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Interaction pattern of Arg 62 in the A-pocket of differentially disease-associated HLA-B27 subtypes suggests distinct TCR binding modes. PLoS One 2012; 7:e32865. [PMID: 22403718 PMCID: PMC3293911 DOI: 10.1371/journal.pone.0032865] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/01/2012] [Indexed: 12/30/2022] Open
Abstract
The single amino acid replacement Asp116His distinguishes the two subtypes HLA-B*2705 and HLA-B*2709 which are, respectively, associated and non-associated with Ankylosing Spondylitis, an autoimmune chronic inflammatory disease. The reason for this differential association is so far poorly understood and might be related to subtype-specific HLA:peptide conformations as well as to subtype/peptide-dependent dynamical properties on the nanoscale. Here, we combine functional experiments with extensive molecular dynamics simulations to investigate the molecular dynamics and function of the conserved Arg62 of the α1-helix for both B27 subtypes in complex with the self-peptides pVIPR (RRKWRRWHL) and TIS (RRLPIFSRL), and the viral peptides pLMP2 (RRRWRRLTV) and NPflu (SRYWAIRTR). Simulations of HLA:peptide systems suggest that peptide-stabilizing interactions of the Arg62 residue observed in crystal structures are metastable for both B27 subtypes under physiological conditions, rendering this arginine solvent-exposed and, probably, a key residue for TCR interaction more than peptide-binding. This view is supported by functional experiments with conservative (R62K) and non-conservative (R62A) B*2705 and B*2709 mutants that showed an overall reduction in their capability to present peptides to CD8+ T cells. Moreover, major subtype-dependent differences in the peptide recognition suggest distinct TCR binding modes for the B*2705 versus the B*2709 subtype.
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Narzi D, Becker CM, Fiorillo MT, Uchanska-Ziegler B, Ziegler A, Böckmann RA. Dynamical Characterization of Two Differentially Disease Associated MHC Class I Proteins in Complex with Viral and Self-Peptides. J Mol Biol 2012; 415:429-42. [DOI: 10.1016/j.jmb.2011.11.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/01/2011] [Accepted: 11/10/2011] [Indexed: 10/15/2022]
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García-Medel N, Sanz-Bravo A, Barnea E, Admon A, López de Castro JA. The origin of proteasome-inhibitor resistant HLA class I peptidomes: a study with HLA-A*68:01. Mol Cell Proteomics 2011; 11:M111.011486. [PMID: 21969608 DOI: 10.1074/mcp.m111.011486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Some HLA class I molecules bind a significant fraction of their constitutive peptidomes in the presence of proteasome inhibitors. In this study, A*68:01-bound peptides, and their parental proteins, were characterized through massive mass spectrometry sequencing to refine its binding motif, including the nearly exclusive preference for C-terminal basic residues. Stable isotope tagging was used to distinguish proteasome-inhibitor sensitive and resistant ligands. The latter accounted for less than 20% of the peptidome and, like in HLA-B27, arose predominantly from small and basic proteins. Under the conditions used for proteasome inhibition in vivo, epoxomicin and MG-132 incompletely inhibited the hydrolysis of fluorogenic substrates specific for the tryptic or for both the tryptic and chymotryptic subspecificities, respectively. This incomplete inhibition was also reflected in the cleavage of synthetic peptide precursors of A*68:01 ligands. For these substrates, the inhibition of the proteasome resulted in altered cleavage patterns. However these alterations did not upset the balance between cleavage at peptide bonds resulting in epitope destruction and those leading to their generation. The results indicate that inhibitor-resistant HLA class I ligands are not necessarily produced by non-proteasomal pathways. However, their generation is not simply explained by decreased epitope destruction upon incomplete proteasomal inhibition and may require additional proteolytic steps acting on incompletely processed proteasomal products.
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Affiliation(s)
- Noel García-Medel
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolas Cabrera N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - Alejandro Sanz-Bravo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolas Cabrera N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - Eilon Barnea
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Arie Admon
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - José A López de Castro
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolas Cabrera N.1, Universidad Autónoma, 28049 Madrid, Spain.
