Advertisement

Peptide Modulation of Class I Major Histocompatibility Complex Protein Molecular Flexibility and the Implications for Immune Recognition*

Open AccessPublished:July 08, 2013DOI:https://doi.org/10.1074/jbc.M113.490664
      T cells use the αβ T cell receptor (TCR) to recognize antigenic peptides presented by class I major histocompatibility complex proteins (pMHCs) on the surfaces of antigen-presenting cells. Flexibility in both TCRs and peptides plays an important role in antigen recognition and discrimination. Less clear is the role of flexibility in the MHC protein; although recent observations have indicated that mobility in the MHC can impact TCR recognition in a peptide-dependent fashion, the extent of this behavior is unknown. Here, using hydrogen/deuterium exchange, fluorescence anisotropy, and structural analyses, we show that the flexibility of the peptide binding groove of the class I MHC protein HLA-A*0201 varies significantly with different peptides. The variations extend throughout the binding groove, impacting regions contacted by TCRs as well as other activating and inhibitory receptors of the immune system. Our results are consistent with statistical mechanical models of protein structure and dynamics, in which the binding of different peptides alters the populations and exchange kinetics of substates in the MHC conformational ensemble. Altered MHC flexibility will influence receptor engagement, impacting conformational adaptations, entropic penalties associated with receptor recognition, and the populations of binding-competent states. Our results highlight a previously unrecognized aspect of the “altered self” mechanism of immune recognition and have implications for specificity, cross-reactivity, and antigenicity in cellular immunity.
      Background: Peptide modulation of MHC flexibility can affect recognition by immune receptors.
      Results: Different peptides alter the flexibility of the MHC protein at sites around the peptide-binding groove.
      Conclusion: Peptide modulation of MHC flexibility is not limited to specific peptides or isolated regions.
      Significance: Peptide modulation of MHC flexibility indicates an extension of antigenicity from the peptide to the MHC.

      Introduction

      αβ T cell receptors (TCRs)
      The abbreviations used are: TCR
      T cell receptor
      pMHC
      peptide·MHC complex
      HDX-MS
      hydrogen/deuterium exchange-mass spectrometry.
      on the surfaces of CD8+ T cells recognize antigenic peptides bound and presented by class I major histocompatibility complex proteins (class I pMHC complexes) to initiate and propagate an antigen-dependent immune response. Both TCR and peptide conformational properties play key roles in antigen recognition and discrimination. Conformational changes in the TCR complementarity-determining region binding loops often accompany binding (
      • Armstrong K.M.
      • Piepenbrink K.H.
      • Baker B.M.
      Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes.
      ), and measurements of complementarity-determining region loop dynamics have directly linked loop flexibility to TCR cross-reactivity (
      • Scott D.R.
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Corcelli S.A.
      • Baker B.M.
      Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism.
      ,
      • Hare B.J.
      • Wyss D.F.
      • Osburne M.S.
      • Kern P.S.
      • Reinherz E.L.
      • Wagner G.
      Structure, specificity, and CDR mobility of a class II restricted single-chain T-cell receptor.
      ). Likewise, conformational changes in peptides often accompany TCR binding (e.g. Refs.
      • Borbulevych O.Y.
      • Santhanagopolan S.M.
      • Hossain M.
      • Baker B.M.
      TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms.
      and
      • Tynan F.E.
      • Reid H.H.
      • Kjer-Nielsen L.
      • Miles J.J.
      • Wilce M.C.J.
      • Kostenko L.
      • Borg N.A.
      • Williamson N.A.
      • Beddoe T.
      • Purcell A.W.
      • Burrows S.R.
      • McCluskey J.
      • Rossjohn J.
      A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule.
      ), and peptide flexibility can be altered through peptide modifications or MHC polymorphisms (
      • Insaidoo F.K.
      • Borbulevych O.Y.
      • Hossain M.
      • Santhanagopolan S.M.
      • Baxter T.K.
      • Baker B.M.
      Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design.
      ,
      • Narzi D.
      • Becker C.M.
      • Fiorillo M.T.
      • Uchanska-Ziegler B.
      • Ziegler A.
      • Böckmann R.A.
      Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides.
      ,
      • Pöhlmann T.
      • Böckmann R.A.
      • Grubmüller H.
      • Uchanska-Ziegler B.
      • Ziegler A.
      • Alexiev U.
