Model for the Peptide-Free Conformation of Class II MHC Proteins

Background Major histocompatibility complex proteins are believed to undergo significant conformational changes concomitant with peptide binding, but structural characterization of these changes has remained elusive. Methodology/Principal Findings Here we use molecular dynamics simulations and experimental probes of protein conformation to investigate the peptide-free state of class II MHC proteins. Upon computational removal of the bound peptide from HLA-DR1-peptide complex, the α50-59 region folded into the P1-P4 region of the peptide binding site, adopting the same conformation as a bound peptide. Strikingly, the structure of the hydrophobic P1 pocket is maintained by engagement of the side chain of Phe α54. In addition, conserved hydrogen bonds observed in crystal structures between the peptide backbone and numerous MHC side chains are maintained between the α51-55 region and the rest of the molecule. The model for the peptide-free conformation was evaluated using conformationally-sensitive antibody and superantigen probes predicted to show no change, moderate change, or dramatic changes in their interaction with peptide-free DR1 and peptide-loaded DR1. The binding observed for these probes is in agreement with the movements predicted by the model. Conclusion/Significance This work presents a molecular model for peptide-free class II MHC proteins that can help to interpret the conformational changes known to occur within the protein during peptide binding and release, and can provide insight into possible mechanisms for DM action.

[1]  D. Wiley,et al.  The human class II MHC protein HLA-DR1 assembles as empty αβ heterodimers in the absence of antigenic peptide , 1992, Cell.

[2]  T. Schneider,et al.  Objective comparison of protein structures: error-scaled difference distance matrices. , 2000, Acta crystallographica. Section D, Biological crystallography.

[3]  M. 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.

[4]  D. Thirumalai,et al.  Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. , 2007, Biophysical journal.

[5]  J. Cochran,et al.  A diverse set of oligomeric class II MHC-peptide complexes for probing T-cell receptor interactions. , 2000, Chemistry & biology.

[6]  N. Allbritton,et al.  Evidence for a conformational change in a class II major histocompatibility complex molecule occurring in the same pH range where antigen binding is enhanced , 1996, The Journal of experimental medicine.

[7]  L. Stern,et al.  Sodium dodecyl sulfate stability of HLA-DR1 complexes correlates with burial of hydrophobic residues in pocket 1. , 1999, Journal of immunology.

[8]  Matthew W. Anderson,et al.  A polymorphic pocket at the P10 position contributes to peptide binding specificity in class II MHC proteins. , 2004, Chemistry & biology.

[9]  Wilfred F van Gunsteren,et al.  Molecular dynamics simulations of the native and partially folded states of ubiquitin: Influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics , 2007, Protein science : a publication of the Protein Society.

[10]  D. Wiley,et al.  MHC class II function preserved by low-affinity peptide interactions preceding stable binding , 1994, Nature.

[11]  Kedar Narayan,et al.  HLA-DM targets the hydrogen bond between the histidine at position β81 and peptide to dissociate HLA-DR–peptide complexes , 2007, Nature Immunology.

[12]  G J Kleywegt,et al.  Experimental assessment of differences between related protein crystal structures. , 1999, Acta crystallographica. Section D, Biological crystallography.

[13]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[14]  M. Davis,et al.  Conformational isomers of a class II MHC-peptide complex in solution. , 1999, Journal of molecular biology.

[15]  Monique Laberge,et al.  Molecular dynamics simulations of hemoglobin A in different states and bound to DPG: effector-linked perturbation of tertiary conformations and HbA concerted dynamics. , 2008, Biophysical journal.

[16]  David M. Kranz,et al.  Role of the T Cell Receptor α Chain in Stabilizing TCR-Superantigen-MHC Class II Complexes , 1999 .

[17]  L. Stern,et al.  The kinetic basis of peptide exchange catalysis by HLA-DM , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Sadegh-Nasseri,et al.  Stable peptide binding to MHC class II molecule is rapid and is determined by a receptive conformation shaped by prior association with low affinity peptides. , 1999, Journal of immunology.

[19]  P. Cresswell,et al.  HLA-DM Interactions with Intermediates in HLA-DR Maturation and a Role for HLA-DM in Stabilizing Empty HLA-DR Molecules , 1996, The Journal of experimental medicine.

[20]  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.

[21]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[22]  P. Bjorkman,et al.  Thermal stability comparison of purified empty and peptide-filled forms of a class I MHC molecule. , 1992, Science.

[23]  H. Mcconnell,et al.  Formation of two peptide/MHC II isomers is catalyzed differentially by HLA-DM. , 2003, Biochemistry.

[24]  P. S. Andersen,et al.  Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation. , 2003, Structure.

[25]  Ira Mellman,et al.  Cell biology of antigen processing in vitro and in vivo. , 2005, Annual review of immunology.

