Molecular dynamics at the receptor level of immunodominant myelin basic protein epitope 87-99 implicated in multiple sclerosis and its antagonists altered peptide ligands: Triggering of immune response

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 2, 2007, Pages 471-481

  Mantzourani, Efthimia D ^a,b   Platts, James A ^c   Brancale, Andrea ^d   Mavromoustakos, Thomas M ^a   Tselios, Theodore V ^b  

^a INSTITUTE OF BIOLOGY   (Greece)

^b UNIVERSITY OF PATRAS   (Greece)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Altered peptide ligands; Molecular dynamics; Molecular recognition; Peptides; Receptors

Indexed keywords

AMINO ACIDS; ANTIGENS; IMMUNOLOGY; LIGANDS; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION;

IMMUNE RESPONSE; IMMUNODOMINANT MYELIN BASIC PROTEIN (MBP) EPITOPE; MULTIPLE SCLEROSIS; RECEPTOR LEVEL; RECEPTORS; X-RAY STRUCTURE;

PEPTIDES;

ALANINE; ARGININE; EPITOPE; HISTIDINE; HLA DR2 ANTIGEN; LEUKOCYTE ANTIGEN; LIGAND; MYELIN BASIC PROTEIN; PEPTIDE; PHENYLALANINE; T LYMPHOCYTE RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; COMPLEX FORMATION; HYDROGEN BOND; IMMUNE RESPONSE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MULTIPLE SCLEROSIS; PRIORITY JOURNAL; PROTEIN STRUCTURE; RECEPTOR BINDING; X RAY;

COMPUTER SIMULATION; HLA-DR2 ANTIGEN; IMMUNODOMINANT EPITOPES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MULTIPLE SCLEROSIS; MYELIN BASIC PROTEINS; PEPTIDE FRAGMENTS; PROTEIN CONFORMATION; RECEPTORS, ANTIGEN, T-CELL; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 34548306797     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2007.02.004     Document Type: Article

References (62)