      Differential peptide dynamics is linked to major histocompatibility complex polymorphism.
      ).
      Less appreciated, however, is the role that MHC flexibility plays in TCR recognition. Examples of conformational changes in MHC peptide-binding domains occurring upon TCR binding are mostly limited to small shifts in the shapes and positions of the α1 or α2 helices (e.g. Ref.
      • Mazza C.
      • Auphan-Anezin N.
      • Gregoire C.
      • Guimezanes A.
      • Kellenberger C.
      • Roussel A.
      • Kearney A.
      • van der Merwe P.A.
      • Schmitt-Verhulst A.M.
      • Malissen B.
      How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?.
      ). In one telling case, however, the conformation of the α2 helix of the human class I MHC protein HLA-A*0201 (HLA-A2) was shown to undergo a large reorganization upon binding of the A6 TCR (
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Gloor B.E.
      • Scott D.R.
      • Sommese R.F.
      • Cole D.K.
      • Sewell A.K.
      • Baker B.M.
      T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
      ). Notably, this reorganization is dependent on the peptide as it has not been observed upon recognition of other HLA-A2-presented peptides by the same TCR (
      • Garboczi D.N.
      • Ghosh P.
      • Utz U.
      • Fan Q.R.
      • Biddison W.E.
      • Wiley D.C.
      Structure of the complex between human T-cell receptor, viral peptide and HLA-A2.
      ,
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Baker B.M.
      Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics.
      ).
      In protein binding, crystallographically observed conformational differences have been shown to occur in regions with enhanced motions as the lower energy barriers that facilitate conformational changes translate into faster rates of conformational exchange (
      • Csermely P.
      • Palotai R.
      • Nussinov R.
      Induced fit, conformational selection, and independent dynamic segments: an extended view of binding events.
      ). Indeed, with HLA-A2, the mobility of the region that undergoes a structural change upon binding of the A6 TCR was shown to vary with different peptides (
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Gloor B.E.
      • Scott D.R.
      • Sommese R.F.
      • Cole D.K.
      • Sewell A.K.
      • Baker B.M.
      T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
      ). This may not be a unique observation as similar effects are believed to contribute to differential T cell recognition of native and modified MART-1 peptides (
      • Insaidoo F.K.
      • Borbulevych O.Y.
      • Hossain M.
      • Santhanagopolan S.M.
      • Baxter T.K.
      • Baker B.M.
      Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design.
      ), and MHC flexibility can be altered by micropolymorphisms (
      • Narzi D.
      • Becker C.M.
      • Fiorillo M.T.
      • Uchanska-Ziegler B.
      • Ziegler A.
      • Böckmann R.A.
      Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides.
      ,
      • Fabian H.
      • Loll B.
      • Huser H.
      • Naumann D.
      • Uchanska-Ziegler B.
      • Ziegler A.
      Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy.
      ,
      • Fabian H.
      • Huser H.
      • Narzi D.
      • Misselwitz R.
      • Loll B.
      • Ziegler A.
      • Böckmann R.A.
      • Uchanska-Ziegler B.
      • Naumann D.
      HLA-B27 subtypes differentially associated with disease exhibit conformational differences in solution.
      ). As demonstrated by the A6 TCR, peptide-dependent MHC dynamics can impact TCR recognition by altering the barriers for conformational adjustments, influencing the entropic costs for receptor binding and shifting the populations of binding-competent states. Although altered MHC flexibility has not been apparent structurally, differences in flexibility are generally difficult to ascertain from examination of structure alone.
      Here, we explore the extent to which different peptides modify the flexibility of the peptide-binding domain of the class I MHC protein in detail. Using hydrogen/deuterium exchange, fluorescence anisotropy, and an analysis of the class I pMHC structural database, we found a surprising degree of peptide dependence to the motional properties of the HLA-A2 peptide-binding groove. The results were not limited to one region, but extended throughout both α-helices as well as the β-sheet floor of the groove. Regions affected included those that interact with TCRs as well as other activating and inhibitory receptors of the immune system, such as the CD8 coreceptor and natural killer receptors. Our observations emphasize that association of peptides with HLA-A2 proteins physically alters the properties of the protein. Indeed, our results encompass yet broaden the “altered self” model of immune recognition, which emerged from the finding that receptors of the cellular immune system recognize MHC proteins altered through the binding and presentation of antigens (
      • Zinkernagel R.M.
      • Doherty P.C.
      Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis.
      ). Our findings have implications for immunological specificity, cross-reactivity, and ultimately, the determinants of antigenicity for class I MHC-presented peptides.

      DISCUSSION

      Studying recognition of the Tel1p and Tax peptides by the A6 TCR, we previously observed that peptide-dependent motions of the HLA-A2 peptide-binding groove could influence TCR recognition, specificity, and cross-reactivity (
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Gloor B.E.
      • Scott D.R.
      • Sommese R.F.
      • Cole D.K.
      • Sewell A.K.
      • Baker B.M.
      T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
      ). Here, we provide concrete evidence that the “tuning” of the flexibility of class I MHC proteins by different peptides is a general phenomenon and not localized to certain peptides or a single region of the protein.
      The alteration of protein motions by ligand binding can be interpreted in the context of energy landscapes, which relate protein conformation and energy and define the populations and transition kinetics for the conformational substates that make up the structural ensemble of a protein (
      • Tsai C.-J.
      • Ma B.
      • Nussinov R.
      Folding and binding cascades: shifts in energy landscapes.
      ,
      • Miller D.W.
      • Dill K.A.
      Ligand binding to proteins: the binding landscape model.
      ). In altering flexibility, the binding of a ligand to a particular set of substates stabilizes those and destabilizes others, altering the energy landscape and thus entropy and protein dynamics (
      • Wrabl J.O.
      • Gu J.
      • Liu T.
      • Schrank T.P.
      • Whitten S.T.
      • Hilser V.J.
      The role of protein conformational fluctuations in allostery, function, and evolution.
      ). Importantly, the binding of different ligands can stabilize or destabilize different sets of substates, resulting in ligand-dependent changes in protein motions (
      • Frederick K.K.
      • Marlow M.S.
      • Valentine K.G.
      • Wand A.J.
      Conformational entropy in molecular recognition by proteins.
      ,
      • Masterson L.R.
      • Shi L.
      • Metcalfe E.
      • Gao J.
      • Taylor S.S.
      • Veglia G.
      Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy.
      ,
      • Boehr D.D.
      • McElheny D.
      • Dyson H.J.
      • Wright P.E.
      Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands.
      ). In addition to our results here, this behavior has been demonstrated for a variety of proteins, with differential motions impacting processes as diverse as signaling, enzyme activity, and allostery (reviewed in Ref.
      • Smock R.G.
      • Gierasch L.M.
      Sending signals dynamically.
      ). In structural terms, the stabilization/destabilization of different states by various ligands can arise from formation of different types, strengths, and numbers of noncovalent interactions, as well as different steric limitations on what conformations can be sampled as the protein moves. Given that peptide binding is coupled to class I MHC folding, with the peptide deeply integrated into the structure of the protein, opportunities exist for peptides to impact the stability and thus populations of numerous states (as a simple example, when the structures of the Tax and Flu M1 peptides bound to HLA-A2 are compared, there are 11 amino acids that are uniquely contacted in the two structures (supplemental Fig. S4)). Our results are interpreted in this context in Fig. 4, which shows a stylized class I MHC folding funnel and stylized variations in the folded state energy landscape with different peptides.
      Figure thumbnail gr4
      FIGURE 4Variations in the HLA-A2 energy landscape can explain the peptide dependence of flexibility. Left, a hypothetical, simplified folding funnel for a class I MHC protein, with conformation reflected by the width and free energy reflected by the height. Association of β2-microglobulin and peptide is represented implicitly. The tip of the funnel reflects the crystallographically observed, low energy native state. Right, the sampling of different conformational substates in the native state, or the “breathing” of protein, is dictated by the energy landscape, in which the depths of the wells define the populations of the various substates and thus the entropy, and the heights of the separating barriers give the kinetics for transitioning between substates. Different peptides affect the stability of different substates, as indicated in , altering the shape of the energy landscape.
      It may be notable that beyond showing peptide-specific differences, the correlation between the differences measured by HDX-MS and fluorescence anisotropy is not strong. However, it is important to note that the two experiments probe very different time and length scales. The HDX-MS experiments probe motions indirectly on the millisecond timescale and more slowly, and cannot localize the motions to specific amino acids within the peptidic fragments, which range from 7 to 20 amino acids. Conversely, the fluorescence anisotropy experiments probe motions on the fast, nanosecond timescale directly at the labeled positions. Thus, correlations between the HDX-MS and fluorescence anisotropy results need not be expected. The variation across timescales, however, is important as it speaks to the potential for altered MHC flexibility to impact TCR recognition through multiple ways, including binding entropies (fast timescales), conformational changes (fast and slow timescales), and altered populations of binding-competent states (slow timescales).