[26]  L. Stern,et al.  Empty and peptide-loaded class II major histocompatibility complex proteins produced by expression in Escherichia coli and folding in vitro. , 1999, Protein expression and purification.

[27]  Craig Beeson,et al.  Binding interactions between peptides and proteins of the class II Major Histocompatibility Complex , 2002, Medicinal research reviews.

[28]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[29]  D. Fremont,et al.  Recognition of open conformers of classical MHC by chaperones and monoclonal antibodies , 2005, Immunological reviews.

[30]  Leah M. Octavio,et al.  Empty Class II Major Histocompatibility Complex Created by Peptide Photolysis Establishes the Role of DM in Peptide Association* , 2007, Journal of Biological Chemistry.

[31]  R W Chesnut,et al.  Characterization of the specificity of peptide binding to four DR haplotypes. , 1990, Journal of immunology.

[32]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997 .

[33]  F. Sinigaglia,et al.  Identification of a motif for HLA-DR1 binding peptides using M13 display libraries , 1992, The Journal of experimental medicine.

[34]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[35]  K. Schulten,et al.  Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Scheherazade Sadegh-Nasseri,et al.  Hla-Dm Recognizes the Flexible Conformation of Major Histocompatibility Complex Class II , 2000, The Journal of experimental medicine.

[37]  R. Mariuzza,et al.  TCR recognition of peptide/MHC class II complexes and superantigens. , 2007, Seminars in immunology.

[38]  P. S. Andersen,et al.  Role of the T cell receptor alpha chain in stabilizing TCR-superantigen-MHC class II complexes. , 1999, Immunity.

[39]  Bernd Rupp,et al.  Anchor Side Chains of Short Peptide Fragments Trigger Ligand-Exchange of Class II MHC Molecules , 2008, PloS one.

[40]  R. Karr,et al.  HLA-DR alpha chain residues located on the outer loops are involved in nonpolymorphic and polymorphic antibody-binding epitopes. , 1994, Human immunology.

[41]  Mayuko Takeda-Shitaka,et al.  Dynamic flexibility of a peptide-binding groove of human HLA-DR1 class II MHC molecules: normal mode analysis of the antigen peptide-class II MHC complex. , 2003, Chemical & pharmaceutical bulletin.

[42]  R. Doebele,et al.  Determination of the HLA-DM interaction site on HLA-DR molecules. , 2000, Immunity.

[43]  P. Jensen,et al.  A structural transition in class II major histocompatibility complex proteins at mildly acidic pH , 1996, The Journal of experimental medicine.

[44]  D. Wiley,et al.  Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1 , 1993, Nature.

[45]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[46]  Michelle Palmer,et al.  Monoclonal Antibodies Specific for the Empty Conformation of HLA-DR1 Reveal Aspects of the Conformational Change Associated with Peptide Binding* , 2004, Journal of Biological Chemistry.

[47]  G. Benedek,et al.  A conformational change in the human major histocompatibility complex protein HLA-DR1 induced by peptide binding. , 1999, Biochemistry.

[48]  M. Vrljic,et al.  Formation of a highly peptide-receptive state of class II MHC. , 1998, Immunity.

[49]  T. Elliott,et al.  The Crystal Structure of H-2Db Complexed with a Partial Peptide Epitope Suggests a Major Histocompatibility Complex Class I Assembly Intermediate* , 2006, Journal of Biological Chemistry.

[50]  R Crowther,et al.  Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures. , 2000, Journal of medicinal chemistry.

[51]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[52]  D. Wiley,et al.  The human class II MHC protein HLA-DR1 assembles as empty alpha beta heterodimers in the absence of antigenic peptide. , 1992, Cell.

[53]  J. Altman,et al.  Stability of empty and peptide-loaded class II major histocompatibility complex molecules at neutral and endosomal pH: comparison to class I proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[54]  L. Stern,et al.  A three-step kinetic mechanism for peptide binding to MHC class II proteins. , 2000, Biochemistry.

[55]  Don C. Wiley,et al.  Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide , 1994, Nature.

[56]  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.

[57]  E. Unanue,et al.  Conformational isomers of a peptide–class II major histocompatibility complex , 2005, Immunological reviews.

[58]  Philip J Norris,et al.  A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[59]  G. Hämmerling,et al.  HLA-DM acts as a molecular chaperone and rescues empty HLA-DR molecules at lysosomal pH. , 1997, Immunity.

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

[61]  G. Benedek,et al.  Determinants of the Peptide-induced Conformational Change in the Human Class II Major Histocompatibility Complex Protein HLA-DR1* , 2000, The Journal of Biological Chemistry.

[62]  L. Stern,et al.  Probing the ligand-induced conformational change in HLA-DR1 by selective chemical modification and mass spectrometric mapping. , 2005, Biochemistry.