1. Mantzourani E.D., Mavromoustakos T.M., Platts J.A., Matsoukas J.M., and Tselios T. Structural requirements for binding of myelin basic protein (MBP) peptides to MHC II: Effects on immune regulation. Curr. Med. Chem. 12 (2005) 1521-1535
2. Margulies D.H. Interactions of TCRs with MHC-peptide complexes: a quantitative basis for mechanistic models. Curr. Opin. Immunol. 9 (1997) 390
3. Von Boehmer H. Positive and negative selection of the alpha beta T-cell repertoire in vivo. Curr. Opin. Immunol. 3 (1991) 210
4. Bell R.B., Lindsey J.W., Sobel R.A., Hodgkinson S., Steinman L., and Diverse T. Cell receptor V beta gene usage in the central nervous system in experimental allergic encephalomyelitis. J. Immunol. 150 (1993) 4085
5. MHC sequence consortium. Complete sequence and gene map of a human MHC complex. Nature 1999, 401, 921.
6. Compston A., and Coles A. Multiple sclerosis. Lancet 359 (2002) 1221
7. Prat E., and Martin R. The immunopathogenesis of MS. J. Rehab. Res. Devel. 39 (2002) 187-200
8. Barcellos L., and Thomson G. Genetic analysis of MS in Europeans. J. Neuroimmunol. 143 (2003) 1-6
9. Muraro P.A., Vergelli M., Kalbus M., Banks D.E., Nagle J., Tranquill L.R., Nepom G.T., Biddison W.E., McFarland H.F., and Martin R. Immunodominance of a low-affinity major histocompatibility complex-binding myelin basic protein epitope in HLA-DR4 subjects is associated with a restricted T cell receptor repertoire. J. Clin. Invest. 100 (1997) 339-349
10. Madden D.R. The three-dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13 (1995) 587
11. Steinman L. Assessment of animal models for MS and demyelinating disease in the design of rational therapy. Neuron 24 (1999) 511-514
12. Zamvil S.S., and Steinman L. The T lymphocyte in experimental allergic encephalomyelitis. Annu. Rev. Immunol. 8 (1990) 579-621
13. Ota K., Matsui M., Milford E.L., Mackin G.A., Weiner H.L., and Hafler D.A. T-cell recognition of an immunodominant myelin basic protein epitope in multiple sclerosis. Nature 346 (1990) 183-187
14. Valli A., Sette A., Kappos L., Oseroff C., Sidney J., Miescher G., Hochberger M., Albert E.D., and Adorini L. Binding of myelin basic protein peptides to human histocompatibility leukocyte antigen class II molecules and their recognition by T cells from multiple sclerosis patients. J. Clin. Invest. 91 (1993) 616-628
15. Martin R., Howell M.D., Jaraquemada D., Flerlage M., Richert J., Brostoff S., Long E.O., McFarlin D.E., and McFarland H.F. A myelin basic protein peptide is recognized by cytotoxic T cells in the context of four HLA-DR types associated with multiple sclerosis. J. Exp. Med. 173 (1991) 19-24
16. Davis M.M., et al. Ligand recognition by αβ T-cell receptors. Annu. Rev. Immunol. 16 (1998) 523-544
17. Rudolph M.G., and Wilson I.A. The specificity of TCR/pMHC interaction. Curr. Opin. Immunol. 14 (2002) 1043-1052
18. Hare B.J., et al. Structure, specificity and CDR mobility of a class II restricted single-chain T-cell receptor. Nature Struct. Biol. 6 (1999) 574-581
19. Willcox B.E., et al. TCR binding to peptide-MHC stabilizes a flexible recognition interface. Immunity 10 (1999) 357-365
20. Smith K.J., Pyrdol J., Gauthier L., Wiley D.C., and Wucherpfennig K.W. Crystal structure of HLA-DR2 (DRA*0101, DRB1*1501) complexed with a peptide from human myelin basic protein. J. Exp. Med. 188 8 (1998) 1511
21. Hahn M., Nicholson M.J., Pyrdol J., and Wucherpfennig K.W. Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor. Nat. Immunol. 6 5 (2005) 490-496
22. Wucherpfennig K.W., Sette A., Southwood S.S., Oseroff S.C., Matsui M., Strominger J.L., and Haffler D.A. Structural requirements for binding of an immunodominant myelin basic protein peptide to DR2 isotypes and for its recognition by human T cell clones. J. Exp. Med. 179 (1994) 279-290
23. Wucherpfennig K.W., Zhang J., Witek C., Matsui M., Modabber Y., Ota K., and Hafler D.A. Clonal expansion and persistence of human T cells specific for an immunodominant myelin basic protein peptide. J. Immunol. 152 (1994) 5581-5592
24. Garcia K.C., Degano M., Pease L.R., Huang M., Peterson P.A., Teyton L., and Wilson I.A. Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen. Science 279 (1998) 1166-1172
25. Stewat-Jones G.B., McMichael A.J., Bell J.I., Stuart D.I., and Jones E.Y. A structural basis for immunodominant human T cell receptor recognition. Nat. Immunol. 8 (2003) 403-411
26. Hennecke J., Carfi A., and Wiley D.C. Structure of a covalently stabilized complex of a human αβ T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1. EMBO J. 19 (2000) 5611-5624
27. Li Y., Huang Y., Lue J., Quandt J.A., Martin R., and Mariuzza R.A. Structure of a human autoimmune TCR bound to a myelin basic protein self-peptide and a multiple sclerosis-associated MHC class II molecule. EMBO 24 (2005) 2968-2979
28. 87-99. Bioorg. Med. Chem. 8 (2000) 1903-1909
29. 87-99 associated with Multiple Sclerosis, 2001.
30. 87-99. J. Mol. Graph. Mod. 25/1 (2005) 17-29
