of Biochemistry, 218(1), 239–244. https://doi.org/https://doi.org/10.1111/j.1432-1033.1993.tb18370.x
- Kaszuba, K., Michał, G., Adam, O., Reinis, D., Tomasz, R., Kai, S., Ünal, C., & Vattulainen, I. (2015). N-glycosylation as determinant of epidermal growth factor receptor conformation in membranes. Proceedings of the National Academy of Sciences, 112, 4334–4339.
- Kirschner, K. N., Yongye, A. B., Tschampel, S. M., González-Outeiriño, J., Daniels, C. R., Lachele Foley, B., & Woods, R. J. (2008). GLYCAM06: A generalizable biomolecular force field. Carbohydrates. Journal of Computational Chemistry, 29(4), 622–655. https://doi.org/https://doi.org/10.1002/jcc.20820
- Krumm, B., Xiang, Y., & Deng, J. (2014). Structural biology of the IL-1 superfamily: Key cytokines in the regulation of immune and inflammatory responses. Protein Science, 23(5), 526–538. https://doi.org/https://doi.org/10.1002/pro.2441
- Leach, A. R. (2001). Molecular modelling: Principles and applications. Prentice Hall.
- Lee, H. S., Qi, Y., & Im, W. (2015). Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. Scientific Reports, 5, 8926. https://doi.org/https://doi.org/10.1038/srep08926
- Lee, J.-H., Wang, L.-C., Yu, H.-H., Lin, Y.-T., Yang, Y.-H., & Chiang, B.-L. (2010). Type I IL-1 receptor (IL-1RI) as potential new therapeutic target for bronchial asthma. Mediators of Inflammation, 2010, 567351–567351. https://doi.org/https://doi.org/10.1155/2010/567351
- Loncharich, R. J., Brooks, B. R., & Pastor, R. W. (1992). Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers, 32(5), 523–535. https://doi.org/https://doi.org/10.1002/bip.360320508
- Lopez-Castejon, G., & Brough, D. (2011). Understanding the mechanism of IL-1β secretion. Cytokine & Growth Factor Reviews, 22(4), 189–195. https://doi.org/https://doi.org/10.1016/j.cytogfr.2011.10.001
- Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00255
- Mantovani, A., Dinarello, C. A., Molgora, M., & Garlanda, C. (2019). IL-1 and related cytokines in innate and adaptive immunity in health and disease. Immunity, 50(4), 778–795.
- Mariño, K., Bones, J., Kattla, J. J., & Rudd, P. M. (2010). A systematic approach to protein glycosylation analysis: A path through the maze. Nature Chemical Biology, 6(10), 713–723. https://doi.org/https://doi.org/10.1038/nchembio.437
- Pastor, R. W., Brooks, B. R., & Szabo, A. (1988). An analysis of the accuracy of Langevin and molecular dynamics algorithms. Molecular Physics, 65(6), 1409–1419. https://doi.org/https://doi.org/10.1080/00268978800101881
- Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1-3), 1–41.
- Peters, V. A., Joesting, J. J., & Freund, G. G. (2013). IL-1 receptor 2 (IL-1R2) and its role in immune regulation. Brain, Behavior, and Immunity, 32, 1–8. https://doi.org/https://doi.org/10.1016/j.bbi.2012.11.006
- Pierce, L. C. T., Salomon-Ferrer, R., de Oliveira, C. A. F., McCammon, J. A., & Walker, R. C. (2012). Routine access to millisecond time scale events with accelerated molecular dynamics. Journal of Chemical Theory and Computation, 8(9), 2997–3002. https://doi.org/https://doi.org/10.1021/ct300284c
- Poger, D., & Mark, A. E. (2014). Activation of the epidermal growth factor receptor: A series of twists and turns. Biochemistry, 53(16), 2710–2721. https://doi.org/https://doi.org/10.1021/bi401632z
- Quiniou, C., Sapieha, P., Lahaie, I., Hou, X., Brault, S., Beauchamp, M., Leduc, M., Rihakova, L., Joyal, J.-S., Nadeau, S., Heveker, N., Lubell, W., Sennlaub, F., Gobeil, F., Miller, G., Pshezhetsky, A. V., & Chemtob, S. (2008). Development of a novel noncompetitive antagonist of IL-1 receptor. Journal of Immunology, 180(10), 6977–6987. https://doi.org/https://doi.org/10.4049/jimmunol.180.10.6977
- Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
- Sanders, J. M., Wampole, M. E., Thakur, M. L., & Wickstrom, E. (2013). Molecular determinants of epidermal growth factor binding: A molecular dynamics study. PLoS One, 8(1), e54136.
- Schrodinger LLC. (2010). The PyMOL molecular graphics system. Version 1, (5). http://pymol.sourceforge.net/faq.html#CITE
- Schulz, B. L. (2012). Beyond the sequon: Sites of N-glycosylation (pp. 21–39). INTECH.