      A limitation of our experiments is that they do not provide information about what conformational states are sampled. At the nanosecond timescale, some insight can be gained from prior molecular dynamics simulations of the same class I MHC protein with different peptides bound, each of which showed peptide-dependent variations in the overall shape, positions, and stabilities of the α-helices of the peptide-binding groove (
      • Insaidoo F.K.
      • Borbulevych O.Y.
      • Hossain M.
      • Santhanagopolan S.M.
      • Baxter T.K.
      • Baker B.M.
      Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design.
      ,
      • Narzi D.
      • Becker C.M.
      • Fiorillo M.T.
      • Uchanska-Ziegler B.
      • Ziegler A.
      • Böckmann R.A.
      Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides.
      ,
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Gloor B.E.
      • Scott D.R.
      • Sommese R.F.
      • Cole D.K.
      • Sewell A.K.
      • Baker B.M.
      T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
      ). Although these studies did not address variation in the β-sheet floor of the binding groove, given the tight connectivity between peptides, the helices, and the β-sheet, a peptide dependence to motion within individual β-strands should not be surprising (indeed, the differences in peptide-HLA-A2 contacts in different complexes include multiple residues of the β-sheet (supplemental Fig. S4)). A more direct comparison between our results and these simulations is limited by the finite simulation times of the simulations (50–400 ns); advanced sampling methods that extend the range of molecular simulations should be expected to provide further insight.
      Our findings have implications for the determinants of antigenicity and the functional distinctions that are often made between a peptide and a presenting class I MHC protein. When considered alongside our previous findings with the Tax and Tel1p peptides (
      • Borbulevych O.Y.
      • Piepenbrink K.H.
      • Gloor B.E.
      • Scott D.R.
      • Sommese R.F.
      • Cole D.K.
      • Sewell A.K.
      • Baker B.M.
      T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
      ), our results imply that there can be an “extension of antigenicity” from the peptide to the MHC and that distinctions commonly made between the two weaken at the atomic level (
      • Baker B.M.
      • Scott D.R.
      • Blevins S.J.
      • Hawse W.F.
      Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism.
      ). For example, patterns of similar TCR-MHC interatomic interactions in structures of TCRs sharing variable gene segments bound to the same MHC have been used to help argue that TCRs maintain an intrinsic affinity toward MHC proteins (
      • Garcia K.C.
      • Adams J.J.
      • Feng D.
      • Ely L.K.
      The molecular basis of TCR germline bias for MHC is surprisingly simple.
      ). However, if the strength of TCR-MHC contacts can vary due to altered MHC dynamics, this limits the extent to which evolution can have imparted an MHC bias onto TCR gene segments. This could help explain why clear patterns of conserved TCR-MHC contacts have been difficult to identify, even in structures where the same TCR is engaged to the same MHC protein presenting different peptides (
      • Borbulevych O.Y.
      • Santhanagopolan S.M.
      • Hossain M.
      • Baker B.M.
      TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms.
      ).
      Our results are also relevant to the surprising degree of specificity seen in many TCR-pMHC interactions. Although TCR cross-reactivity is well appreciated (
      • Mason D.
      A very high level of crossreactivity is an essential feature of the T-cell receptor.
      ), in many cases, TCRs have been shown to be highly sensitive to changes in peptide structure or composition, sometimes with no clear structural explanation. Such fine specificity has been implicated in T cell antagonism as well as the poor performance of modified peptides as vaccine candidates (
      • Ding Y.H.
      • Baker B.M.
      • Garboczi D.N.
      • Biddison W.E.
      • Wiley D.C.
      Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical.
      ,
      • Cole D.K.
      • Edwards E.S.
      • Wynn K.K.
      • Clement M.
      • Miles J.J.
      • Ladell K.
      • Ekeruche J.
      • Gostick E.
      • Adams K.J.
      • Skowera A.
      • Peakman M.
      • Wooldridge L.
      • Price D.A.
      • Sewell A.K.
      Modification of MHC anchor residues generates heteroclitic peptides that alter TCR binding and T cell recognition.
