The first step of peptide selection in antigen presentation by MHC class I molecules

Significance MHC class I molecules select and present a limited set of peptides from a broad repertoire provided by TAP. How MHC class I makes this selection is unclear. We show that MHC class I H-2Kb molecules initially bind many peptides because of highly flexible binding pockets. Peptide binding is followed by a selection step wherein a large fraction of these peptides is released, leaving the canonical peptides for presentation. The peptide presentation has a remarkable temperature dependency and explains the low-affinity peptides found associated to MHC class I molecules in cells cultured at low temperature. Our data suggest that MHC class I goes through rounds of considering and rejecting peptides until peptides with high affinity are acquired for presentation. MHC class I molecules present a variable but limited repertoire of antigenic peptides for T-cell recognition. Understanding how peptide selection is achieved requires mechanistic insights into the interactions between the MHC I and candidate peptides. We find that, at first encounter, MHC I H-2Kb considers a wide range of peptides, including those with expanded N termini and unfitting anchor residues. Discrimination occurs in the second step, when noncanonical peptides dissociate with faster exchange rates. This second step exhibits remarkable temperature sensitivity, as illustrated by numerous noncanonical peptides presented by H-2Kb in cells cultured at 26 °C relative to 37 °C. Crystallographic analyses of H-2Kb–peptide complexes suggest that a conformational adaptation of H-2Kb drives the decisive step in peptide selection. We propose that MHC class I molecules consider initially a large peptide pool, subsequently refined by a temperature-sensitive induced-fit mechanism to retain the canonical peptide repertoire.

[1]  Natalie A Borg,et al.  T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I–bound peptide , 2005, Nature Immunology.

[2]  M R Jackson,et al.  In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells. , 1992, The Journal of biological chemistry.

[3]  Morten Nielsen,et al.  NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11 , 2008, Nucleic Acids Res..

[4]  G. Fleuren,et al.  Tumor Eradication by Wild-type p53-specific Cytotoxic T Lymphocytes , 1997, The Journal of experimental medicine.

[5]  T. Elliott,et al.  Peptide-independent stabilization of MHC class I molecules breaches cellular quality control , 2014, Journal of Cell Science.

[6]  T. Straatsma,et al.  Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation study. , 2008, Molecular immunology.

[7]  William S. Lane,et al.  Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle , 1992, Nature.

[8]  Morten Nielsen,et al.  Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers , 2008, Bioinform..

[9]  C DeLisi,et al.  Structural principles that govern the peptide-binding motifs of class I MHC molecules. , 1998, Journal of molecular biology.

[10]  Paul D Adams,et al.  Modelling dynamics in protein crystal structures by ensemble refinement , 2012, eLife.

[11]  J. Neefjes,et al.  Folding and assembly of major histocompatibility complex class I heterodimers in the endoplasmic reticulum of intact cells precedes the binding of peptide , 1993, The Journal of experimental medicine.

[12]  Hidde L. Ploegh,et al.  Direct binding of peptide to empty MHC class I molecules on intact cells and in vitro , 1990, Cell.

[13]  J. Leunissen,et al.  The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes* , 2013, Molecular & Cellular Proteomics.

[14]  M. Zacharias,et al.  Comparative molecular dynamics analysis of tapasin‐dependent and ‐independent MHC class I alleles , 2006, Protein science : a publication of the Protein Society.

[15]  L. K. Ely,et al.  Natural HLA Class I Polymorphism Controls the Pathway of Antigen Presentation and Susceptibility to Viral Evasion , 2004, The Journal of experimental medicine.

[16]  J. McCluskey,et al.  The Energetic Basis Underpinning T-cell Receptor Recognition of a Super-bulged Peptide Bound to a Major Histocompatibility Complex Class I Molecule* , 2012, The Journal of Biological Chemistry.

[17]  D. Wiley,et al.  Structural characterization of a soluble and partially folded class I major histocompatibility heavy chain/β2m heterodimer , 1998, Nature Structural Biology.

[18]  P. A. Peterson,et al.  Crystal structures of two viral peptides in complex with murine MHC class I H-2Kb. , 1994, Science.

[19]  D. Margulies,et al.  The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics , 2012, The Journal of Immunology.

[20]  J. Sacchettini,et al.  The three-dimensional structure of H-2Db at 2.4 Å resolution: Implications for antigen-determinant selection , 1994, Cell.

[21]  M. Zacharias,et al.  Conformational Flexibility of the MHC Class I α1-α2 Domain in Peptide Bound and Free States: A Molecular Dynamics Simulation Study , 2004 .

[22]  J. Drijfhout,et al.  Structural basis for the killing of human beta cells by CD 8 + T cells in type 1 diabetes , 2012 .

[23]  J. Neefjes,et al.  Towards a systems understanding of MHC class I and MHC class II antigen presentation , 2011, Nature Reviews Immunology.

[24]  Martin Zacharias,et al.  Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study. , 2004, Biophysical journal.

[25]  S. Saini,et al.  Not all empty MHC class I molecules are molten globules: tryptophan fluorescence reveals a two-step mechanism of thermal denaturation. , 2013, Molecular immunology.

[26]  O. Lund,et al.  novel sequence representations Reliable prediction of T-cell epitopes using neural networks with , 2003 .

[27]  P. Barry,et al.  Mamu-A01/K(b) transgenic and MHC Class I knockout mice as a tool for HIV vaccine development. , 2009, Virology.

[28]  Hidde L. Ploegh,et al.  Empty MHC class I molecules come out in the cold , 1990, Nature.

[29]  N. Nagarajan,et al.  ERAAP and Tapasin Independently Edit the Amino and Carboxyl Termini of MHC Class I Peptides , 2013, The Journal of Immunology.

[30]  E. Harhaj,et al.  Thermolabile H-2Kb molecules expressed by transporter associated with antigen processing-deficient RMA-S cells are occupied by low-affinity peptides. , 1999, Journal of immunology.

[31]  N. Nagarajan,et al.  Endoplasmic Reticulum Aminopeptidase Associated with Antigen Processing Defines the Composition and Structure of MHC Class I Peptide Repertoire in Normal and Virus-Infected Cells , 2010, The Journal of Immunology.

[32]  James McCluskey,et al.  Optimization of the MHC class I peptide cargo is dependent on tapasin. , 2002, Immunity.

[33]  H. Rammensee,et al.  Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules , 1991, Nature.

[34]  M. Zacharias,et al.  Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[35]  J. Sidney,et al.  Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity , 2014, The Journal of experimental medicine.

[36]  S. Rowland-Jones,et al.  Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms , 2012, Proceedings of the National Academy of Sciences.