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Loll B, Rückert C, Hee CS, Saenger W, Uchanska-Ziegler B, Ziegler A. Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide. Protein Sci 2011; 20:278-90. [PMID: 21280120 PMCID: PMC3048413 DOI: 10.1002/pro.559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/10/2010] [Accepted: 11/10/2010] [Indexed: 01/07/2023]
Abstract
The human major histocompatibility complex class I antigen HLA-B*2705 binds several sequence-related peptides (pVIPR, RRKWRRWHL; pLPM2, RRRWRRLTV; pGR, RRRWHRWRL). Cross-reactivity of cytotoxic T cells (CTL) against these HLA-B*2705:peptide complexes seemed to depend on a particular peptide conformation that is facilitated by the engagement of a crucial residue within the binding groove (Asp116), associated with a noncanonical bulging-in of the middle portion of the bound peptide. We were interested whether a conformational reorientation of the ligand might contribute to the lack of cross-reactivity of these CTL with a peptide derived from voltage-dependent calcium channel α1 subunit (pCAC, SRRWRRWNR), in which the C-terminal peptide residue pArg9 could engage Asp116. Analyses of the HLA-B*2705:pCAC complex by X-ray crystallography at 1.94 Å resolution demonstrated that the peptide had indeed undergone a drastic reorientation, leading it to adopt a canonical binding mode accompanied by the loss of molecular mimicry between pCAC and sequence-related peptides such as pVIPR, pLMP2, and pGR. This was clearly a consequence of interactions of pArg9 with Asp116 and other F-pocket residues. Furthermore, we observed an unprecedented reorientation of several additional residues of the HLA-B*2705 heavy chain near the N-terminal region of the peptide, including also the presence of double conformations of two glutamate residues, Glu63 and Glu163, on opposing sides of the peptide binding groove. Together with the Arg-Ser exchange at peptide position 1, there are thus multiple structural reasons that may explain the observed failure of pVIPR-directed, HLA-B*2705-restricted CTL to cross-react with HLA-B*2705:pCAC complexes.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany,*Correspondence to: Bernhard Loll, Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, Berlin 14195, Germany. E-mail:
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Chee Seng Hee
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie, Abteilung Kristallographie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
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Abstract
The two most frequent HLA-B27 subtypes worldwide are B*2704 and B*2705. In the Han population of China B*2704 and, to a lower extent, B*2705 are found with significant frequency, and both are associated to ankylosing spondylitis (AS). Two articles in this issue report that the association to AS in this ethnic group is stronger for B*2704 than for B*2705. Thus, at least among the Han, B*2704 would be the strongest known susceptibility factor for AS.
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Affiliation(s)
- J A López de Castro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
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Nurzia E, Panimolle F, Cauli A, Mathieu A, Magnacca A, Paladini F, Sorrentino R, Fiorillo MT. CD8+ T-cell mediated self-reactivity in HLA-B27 context as a consequence of dual peptide conformation. Clin Immunol 2010; 135:476-82. [PMID: 20167541 DOI: 10.1016/j.clim.2010.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/18/2010] [Accepted: 01/21/2010] [Indexed: 12/11/2022]
Abstract
HLA-B2709 does not predispose for Ankylosing Spondylitis although it differs from B2705, the most common and AS-associated subtype in different ethnic groups, only for the substitution His116Asp. Therefore, a productive approach to elucidate the molecular mechanisms of the disease could be the comparison of these alleles. B2705 has been shown to display certain self-peptides enriched in basic residues i.e., pVIPR and pGR, in a dual conformation and this is accompanied by the presence of specific cytotoxic T cells in patients with AS. In this study, we convalidate our previous observation that B2709 healthy subjects do not possess primary reactivity towards pVIPR while showing a prompt CD8+ T cell response driven by pGR. Notably, in the B2709 context of presentation, pVIPR assumes only a single conformation in contrast with pGR which is dimorphic. These results suggest a possible general connection between the occurrence of double peptide conformation and the property of inducing specific autoimmune responses.
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Affiliation(s)
- Elisa Nurzia
- Department of Cell Biology and Development, Sapienza University of Rome, 00185 Roma, Italy
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López de Castro JA. The HLA-B27 peptidome: Building on the cornerstone. ACTA ACUST UNITED AC 2010; 62:316-9. [DOI: 10.1002/art.27188] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mou Y, Wu Z, Gu J, Liao Z, Lin Z, Wei Q, Huang J, Li Q. HLA-B27 polymorphism in patients with juvenile and adult-onset ankylosing spondylitis in Southern China. ACTA ACUST UNITED AC 2010; 75:56-60. [DOI: 10.1111/j.1399-0039.2009.01406.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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