      ). Our findings suggest that in some cases, TCR specificity could arise from dynamical changes resulting from peptide modification.
      We focused largely on a single human class I MHC allele, HLA-A*0201. Although the structural analysis suggests similar behavior with the murine class I MHC H-2Kb, an important question to resolve is whether and how MHC micropolymorphisms influence the peptide dependence of dynamics. This may be particularly likely for polymorphic positions whose side chains are embedded within the peptide-binding groove (
      • Fabian H.
      • Huser H.
      • Narzi D.
      • Misselwitz R.
      • Loll B.
      • Ziegler A.
      • Böckmann R.A.
      • Uchanska-Ziegler B.
      • Naumann D.
      HLA-B27 subtypes differentially associated with disease exhibit conformational differences in solution.
      ). Less clear is the extent to which peptide-dependent dynamics occur in class II MHC proteins. Although peptide association with class II molecules is less of a folding reaction and peptide termini in class II are not embedded in the protein as with class I, a recent examination of a large database of class II pMHC structures revealed structural variations resembling those seen with class I MHC proteins (
      • Painter C.A.
      • Stern L.J.
      Conformational variation in structures of classical and non-classical MHCII proteins and functional implications.
      ), possibly reflecting intrinsic class II MHC dynamics that could be modulated by peptide.
      In addition to T cell receptors, a variety of other molecules interact with MHC proteins. These include the CD4/CD8 coreceptors expressed by T cells, and for class I MHC molecules, a range of activating and inhibitory receptors expressed by natural killer and other cell types (
      • Natarajan K.
      • Dimasi N.
      • Wang J.
      • Mariuzza R.A.
      • Margulies D.H.
      Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
      ). Structural and binding data indicate that these molecules interact with class I MHC molecules in a way distinct from T cell receptors, making few, if any contacts to peptides (
      • Gao G.F.
      • Tormo J.
      • Gerth U.C.
      • Wyer J.R.
      • McMichael A.J.
      • Stuart D.I.
      • Bell J.I.
      • Jones E.Y.
      • Jakobsen B.K.
      Crystal structure of the complex between human CD8αα and HLA-A2.
      ,
      • Deng L.
      • Cho S.
      • Malchiodi E.L.
      • Kerzic M.C.
      • Dam J.
      • Mariuzza R.A.
      Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors.
      ,
      • Boyington J.C.
      • Motyka S.A.
      • Schuck P.
      • Brooks A.G.
      • Sun P.D.
      Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand.
      ,
      • Vivian J.P.
      • Duncan R.C.
      • Berry R.
      • O'Connor G.M.
      • Reid H.H.
      • Beddoe T.
      • Gras S.
      • Saunders P.M.
      • Olshina M.A.
      • Widjaja J.M.L.
      • Harpur C.M.
      • Lin J.
      • Maloveste S.M.
      • Price D.A.
      • Lafont B.A.P.
      • McVicar D.W.
      • Clements C.S.
      • Brooks A.G.
      • Rossjohn J.
      Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B.
      ,
      • Dam J.
      • Guan R.
      • Natarajan K.
      • Dimasi N.
      • Chlewicki L.K.
      • Kranz D.M.
      • Schuck P.
      • Margulies D.H.
      • Mariuzza R.A.
      Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2Kb.
      ). Key contact regions include the short arm of the α2 helix and the N-terminal end of the α1 helix, as well as the sides or bottoms of the β-sheet floor of the peptide-binding groove. Our data indicate that peptides can modulate the flexibility of each of these regions, suggesting a mechanism for the paradoxical peptide dependence that has been reported for some of these interactions (e.g. Ref.
      • Dam J.
      • Guan R.
      • Natarajan K.
      • Dimasi N.
      • Chlewicki L.K.
      • Kranz D.M.
      • Schuck P.
      • Margulies D.H.
      • Mariuzza R.A.
      Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2Kb.
      ). Thus it may be possible that the tuning of MHC dynamics by different peptides reflects a fundamental mechanism for modulating antigenicity.

      REFERENCES

        • Armstrong K.M.
        • Piepenbrink K.H.
        • Baker B.M.
        Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes.
        Biochem. J. 2008; 415: 183-196
        • Scott D.R.
        • Borbulevych O.Y.
        • Piepenbrink K.H.
        • Corcelli S.A.
        • Baker B.M.
        Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism.
        J. Mol. Biol. 2011; 414: 385-400
        • Hare B.J.
