344
Views
5
CrossRef citations to date
0
Altmetric
Research Articles

In silico study of the association of the HLA-A*31:01 allele (human leucocyte antigen allele 31:01) with neuroantigenic epitopes of PLP (proteolipid protein), MBP (myelin basic protein) and MOG proteins (myelin oligodendrocyte glycoprotein) for studying the multiple sclerosis disease pathogenesis

, &
Pages 2526-2542 | Received 03 Jan 2020, Accepted 25 Mar 2020, Published online: 13 Apr 2020

References

  • Abualrous, E. T., Saini, S. K., Ramnarayan, V. R., Ilca, F. T., Zacharias, M., & Springer, S. (2015). The carboxy terminus of the ligand peptide determines the stability of the MHC class I molecule H-2Kb: A combined molecular dynamics and experimental study. PloS One, 10(8), e0135421. doi:10.1371/journal.pone.0135421
  • Amor, S., Groome, N., Linington, C., Morris, M. M., Dornmair, K., Gardinier, M. V., Matthieu, J. M., & Baker, D. (1994). Identification of epitopes of myelin oligodendrocyte glycoprotein for the induction of experimental allergic encephalomyelitis in SJL and Biozzi AB/H mice. Journal of Immunology (Baltimore, Md. : 1950), 153(10), 4349–4356.
  • Basu, S., & Sen, S. (2013). Do homologous thermophilic–mesophilic proteins exhibit similar structures and dynamics at optimal growth temperatures? a molecular dynamics simulation study. Journal of Chemical Information and Modeling, 53(2), 423–434. doi:10.1021/ci300474h
  • Borghans, J. A., Beltman, J. B., & De Boer, R. J. (2004). MHC polymorphism under host-pathogen coevolution. Immunogenetics, 55(11), 732–739. doi:10.1007/s00251-003-0630-5
  • Boyle, L. H., Traherne, J. A., Plotnek, G., Ward, R., & Trowsdale, J. (2007). Splice variation in the cytoplasmic domains of myelin oligodendrocyte glycoprotein affects its cellular localisation and transport 1. Journal of Neurochemistry, 102(6), 1853–1862. doi:10.1111/j.1471-4159.2007.04687.x
  • Case, D., Babin, V., Berryman, J., Betz, R., Cai, Q., Cerutti, D., … Gohlke, H. (2014). AMBER 14 Reference Manual, 2014. Table of Contents Graphic, 1(2), 3.
  • Collins, E. J., Garboczi, D. N., Karpusas, M. N., & Wiley, D. C. (1995). The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain. Proceedings of the National Academy of Sciences, 92(4), 1218–1221. doi:10.1073/pnas.92.4.1218
  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅ log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • Denic, A., Wootla, B., & Rodriguez, M. (2013). CD8+ T cells in multiple sclerosis. Expert Opinion on Therapeutic Targets, 17(9), 1053–1066. doi:10.1517/14728222.2013.815726
  • DiBrino, M., Parker, K. C., Shiloach, J., Knierman, M., Lukszo, J., Turner, R. V., Biddison, W. E., & Coligan, J. E. (1993). Endogenous peptides bound to HLA-A3 possess a specific combination of anchor residues that permit identification of potential antigenic peptides. Proceedings of the National Academy of Sciences, 90(4), 1508–1512. doi:10.1073/pnas.90.4.1508
  • Falk, K., Rötzschke, O., Takiguchi, M., Grahovac, B., Gnau, V., Stevanović, S., Jung, G., & Rammensee, H.-G. (1994). Peptide motifs of HLA-A1,-A11,-A31, and-A33 molecules. Immunogenetics, 40(3), 238–241. doi:10.1007/BF00167086
  • Friese, M. A., & Fugger, L. (2005). Autoreactive CD8+ T cells in multiple sclerosis: A new target for therapy? Brain, 128(8), 1747–1763. doi:10.1093/brain/awh578
  • Gaba, M., Gaba, P., Singh, S., & Gupta, G. (2010). An overview on molecular docking. International Journal of Drug Development Research, 2(2), 219–231.
  • Hakenberg, J., Nussbaum, A. K., Schild, H., Rammensee, H.-G., Kuttler, C., Holzhütter, H.-G., Kloetzel, P.-M., Kaufmann, S. H. E., & Mollenkopf, H.-J. (2003). MAPPP: MHC class I antigenic peptide processing prediction. Applied Bioinformatics, 2(3), 155–158.
  • Hassan, M. I., & Ahmad, F. (2011). Structural diversity of class I MHC-like molecules and its implications in binding specificities. Advances in protein chemistry and structural biology (Vol. 83, pp. 223–270). Elsevier.
