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Decamer-like conformation of a nona-peptide bound to HLA-B*3501 due to non-standard positioning of the C terminus.

Menssen R, Orth P, Ziegler A, Saenger W
J Mol Biol 285 645-53 (1999)
Cited: 34 times
EuropePMC logo PMID: 9878435

Abstract

The N and C termini of peptides presented by major histocompatibility complex (MHC) class I molecules are held within the peptide binding groove by a network of hydrogen bonds to conserved MHC residues. However, the published structure of the human allele HLA-B*3501 complexed with the nef octa-peptide VPLRPMTY, revealed non-standard positioning for both peptide termini. To investigate whether these deviations are indeed related to the length of the nef-peptide, we have determined the structure of HLA-B*3501 presenting a nona-peptide to 2.5 A resolution. A comparison of HLA-B*3501/peptide complexes with structures of other HLA molecules exhibits allele-specific properties of HLA-B*3501, as well as peptide-induced structural changes. Independent of the length of the bound peptide, HLA-B*3501 positions the peptide C terminus significantly closer to the alpha1-helix and nearer to the A pocket than observed for other HLA class I/peptide complexes. This reorientation is accompanied by a shift within the N-terminal part of the alpha2-helix towards the middle of the binding groove. Due to the short distance between the N and C termini, the nona-peptide is compressed and forced to zig-zag vertically within the binding groove. Its conformation rather resembles that of a deca-peptide than of other nona-peptides bound to class I molecules. Superposition of both HLA-B*3501/peptide complexes additionally reveals a significant, peptide-dependent deviation between the N-terminal parts of the alpha1-helices which might be due to different positioning of the peptide N termini. Taken together, these data illustrate the strong interdependence between the HLA class I molecule and the bound peptide.

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  1. Alternate states of proteins revealed by detailed energy landscape mapping. Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D. J Mol Biol 405 607-618 (2011)
  2. An improved hydrogen bond potential: impact on medium resolution protein structures. Fabiola F, Bertram R, Korostelev A, Chapman MS. Protein Sci 11 1415-1423 (2002)
  3. Modeling the structure of bound peptide ligands to major histocompatibility complex. Tong JC, Tan TW, Ranganathan S. Protein Sci 13 2523-2532 (2004)
  4. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. Yanaka S, Ueno T, Shi Y, Qi J, Gao GF, Tsumoto K, Sugase K. J Biol Chem 289 24680-24690 (2014)
  5. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X. J Mol Biol 340 695-706 (2004)
  6. T and B cell Epitope analysis of SARS-CoV-2 S protein based on immunoinformatics and experimental research. Chen Z, Ruan P, Wang L, Nie X, Ma X, Tan Y. J Cell Mol Med 25 1274-1289 (2021)
  7. Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data. Adrian PE, Rajaseger G, Mathura VS, Sakharkar MK, Kangueane P. BMC Struct Biol 2 2 (2002)
  8. Analysis of the different subpeptidomes presented by the HLA class I molecules of the B7 supertype. Tirado-Herranz A, Guasp P, Pastor-Moreno A, Area-Navarro M, Alvarez I. Cell Immunol 387 104707 (2023)