        • Wyss D.F.
        • Osburne M.S.
        • Kern P.S.
        • Reinherz E.L.
        • Wagner G.
        Structure, specificity, and CDR mobility of a class II restricted single-chain T-cell receptor.
        Nat Struct Biol. 1999; 6: 574-581
        • Borbulevych O.Y.
        • Santhanagopolan S.M.
        • Hossain M.
        • Baker B.M.
        TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms.
        J. Immunol. 2011; 187: 2453-2463
        • Tynan F.E.
        • Reid H.H.
        • Kjer-Nielsen L.
        • Miles J.J.
        • Wilce M.C.J.
        • Kostenko L.
        • Borg N.A.
        • Williamson N.A.
        • Beddoe T.
        • Purcell A.W.
        • Burrows S.R.
        • McCluskey J.
        • Rossjohn J.
        A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule.
        Nat Immunol. 2007; 8: 268-276
        • Insaidoo F.K.
        • Borbulevych O.Y.
        • Hossain M.
        • Santhanagopolan S.M.
        • Baxter T.K.
        • Baker B.M.
        Loss of T cell antigen recognition arising from changes in peptide and major histocompatibility complex protein flexibility: implications for vaccine design.
        J. Biol. Chem. 2011; 286: 40163-40173
        • Narzi D.
        • Becker C.M.
        • Fiorillo M.T.
        • Uchanska-Ziegler B.
        • Ziegler A.
        • Böckmann R.A.
        Dynamical characterization of two differentially disease associated MHC class I proteins in complex with viral and self-peptides.
        J. Mol. Biol. 2012; 415: 429-442
        • Pöhlmann T.
        • Böckmann R.A.
        • Grubmüller H.
        • Uchanska-Ziegler B.
        • Ziegler A.
        • Alexiev U.
        Differential peptide dynamics is linked to major histocompatibility complex polymorphism.
        J. Biol. Chem. 2004; 279: 28197-28201
        • Mazza C.
        • Auphan-Anezin N.
        • Gregoire C.
        • Guimezanes A.
        • Kellenberger C.
        • Roussel A.
        • Kearney A.
        • van der Merwe P.A.
        • Schmitt-Verhulst A.M.
        • Malissen B.
        How much can a T-cell antigen receptor adapt to structurally distinct antigenic peptides?.
        EMBO J. 2007; 26: 1972-1983
        • Borbulevych O.Y.
        • Piepenbrink K.H.
        • Gloor B.E.
        • Scott D.R.
        • Sommese R.F.
        • Cole D.K.
        • Sewell A.K.
        • Baker B.M.
        T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
        Immunity. 2009; 31: 885-896
        • Garboczi D.N.
        • Ghosh P.
        • Utz U.
        • Fan Q.R.
        • Biddison W.E.
        • Wiley D.C.
        Structure of the complex between human T-cell receptor, viral peptide and HLA-A2.
        Nature. 1996; 384: 134-141
        • Borbulevych O.Y.
        • Piepenbrink K.H.
        • Baker B.M.
        Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics.
        J. Immunol. 2011; 186: 2950-2958
        • Csermely P.
        • Palotai R.
        • Nussinov R.
        Induced fit, conformational selection, and independent dynamic segments: an extended view of binding events.
        Trends Biochem. Sci. 2010; 35: 539-546
        • Fabian H.
        • Loll B.
        • Huser H.
        • Naumann D.
        • Uchanska-Ziegler B.
        • Ziegler A.
        Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy.
        FEBS J. 2011; 278: 1713-1727
        • Fabian H.
        • Huser H.
        • Narzi D.
        • Misselwitz R.
        • Loll B.
        • Ziegler A.
        • Böckmann R.A.
        • Uchanska-Ziegler B.
        • Naumann D.
        HLA-B27 subtypes differentially associated with disease exhibit conformational differences in solution.
        J. Mol. Biol. 2008; 376: 798-810
        • Zinkernagel R.M.
        • Doherty P.C.
        Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis.
        Nature. 1974; 251: 547-548
        • Davis-Harrison R.L.
        • Armstrong K.M.
        • Baker B.M.
        Two different T cell receptors use different thermodynamic strategies to recognize the same peptide/MHC ligand.
        J. Mol. Biol. 2005; 346: 533-550
        • Hawse W.F.
        • Champion M.M.
        • Joyce M.V.