- Schwarz, F., & Aebi, M. (2011). Mechanisms and principles of N-linked protein glycosylation. Current Opinion in Structural Biology, 21(5), 576–582. https://doi.org/https://doi.org/10.1016/j.sbi.2011.08.005
- Shaftel, S. S., Sue, W., Griffin, T., & O’Banion, M. K. (2008). The role of interleukin-1 in neuroinflammation and Alzheimer disease: An evolving perspective. Journal of Neuroinflammation, 5(1), 7. https://doi.org/https://doi.org/10.1186/1742-2094-5-7
- Shental-Bechor, D., Levy, Y. (2008). Effect of glycosylation on protein folding: A close look at thermodynamic stabilization. Proceedings of the National Academy of Sciences, 105, 8256–8261.
- Sims, J. E., & Smith, D. E. (2010). The IL-1 family: Regulators of immunity. Nature Reviews. Immunology, 10(2), 89–102. https://doi.org/https://doi.org/10.1038/nri2691
- Sivasubramanian, A., Chao, G., Pressler, H. M., Wittrup, K. D., & Gray, J. J. (2006). Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure, 14(3), 401–414. https://doi.org/https://doi.org/10.1016/j.str.2005.11.022
- Slieker, L. J., Martensen, T. M., & Lane, M. D. (1986). Synthesis of epidermal growth factor receptor in human A431 cells. Glycosylation-dependent acquisition of ligand binding activity occurs post-translationally in the endoplasmic reticulum. The Journal of Biological Chemistry, 261(32), 15233–15241.
- Stanley, P., Taniguchi, N., & Aebi, M. (2017). N-glycans. In Essentials of glycobiology [Internet] (3rd ed.). Cold Spring Harbor Laboratory Press.
- Taylor, M. E., & Drickamer, K. (2011). Introduction to glycobiology. Oxford University Press.
- Thomas, C., Bazan, J. F., & Garcia, K. C. (2012). Structure of the activating IL-1 receptor signaling complex. Nature Structural & Molecular Biology, 19, 455-457.
- Vigers, G. P., Anderson, L. J., Caffes, P., & Brandhuber, B. J. (1997). Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1beta. Nature, 386(6621), 190–194. https://doi.org/https://doi.org/10.1038/386190a0
- Vigers, G. P., Dripps, D. J., Edwards, C. K., & Brandhuber, B. J. (2000). X-ray crystal structure of a small antagonist peptide bound to interleukin-1 receptor type 1. The Journal of Biological Chemistry, 275(47), 36927–36933. https://doi.org/https://doi.org/10.1074/jbc.M006071200
- Wald, D., Qin, J., Zhao, Z., Qian, Y., Naramura, M., Tian, L., Towne, J., Sims, J. E., Stark, G. R., & Li, X. (2003). SIGIRR, a negative regulator of Toll-like receptor-interleukin 1 receptor signaling. Nature Immunology, 4(9), 920–927. https://doi.org/https://doi.org/10.1038/ni968
- Wang, D., Zhang, S., Li, L., Liu, X., Mei, K., & Wang, X. (2010). Structural insights into the assembly and activation of IL-1β with its receptors. Nature Immunology, 11(10), 905–911. https://doi.org/https://doi.org/10.1038/ni.1925
- Wißbrock, A., Goradia, N. B., Kumar, A., Paul George, A. A., Kühl, T., Bellstedt, P., Ramachandran, R., Hoffmann, P., Galler, K., Popp, J., Neugebauer, U., Hampel, K., Zimmermann, B., Adam, S., Wiendl, M., Krönke, G., Hamza, I., Heinemann, S. H., Frey, S., … Imhof, D. (2019). Structural insights into heme binding to IL-36α proinflammatory cytokine. Scientific Reports, 9(1), 1–14. https://doi.org/https://doi.org/10.1038/s41598-019-53231-0
- Woods Group. (2005–XXXX) GLYCAM web. Complex Carbohydrate Research Center, University of Georgia, Athens, GA. http://glycam.org. (2005-2020).
- Woods, R. J. (2018). Predicting the structures of glycans, glycoproteins, and their complexes. Chemical Reviews, 118(17), 8005–8024. https://doi.org/https://doi.org/10.1021/acs.chemrev.8b00032
- Yadav, B. S., Chaturvedi, N., Yadav, P. K., Marina, N., Ganash, M., Barreto, G. E., Ashraf, G. M., Ahmad, K., & Baig, M. H. (2019). Protein modeling, molecular network and molecular dynamics study of newly sequenced interleukin-18 (IL-18) gene in Mus musculus. Journal of Cellular Physiology, 234(8), 14285–14295. https://doi.org/https://doi.org/10.1002/jcp.28127
- Yen, H.-Y., Liu, Y.-C., Chen, N.-Y., Tsai, C.-F., Wang, Y.-T., Chen, Y.-J., Hsu, T.-L., Yang, P.-C., & Wong, C.-H. (2015). Effect of sialylation on EGFR phosphorylation and resistance to tyrosine kinase inhibition. Proceedings of the National Academy of Sciences, 112, 6955–6960.