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  2. High resolution structures of highly bulged viral epitopes bound to major histocompatibility complex class I. Implications for T-cell receptor engagement and T-cell immunodominance. Tynan FE, Borg NA, Miles JJ, Beddoe T, El-Hassen D, Silins SL, van Zuylen WJ, Purcell AW, Kjer-Nielsen L, McCluskey J, Burrows SR, Rossjohn J. J Biol Chem 280 23900-23909 (2005)
  3. Dual, HLA-B27 subtype-dependent conformation of a self-peptide. Hülsmeyer M, Fiorillo MT, Bettosini F, Sorrentino R, Saenger W, Ziegler A, Uchanska-Ziegler B. J Exp Med 199 271-281 (2004)
  4. Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles. Schueler-Furman O, Altuvia Y, Sette A, Margalit H. Protein Sci 9 1838-1846 (2000)
  5. The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation. Tynan FE, Elhassen D, Purcell AW, Burrows JM, Borg NA, Miles JJ, Williamson NA, Green KJ, Tellam J, Kjer-Nielsen L, McCluskey J, Rossjohn J, Burrows SR. J Exp Med 202 1249-1260 (2005)
  6. An alternative open reading frame of the human macrophage colony-stimulating factor gene is independently translated and codes for an antigenic peptide of 14 amino acids recognized by tumor-infiltrating CD8 T lymphocytes. Probst-Kepper M, Stroobant V, Kridel R, Gaugler B, Landry C, Brasseur F, Cosyns JP, Weynand B, Boon T, Van Den Eynde BJ. J Exp Med 193 1189-1198 (2001)
  7. Conformational restraints and flexibility of 14-meric peptides in complex with HLA-B*3501. Probst-Kepper M, Hecht HJ, Herrmann H, Janke V, Ocklenburg F, Klempnauer J, van den Eynde BJ, Weiss S. J Immunol 173 5610-5616 (2004)
  8. Nonstandard peptide binding revealed by crystal structures of HLA-B*5101 complexed with HIV immunodominant epitopes. Maenaka K, Maenaka T, Tomiyama H, Takiguchi M, Stuart DI, Jones EY. J Immunol 165 3260-3267 (2000)
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  11. Polymorphic sites away from the Bw4 epitope that affect interaction of Bw4+ HLA-B with KIR3DL1. Sanjanwala B, Draghi M, Norman PJ, Guethlein LA, Parham P. J Immunol 181 6293-6300 (2008)
  12. Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex. Reboul CF, Meyer GR, Porebski BT, Borg NA, Buckle AM. PLoS Comput Biol 8 e1002404 (2012)
  13. Epitope-based peptide vaccines predicted against novel coronavirus disease caused by SARS-CoV-2. Lin L, Ting S, Yufei H, Wendong L, Yubo F, Jing Z. Virus Res 288 198082 (2020)
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  15. Thermodynamic and structural equivalence of two HLA-B27 subtypes complexed with a self-peptide. Hülsmeyer M, Welfle K, Pöhlmann T, Misselwitz R, Alexiev U, Welfle H, Saenger W, Uchanska-Ziegler B, Ziegler A. J Mol Biol 346 1367-1379 (2005)
  16. Structural prediction of peptides bound to MHC class I. Fagerberg T, Cerottini JC, Michielin O. J Mol Biol 356 521-546 (2006)
  17. Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens. Kumar P, Vahedi-Faridi A, Saenger W, Merino E, López de Castro JA, Uchanska-Ziegler B, Ziegler A. J Biol Chem 284 29784-29797 (2009)
  18. Quantitative online prediction of peptide binding to the major histocompatibility complex. Hattotuwagama CK, Guan P, Doytchinova IA, Zygouri C, Flower DR. J Mol Graph Model 22 195-207 (2004)
  19. Natural MHC class I polymorphism controls the pathway of peptide dissociation from HLA-B27 complexes. Winkler K, Winter A, Rueckert C, Uchanska-Ziegler B, Alexiev U. Biophys J 93 2743-2755 (2007)
  20. A novel MHCp binding prediction model. Zhao B, Mathura VS, Rajaseger G, Moochhala S, Sakharkar MK, Kangueane P. Hum Immunol 64 1123-1143 (2003)
  21. CAR-T cells and TRUCKs that recognize an EBNA-3C-derived epitope presented on HLA-B*35 control Epstein-Barr virus-associated lymphoproliferation. Dragon AC, Zimmermann K, Nerreter T, Sandfort D, Lahrberg J, Klöß S, Kloth C, Mangare C, Bonifacius A, Tischer-Zimmermann S, Blasczyk R, Maecker-Kolhoff B, Uchanska-Ziegler B, Abken H, Schambach A, Hudecek M, Eiz-Vesper B. J Immunother Cancer 8 e000736 (2020)
  22. Function-related regulation of the stability of MHC proteins. Simon A, Dosztányi Zs, Rajnavölgyi E, Simon I. Biophys J 79 2305-2313 (2000)
  23. Molecular Dynamics Simulation Reveals the Selective Binding of Human Leukocyte Antigen Alleles Associated with Behçet's Disease. Kongkaew S, Yotmanee P, Rungrotmongkol T, Kaiyawet N, Meeprasert A, Kaburaki T, Noguchi H, Takeuchi F, Kungwan N, Hannongbua S. PLoS One 10 e0135575 (2015)
  24. Towards the MHC-peptide combinatorics. Kangueane P, Sakharkar MK, Kolatkar PR, Ren EC. Hum Immunol 62 539-556 (2001)
  25. 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. Loll B, Rückert C, Hee CS, Saenger W, Uchanska-Ziegler B, Ziegler A. Protein Sci 20 278-290 (2011)
  26. Molecular modelling of HLA-B*35:132. Longhi E, Crivello P, Mantovani M, Frison S, Fleischhauer K, Crespiatico L, Piccolo G, Poli F. Int J Immunogenet 41 195-197 (2014)


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