        • Hellman L.M.
        • Hossain M.
        • Ryan V.
        • Pierce B.G.
        • Weng Z.
        • Baker B.M.
        Cutting edge: Evidence for a dynamically driven T cell signaling mechanism.
        J. Immunol. 2012; 188: 5819-5823
        • Binz A.K.
        • Rodriguez R.C.
        • Biddison W.E.
        • Baker B.M.
        Thermodynamic and kinetic analysis of a peptide-class I MHC interaction highlights the noncovalent nature and conformational dynamics of the class I heterotrimer.
        Biochemistry. 2003; 42: 4954-4961
        • Kumar P.
        • Bansal M.
        HELANAL-Plus: a web server for analysis of helix geometry in protein structures.
        J. Biomol. Struct. Dyn. 2012; 30: 773-783
        • Laskowski R.A.
        • Swindells M.B.
        LigPlot+: multiple ligand-protein interaction diagrams for drug discovery.
        J. Chem. Inf. Model. 2011; 51: 2778-2786
        • Marcsisin S.R.
        • Engen J.R.
        Hydrogen exchange mass spectrometry: what is it and what can it tell us?.
        Analytical and bioanalytical chemistry. 2010; 397: 967-972
        • Painter C.A.
        • Negroni M.P.
        • Kellersberger K.A.
        • Zavala-Ruiz Z.
        • Evans J.E.
        • Stern L.J.
        Conformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange.
        Proc. Natl. Acad. Sci. U.S.A. 2011; 108: 19329-19334
        • Khan A.R.
        • Baker B.M.
        • Ghosh P.
        • Biddison W.E.
        • Wiley D.C.
        The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site.
        J. Immunol. 2000; 164: 6398-6405
        • Sliz P.
        • Michielin O.
        • Cerottini J.-C.
        • Luescher I.
        • Romero P.
        • Karplus M.
        • Wiley D.C.
        Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes.
        J. Immunol. 2001; 167: 3276-3284
        • Madden D.R.
        • Garboczi D.N.
        • Wiley D.C.
        The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.
        Cell. 1993; 75: 693-708
        • Bouvier M.
        • Guo H.C.
        • Smith K.J.
        • Wiley D.C.
        Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group.
        Proteins. 1998; 33: 97-106
        • Gao G.F.
        • Tormo J.
        • Gerth U.C.
        • Wyer J.R.
        • McMichael A.J.
        • Stuart D.I.
        • Bell J.I.
        • Jones E.Y.
        • Jakobsen B.K.
        Crystal structure of the complex between human CD8αα and HLA-A2.
        Nature. 1997; 387: 630-634
        • Deng L.
        • Cho S.
        • Malchiodi E.L.
        • Kerzic M.C.
        • Dam J.
        • Mariuzza R.A.
        Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors.
        J. Biol. Chem. 2008; 283: 16840-16849
        • Borbulevych O.Y.
        • Baxter T.K.
        • Yu Z.
        • Restifo N.P.
        • Baker B.M.
        Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design.
        J. Immunol. 2005; 174: 4812-4820
        • Wooldridge L.
        • Lissina A.
        • Vernazza J.
        • Gostick E.
        • Laugel B.
        • Hutchinson S.L.
        • Mirza F.
        • Dunbar P.R.
        • Boulter J.M.
        • Glick M.
        • Cerundolo V.
        • van den Berg H.A.
        • Price D.A.
        • Sewell A.K.
        Enhanced immunogenicity of CTL antigens through mutation of the CD8 binding MHC class I invariant region.
        Eur. J. Immunol. 2007; 37: 1323-1333
        • Smith K.J.
        • Reid S.W.
        • Stuart D.I.
        • McMichael A.J.
        • Jones E.Y.
        • Bell J.I.
        An altered position of the α2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501.
        Immunity. 1996; 4: 203-213
        • Cerutti D.S.
        • Le Trong I.
        • Stenkamp R.E.
        • Lybrand T.P.
        Simulations of a protein crystal: explicit treatment of crystallization conditions links theory and experiment in the streptavidin-biotin complex.
        Biochemistry. 2008; 47: 12065-12077
        • Reichert D.
        • Zinkevich T.
        • Saalwächter K.
        • Krushelnitsky A.
        The relation of the X-ray B-factor to protein dynamics: insights from recent dynamic solid-state NMR data.
