NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: Structural implications for the MHC II (I-A^u)-peptide complex from docking calculations

Authors: Tzakos, Andreas G.¹; Fuchs, Patrick²; van Nuland, Nico A. J.²; Troganis, Anastasios³; Tselios, Theodore⁴; Deraos, Spyros⁴; Matsoukas, John⁴; Gerothanassis, Ioannis P.¹; Bonvin, Alexandre M. J. J.²

Source: FEBS Journal, Volume 271, Number 16, August 2004 , pp. 3399-3413(15)

Publisher: Wiley-Blackwell

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Abstract:

Experimental autoimmune encephalomyelitis can be induced in susceptible animals by immunodominant determinants of myelin basic protein (MBP). To characterize the molecular features of antigenic sites important for designing experimental autoimmune encephalomyelitis suppressing molecules, we report structural studies, based on NMR experimental data in conjunction with molecular dynamic simulations, of the potent linear dodecapeptide epitope of guinea pig MBP, Gln74-Lys75-Ser76-Gln77-Arg78-Ser79-Gln80-Asp81-Glu82-Asn83-Pro84-Val85 [MBP(74-85)], and its antagonist analogue Ala81MBP(74-85). The two peptides were studied in both water and Me₂SO in order to mimic solvent-dependent structural changes in MBP. The agonist MBP(74-85) adopts a compact conformation because of electrostatic interactions of Arg78 with the side chains of Asp81 and Glu82. Arg78 is `locked' in a well-defined conformation, perpendicular to the peptide backbone which is practically solvent independent. These electrostatic interactions are, however, absent from the antagonist Ala81MBP(74-85), resulting in great flexibility of the side chain of Arg78. Sequence alignment of the two analogues with several species of MBP suggests a critical role for the positively charged residue Arg78, firstly, in the stabilization of the local microdomains (epitopes) of the integral protein, and secondly, in a number of post-translational modifications relevant to multiple sclerosis, such as the conversion of charged arginine residues to uncharged citrullines. Flexible docking calculations on the binding of the MBP(74-85) antigen to the MHC class II receptor site I-A^u usinghaddockindicate that Gln74, Ser76 and Ser79 are MHC II anchor residues. Lys75, Arg78 and Asp81 are prominent, solvent-exposed residues and, thus, may be of importance in the formation of the trimolecular T-cell receptor-MBP(74-85)-MHC II complex.

Keywords: conformation; docking; major histocompatibility complex; molecular dynamics; myelin basic epitope

Document Type: Research article

DOI: http://dx.doi.org/10.1111/j.1432-1033.2004.04274.x

Affiliations: 1: Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Greece 2: Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht, the Netherlands 3: Department of Biological Applications and Technologies, University of Ioannina, Greece 4: Department of Chemistry, University of Patras, Greece

Publication date: 2004-08-01