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. doi:10.1063/1.445869
  • Kim, Y., Ponomarenko, J., Zhu, Z., Tamang, D., Wang, P., Greenbaum, J., Lundegaard, C., Sette, A., Lund, O., Bourne, P. E., Nielsen, M., & Peters, B. (2012). Immune epitope database analysis resource. Nucleic Acids Research, 40(W1), W525–W530. doi:10.1093/nar/gks438
  • Klein, J., & Sato, A. (2000). The HLA system. New England Journal of Medicine, 343(10), 702–709. doi:10.1056/NEJM200009073431006
  • Kumar, A., Cocco, E., Atzori, L., Marrosu, M. G., & Pieroni, E. (2013). Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: A molecular dynamics simulation study. PloS One., 8(3), e59711. doi:10.1371/journal.pone.0059711
  • Lafuente, E. M., & Reche, P. A. (2009). Prediction of MHC-peptide binding: A systematic and comprehensive overview. Current Pharmaceutical Design, 15(28), 3209–3220. doi:10.2174/138161209789105162
  • 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. doi:10.1107/S0021889892009944
  • Lemus, H. N., Warrington, A. E., & Rodriguez, M. (2018). Multiple sclerosis: Mechanisms of disease and strategies for myelin and axonal repair. Neurologic Clinics, 36(1), 1–11. doi:10.1016/j.ncl.2017.08.002
  • London, N., Raveh, B., Cohen, E., Fathi, G., & Schueler-Furman, O. (2011). Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions. Nucleic Acids Research, 39(suppl_2), W249–W253. doi:10.1093/nar/gkr431
  • Mage, M. G., Dolan, M. A., Wang, R., Boyd, L. F., Revilleza, M. J., Robinson, H., Natarajan, K., Myers, N. B., Hansen, T. H., & Margulies, D. H. (2012). The peptide-receptive transition state of MHC class I molecules: Insight from structure and molecular dynamics. The Journal of Immunology, 189(3), 1391–1399. doi:10.4049/jimmunol.1200831
  • Matsumura, M., Fremont, D. H., Peterson, P. A., & Wilson, I. A. (1992). Emerging principles for the recognition of peptide antigens by MHC class I molecules. Science, 257(5072), 927–934. doi:10.1126/science.1323878
  • McMahon, R. M., Friis, L., Siebold, C., Friese, M. A., Fugger, L., & Jones, E. Y. (2011). Structure of HLA-A* 0301 in complex with a peptide of proteolipid protein: Insights into the role of HLA-A alleles in susceptibility to multiple sclerosis. Acta Crystallographica Section D Biological Crystallography, 67(5), 447–454. doi:10.1107/S0907444911007888
  • Messaoudi, A., Belguith, H., & Hamida, J. B. (2013). Homology modeling and virtual screening approaches to identify potent inhibitors of VEB-1 β-lactamase. Theoretical Biology and Medical Modelling, 10(1), 22. doi:10.1186/1742-4682-10-22
  • Michielin, O., Blanchets, J.-S., Fagerberg, T., Valmori, D., Rubio-Godoy, V., Speiser, D., … Gairin, J.-E. (2005). Tinkering with nature: The tale of optimizing peptide based cancer vaccines. Tumor Immunology and Cancer Vaccines (pp. 267–291). Springer.
  • Miles, J. J., Elhassen, D., Borg, N. A., Silins, S. L., Tynan, F. E., Burrows, J. M., Purcell, A. W., Kjer-Nielsen, L., Rossjohn, J., Burrows, S. R., & McCluskey, J. (2005). CTL recognition of a bulged viral peptide involves biased TCR selection. The Journal of Immunology, 175(6), 3826–3834. doi:10.4049/jimmunol.175.6.3826
  • Muñoz-Culla, M., Irizar, H., & Otaegui, D. (2013). The genetics of multiple sclerosis: Review of current and emerging candidates. The Application of Clinical Genetics, 6, 63–73. doi:10.2147/TACG.S29107
  • Narzi, D., Becker, C. M., Fiorillo, M. T., Uchanska-Ziegler, B., Ziegler, A., & Böckmann, R. A. (2012). Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides. Journal of Molecular Biology, 415(2), 429–442. doi:10.1016/j.jmb.2011.11.021
  • Neefjes, J., Jongsma, M. L., Paul, P., & Bakke, O. (2011). Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nature Reviews Immunology, 11(12), 823–836. doi:10.1038/nri3084
  • Persson, K., & Schneider, G. (2000). Three-dimensional structures of MHC class I-peptide complexes: Implications for peptide recognition. Archivum Immunologiae et Therapiae Experimentalis, 48(3), 135–142.
