Conformational Variants of Class II MHC/Peptide Complexes induced by N- and C-Terminal Extensions of Minimal Peptide Epitopes

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 96; no. 13; pp. 7445 - 7450
• Main Authors: Rötzschke, O., Falk, K., Mack, J., Lau, J. M., Jung, G., Strominger, J. L.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences of the United States of America 22.06.1999; National Acad Sciences; National Academy of Sciences; The National Academy of Sciences
• Subjects: Amino acids; Antigen Presentation; Biological Sciences; Elution; Epitopes; Epitopes - chemistry; Epitopes - immunology; Gels; Glycols; HLA-D Antigens - chemistry; HLA-D Antigens - immunology; Humans; Immunology; Ligands; Molecular weight; Molecules; Peptides; Peptides - chemistry; Peptides - immunology; Protein Conformation; Proteins; Structure-Activity Relationship; Truncation
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.96.13.7445

Class II MHC molecules are known to exist in conformational variants. "Floppy" and "compact" forms of murine MHC molecules, for example, are discriminated by their migration behavior on SDS/PAGE and represent empty and ligand-loaded forms. Here we show that formation of distinctly faster-migrating ligand complexes (F-forms) rather than the normal compact (C-) forms of HLA-DR1 or -DR4 results from extensions of minimal peptide epitopes (such as HA306-318 or IC106-120) by ≈ 10 amino acids at either the N or the C terminus. Two similar but distinct F-forms (FI and FII) were detected, depending on the site of the extension. Both F-forms were characterized by increased surface hydrophobicity and reduced SDS-stability. Native gel separations and size exclusion chromatography indicated that the F-forms had increased hydrodynamic radii compared with the C-form and an apparent size similar to that of empty MHC molecules. The regions on the ligand overhangs responsible for the effect began at a distance of ≈ 5 amino acids on either side of the epitopes, comprised 4-8 amino acids (i.e., a total overhang of 9-14), and did not have a particular sequence preference. The possible functional significance of these forms is discussed.