31. Mantzourani E.D., Tselios T.V., Golič Grdadolnik S., Platts J.A., Brancale A., Deraos G., Matsoukas J.M., and Mavromoustakos T.M. Comparison of proposed putative active conformations of linear altered peptide ligands of myelin basic protein epitope 87-99 by spectroscopic and modelling studies: the role of position 91 and 96 in T-cell receptor activation. J. Med. Chem. 49 23 (2006) 6683-6691
32. Nicklaus M.C., Wang S., Driscoll J.S., and Milne G.W. Conformational changes of small molecules binding to proteins. Bioorg. Med. Chem. 3 4 (1995) 411-428
33. Wan S., Coveney P., and Flower D.R. Large scale molecular dynamics simulations of HLA-A*0201 complexed with a tumour-specific antigenic peptide: can the _3 and _2m domains be neglected?. J. Comput. Chem. 25 (2004) 1803-1813
34. Karin N., Mitchell D.J., Brocke S., Ling N., and Steinman L. Reversal of experimental autoimmune encephalomyelitis by a soluble peptide variant of a myelin basic protein epitope: T cell receptor antagonism and reduction of interferon 3′ and tumor necrosis factor cr production. J. Exp. Med. 180 (1994) 2227-2237
35. 83-96.
36. Berendsen H.J.C., Van der Spoel D., and Van Drunen R. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91 (1995) 43-56
37. Lindahl E., Hess B., and Van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
38. Van Gunsteren W.F., Billeter S.R., Eising A.A., Hünenberger P.H., Krüger P., Mark A.E., Scott W.R.P., and Tironi I.G. Biomolecular Simulation: the GROMOS96 manual and user guide. Zürich, Switzerland: Hochschulverlag AG an der ETH Zürich. (1996)
39. Hockney R.W., Goel S.P.J., and Eastwood J.W. Quite high resolution computer models of a plasma J. Comp. Phys. 14 (1974) 148-158
40. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G., and Lincs E.M. A linear constraint solver for molecular simulations. J. Comp. Chem. 18 (1997) 1463-1472
41. Van Gunsteren W.F., and Berendsen H.J.C. Gromos-87 manual. Biomos BV Nijenborgh 4, 9747 AG Groningen. The Netherlands (1987)
42. Van Buuren A.R., Marrink S.J., and Berendsen H.J.C. A molecular dynamics study of the decane/water interface. J. Phys. Chem. 97 (1993) 9206-9212
43. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
44. Van Buuren A.R., and Berendsen H.J.C. Molecular dynamics simulation of the stability of a 22 residue alpha-helix in water and 30% trifluoroethanol. Biopolymers 33 (1993) 1159-1166
45. Liu H., M̈uller-Plathe F., and Van Gunsteren W.F. A force field for liquid dimethyl sulfoxide and liquid proporties of liquid dimethyl sulfoxide calculated using molecular dynamics simulation. J. Am. Chem. Soc. 117 (1995) 4363-4366
46. Van der Spoel D., Van Buuren A.R., Tieleman D.P., and Berendsen H.J.C. Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions. J. Biomol. NMR 8 (1996) 229-238
47. Smith P.E., and Van Gunsteren W.F. The viscosity of spc and spc/e water. Comp. Phys. Comm. 215 (1993) 315-318
48. Bekker H., Dijkstra E.J., Renardus M.K.R., and Berendsen H.J.C. An efficient, box shape independent non-bonded force and virial algorithm for molecular dynamics. Mol. Sim. 14 (1995) 137-152
49. Darden T., York D., and Pedersen L. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
50. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. A smooth particle mesh ewald potential. J. Chem. Phys. 103 (1995) 8577-8592
51. Nose S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52 (1984) 255-268
52. Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31 (1985) 1695-1697
53. Helix Computation and Visualization Facility http://www.helix.cf.ac.uk/.
54. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
55. Chemical Computing Group Inc. 1010. Sherbrooke Street W, Suite 910; Montreal, Quebec; Canada H3A 2R7.
56. SVL code exchange site for MOE Trade Mark user community http://svl.chemcomp.com/.
57. Fraczkiewicz R., and Braun W. J. Comp. Chem. 19 (1998) 319
58. R. Fraczkiewicz, W. Braun. A New Efficient Algorithm for Calculating Solvent Accessible Surface Areas of Macromolecules, ECCC3 1996, Northern Illinois Univ.
59. Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., and Kollman P.A. A second-generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117 (1995) 5179-5197
60. Matsoukas J., Apostolopoulos V., Kalbacher H., Papini A.M., Tselios T., Chatzantoni K., Biagioli T., Lolli F., Deraos S., Papathanassopoulos P., Troganis A., Mantzourani E., Mavromoustakos T., and Mouzaki A. Design and synthesis of a novel potent myelin basic protein epitope 87-99 cyclic analogue: enhanced stability and biological properties of mimics render them a potentially new class of immunomodulators. J. Med. Chem. 48 (2005) 1470-1480
61. Vergelli M., Hemmer B., Utz U., Vogt A., Kalbus M., Nanquill N., Conlon P., Ling N., Steinman L., McFarland H., and Martin R. Differential activation of human autoreactive T cell clones by altered peptide ligands derived from myelin basic protein peptide (87-99). Eur. J. Immunol. 26 (1996) 2624-2634
62. Falcone M., and Bloom B.R. J. Exp. Med. 185 5 (1997) 901-907