  • Riedhammer, C., & Weissert, R. (2015). Antigen presentation, autoantigens, and immune regulation in multiple sclerosis and other autoimmune diseases. Frontiers in Immunology, 6, 322. doi:10.3389/fimmu.2015.00322
  • Rigney, E., Kojima, M., Glithero, A., & Elliott, T. (1998). A soluble major histocompatibility complex class I peptide-binding platform undergoes a conformational change in response to peptide epitopes. Journal of Biological Chemistry, 273(23), 14200–14204. doi:10.1074/jbc.273.23.14200
  • Sali, A., Sánchez, R., & Badretdinov, A. (1994). MODELLER, A protein structure modeling program. The Rockefeller University. doi:http://salilab.org/modeller/
  • Saper, M., Bjorkman, P., & Wiley, D. (1991). Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 Å resolution. Journal of Molecular Biology, 219(2), 277–319. doi:10.1016/0022-2836(91)90567-P
  • Sieker, F., May, A., & Zacharias, M. (2009). Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules. Current Protein & Peptide Science, 10(3), 286–296. doi:10.2174/138920309788452191
  • Sieker, F., Springer, S., & Zacharias, M. (2006). Comparative molecular dynamics analysis of tapasin‐dependent and‐independent MHC class I alleles. Protein Science, 16(2), 299–308. doi:10.1110/ps.062568407
  • Sinha, S., Boyden, A. W., Itani, F. R., Crawford, M. P., & Karandikar, N. J. (2015). CD8+ T-cells as immune regulators of multiple sclerosis. Frontiers in Immunology, 6, 619. doi:10.3389/fimmu.2015.00619
  • Siu, C. R., Balsor, J. L., Jones, D. G., & Murphy, K. M. (2015). Classic and Golli Myelin Basic Protein have distinct developmental trajectories in human visual cortex. Frontiers in Neuroscience, 9, 138. doi:10.3389/fnins.2015.00138
  • Sospedra, M., & Martin, R. (2005). Immunology of multiple sclerosis. Annual Review of Immunology, 23(1), 683–747. doi:10.1146/annurev.immunol.23.021704.115707
  • Takiguchi, M., Matsuda, T., & Tomiyama, H. (2000). Polarity of the P1 anchor residue determines peptide binding specificity between HLA‐A* 3101 and HLA‐A* 3303. Tissue Antigens, 56(6), 501–506. doi:10.1034/j.1399-0039.2000.560603.x
  • van Deutekom, H. W., & Keşmir, C. (2015). Zooming into the binding groove of HLA molecules: Which positions and which substitutions change peptide binding most?. Immunogenetics, 67(8), 425–436. doi:10.1007/s00251-015-0849-y
  • Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. "Protein Engineering, Design and Selection"", 8(2), 127–134. doi:10.1093/protein/8.2.127
  • Weiser, J., Shenkin, P. S., & Still, W. C. (1999). Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry, 20(2), 217–230. doi:10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
  • Weissert, R., Kuhle, J., de Graaf, K. L., Wienhold, W., Herrmann, M. M., Müller, C., Forsthuber, T. G., Wiesmüller, K.-H., & Melms, A. (2002). High immunogenicity of intracellular myelin oligodendrocyte glycoprotein epitopes. The Journal of Immunology, 169(1), 548–556. doi:10.4049/jimmunol.169.1.548
  • Wieczorek, M., Abualrous, E. T., Sticht, J., Álvaro-Benito, M., Stolzenberg, S., Noé, F., & Freund, C. (2017). Major histocompatibility complex (MHC) class I and MHC class II proteins: Conformational plasticity in antigen presentation. Frontiers in Immunology, 8, 292. doi:10.3389/fimmu.2017.00292
  • Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server), W407–W410. doi:10.1093/nar/gkm290
  • Yu, H., Wang, M-j., Xuan, N-x., Shang, Z-c., & Wu, J. (2015). Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides. Journal of Zhejiang University-SCIENCE B, 16(10), 883–896. doi:10.1631/jzus.B1500106
  • Zacharias, M., & Springer, S. (2004). Conformational flexibility of the MHC class I α1-α2 domain in peptide bound and free states: A molecular dynamics simulation study. Biophysical Journal, 87(4), 2203–2214. doi:10.1529%2Fbiophysj.104.044743

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.