        J. Biomol. Struct. Dyn. 2012; 30: 617-627
        • Tsai C.-J.
        • Ma B.
        • Nussinov R.
        Folding and binding cascades: shifts in energy landscapes.
        Proc. Natl. Acad. Sci. U.S.A. 1999; 96: 9970-9972
        • Miller D.W.
        • Dill K.A.
        Ligand binding to proteins: the binding landscape model.
        Protein Sci. 1997; 6: 2166-2179
        • Wrabl J.O.
        • Gu J.
        • Liu T.
        • Schrank T.P.
        • Whitten S.T.
        • Hilser V.J.
        The role of protein conformational fluctuations in allostery, function, and evolution.
        Biophys Chem. 2011; 159: 129-141
        • Frederick K.K.
        • Marlow M.S.
        • Valentine K.G.
        • Wand A.J.
        Conformational entropy in molecular recognition by proteins.
        Nature. 2007; 448: 325-329
        • Masterson L.R.
        • Shi L.
        • Metcalfe E.
        • Gao J.
        • Taylor S.S.
        • Veglia G.
        Dynamically committed, uncommitted, and quenched states encoded in protein kinase A revealed by NMR spectroscopy.
        Proc. Natl. Acad. Sci. U.S.A. 2011; 108: 6969-6974
        • Boehr D.D.
        • McElheny D.
        • Dyson H.J.
        • Wright P.E.
        Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands.
        Proc. Natl. Acad. Sci. U.S.A. 2010; 107: 1373-1378
        • Smock R.G.
        • Gierasch L.M.
        Sending signals dynamically.
        Science. 2009; 324: 198-203
        • Baker B.M.
        • Scott D.R.
        • Blevins S.J.
        • Hawse W.F.
        Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism.
        Immunological Reviews. 2012; 250: 10-31
        • Garcia K.C.
        • Adams J.J.
        • Feng D.
        • Ely L.K.
        The molecular basis of TCR germline bias for MHC is surprisingly simple.
        Nat Immunol. 2009; 10: 143-147
        • Mason D.
        A very high level of crossreactivity is an essential feature of the T-cell receptor.
        Immunology Today. 1998; 19: 395-404
        • Ding Y.H.
        • Baker B.M.
        • Garboczi D.N.
        • Biddison W.E.
        • Wiley D.C.
        Four A6-TCR/peptide/HLA-A2 structures that generate very different T cell signals are nearly identical.
        Immunity. 1999; 11: 45-56
        • Cole D.K.
        • Edwards E.S.
        • Wynn K.K.
        • Clement M.
        • Miles J.J.
        • Ladell K.
        • Ekeruche J.
        • Gostick E.
        • Adams K.J.
        • Skowera A.
        • Peakman M.
        • Wooldridge L.
        • Price D.A.
        • Sewell A.K.
        Modification of MHC anchor residues generates heteroclitic peptides that alter TCR binding and T cell recognition.
        J. Immunol. 2010; 185: 2600-2610
        • Painter C.A.
        • Stern L.J.
        Conformational variation in structures of classical and non-classical MHCII proteins and functional implications.
        Immunological Reviews. 2012; 250: 144-157
        • Natarajan K.
        • Dimasi N.
        • Wang J.
        • Mariuzza R.A.
        • Margulies D.H.
        Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
        Annual Review of Immunology. 2002; 20: 853-885
        • Boyington J.C.
        • Motyka S.A.
        • Schuck P.
        • Brooks A.G.
        • Sun P.D.
        Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand.
        Nature. 2000; 405: 537-543
        • Vivian J.P.
        • Duncan R.C.
        • Berry R.
        • O'Connor G.M.
        • Reid H.H.
        • Beddoe T.
        • Gras S.
        • Saunders P.M.
        • Olshina M.A.
        • Widjaja J.M.L.
        • Harpur C.M.
        • Lin J.
        • Maloveste S.M.
        • Price D.A.
        • Lafont B.A.P.
        • McVicar D.W.
        • Clements C.S.
        • Brooks A.G.
        • Rossjohn J.
        Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B.
        Nature. 2011; 479: 401-405
        • Dam J.
        • Guan R.
        • Natarajan K.
        • Dimasi N.
        • Chlewicki L.K.
        • Kranz D.M.
        • Schuck P.
        • Margulies D.H.
        • Mariuzza R.A.
        Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2Kb.
        Nat Immunol. 2003; 4: 1213-1222