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Knapp B, Dorffner G, Schreiner W. Early relaxation dynamics in the LC 13 T cell receptor in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS One 2013; 8:e64464. [PMID: 23762240 PMCID: PMC3675092 DOI: 10.1371/journal.pone.0064464] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/15/2013] [Indexed: 01/24/2023] Open
Abstract
The interaction between the T cell receptor and the major histocompatibility complex is one of the most important events in adaptive immunology. Although several different models for the activation process of the T cell via the T cell receptor have been proposed, it could not be shown that a structural mechanism, which discriminates between peptides of different immunogenicity levels, exists within the T cell receptor. In this study, we performed systematic molecular dynamics simulations of 172 closely related altered peptide ligands in the same T cell receptor/major histocompatibility complex system. Statistical evaluations yielded significant differences in the initial relaxation process between sets of peptides at four different immunogenicity levels.
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Affiliation(s)
- Bernhard Knapp
- Center for Medical Statistics, Informatics and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria.
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52
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Hischenhuber B, Havlicek H, Todoric J, Höllrigl-Binder S, Schreiner W, Knapp B. Differential geometric analysis of alterations in MH α-helices. J Comput Chem 2013; 34:1862-79. [PMID: 23703160 PMCID: PMC3739936 DOI: 10.1002/jcc.23328] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/12/2013] [Accepted: 04/13/2013] [Indexed: 01/03/2023]
Abstract
Antigen presenting cells present processed peptides via their major histocompatibility (MH) complex to the T cell receptors (TRs) of T cells. If a peptide is immunogenic, a signaling cascade can be triggered within the T cell. However, the binding of different peptides and/or different TRs to MH is also known to influence the spatial arrangement of the MH α-helices which could itself be an additional level of T cell regulation. In this study, we introduce a new methodology based on differential geometric parameters to describe MH deformations in a detailed and comparable way. For this purpose, we represent MH α-helices by curves. On the basis of these curves, we calculate in a first step the curvature and torsion to describe each α-helix independently. In a second step, we calculate the distribution parameter and the conical curvature of the ruled surface to describe the relative orientation of the two α-helices. On the basis of four different test sets, we show how these differential geometric parameters can be used to describe changes in the spatial arrangement of the MH α-helices for different biological challenges. In the first test set, we illustrate on the basis of all available crystal structures for (TR)/pMH complexes how the binding of TRs influences the MH helices. In the second test set, we show a cross evaluation of different MH alleles with the same peptide and the same MH allele with different peptides. In the third test set, we present the spatial effects of different TRs on the same peptide/MH complex. In the fourth test set, we illustrate how a severe conformational change in an α-helix can be described quantitatively. Taken together, we provide a novel structural methodology to numerically describe subtle and severe alterations in MH α-helices for a broad range of applications.
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Affiliation(s)
- Birgit Hischenhuber
- Center for Medical Statistics, Informatics, and Intelligent Systems, Section for Biosimulation and Bioinformatics, Medical University of Vienna, Vienna, Austria
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53
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Deng L, Luo M, Velikovsky A, Mariuzza RA. Structural Insights into the Evolution of the Adaptive Immune System. Annu Rev Biophys 2013; 42:191-215. [DOI: 10.1146/annurev-biophys-083012-130422] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lu Deng
- Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Ming Luo
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850;
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Alejandro Velikovsky
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Roy A. Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, W.M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
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54
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Kumar A, Cocco E, Atzori L, Marrosu MG, Pieroni E. Structural and dynamical insights on HLA-DR2 complexes that confer susceptibility to multiple sclerosis in Sardinia: a molecular dynamics simulation study. PLoS One 2013; 8:e59711. [PMID: 23555757 PMCID: PMC3608583 DOI: 10.1371/journal.pone.0059711] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 02/17/2013] [Indexed: 12/28/2022] Open
Abstract
Sardinia is a major Island in the Mediterranean with a high incidence of multiple sclerosis, a chronic autoimmune inflammatory disease of the central nervous system. Disease susceptibility in Sardinian population has been associated with five alleles of major histocompatibility complex (MHC) class II DRB1 gene. We performed 120 ns of molecular dynamics simulation on one predisposing and one protective alleles, unbound and in complex with the two relevant peptides: Myelin Basic Protein and Epstein Barr Virus derived peptide. In particular we focused on the MHC peptide binding groove dynamics. The predisposing allele was found to form a stable complex with both the peptides, while the protective allele displayed stability only when bound with myelin peptide. The local flexibility of the MHC was probed dividing the binding groove into four compartments covering the well known peptide anchoring pockets. The predisposing allele in the first half cleft exhibits a narrower and more rigid groove conformation in the presence of myelin peptide. The protective allele shows a similar behavior, while in the second half cleft it displays a narrower and more flexible groove conformation in the presence of viral peptide. We further characterized these dynamical differences by evaluating H-bonds, hydrophobic and stacking interaction networks, finding striking similarities with super-type patterns emerging in other autoimmune diseases. The protective allele shows a defined preferential binding to myelin peptide, as confirmed by binding free energy calculations. All together, we believe the presented molecular analysis could help to design experimental assays, supports the molecular mimicry hypothesis and suggests that propensity to multiple sclerosis in Sardinia could be partly linked to distinct peptide-MHC interaction and binding characteristics of the antigen presentation mechanism.
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Affiliation(s)
- Amit Kumar
- Multiple Sclerosis Center, Department of Public Health and Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
- CRS4 Science and Technology Park Polaris, Bio-Engineering Group, Piscina Manna, Pula (CA) Italy
- Department of Biomedical Sciences, Oncology and Molecular Pathology Unit, University of Cagliari, Cagliari, Italy
- * E-mail: (AK); (EP)
| | - Eleonora Cocco
- Multiple Sclerosis Center, Department of Public Health and Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Luigi Atzori
- Department of Biomedical Sciences, Oncology and Molecular Pathology Unit, University of Cagliari, Cagliari, Italy
| | - Maria Giovanna Marrosu
- Multiple Sclerosis Center, Department of Public Health and Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Enrico Pieroni
- CRS4 Science and Technology Park Polaris, Bio-Engineering Group, Piscina Manna, Pula (CA) Italy
- * E-mail: (AK); (EP)
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55
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Baker BM, Scott DR, Blevins SJ, Hawse WF. Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunol Rev 2013; 250:10-31. [PMID: 23046120 DOI: 10.1111/j.1600-065x.2012.01165.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past two decades, structural biology has shown how T-cell receptors engage peptide/major histocompatibility complex (MHC) complexes and provided insight into the mechanisms underlying antigen specificity and cross-reactivity. Here we review and contextualize our contributions, which have emphasized the influence of structural changes and molecular flexibility. A repeated observation is the presence of conformational melding, in which the T-cell receptor (TCR), peptide, and in some cases, MHC protein cooperatively adjust in order for recognition to proceed. The structural changes reflect the intrinsic dynamics of the unligated proteins. Characterization of the dynamics of unligated TCR shows how binding loop motion can influence TCR cross-reactivity as well as specificity towards peptide and MHC. Examination of peptide dynamics indicates not only peptide-specific variation but also a peptide dependence to MHC flexibility. This latter point emphasizes that the TCR engages a composite peptide/MHC surface and that physically the receptor makes little distinction between the peptide and MHC. Much additional evidence for this can be found within the database of available structures, including our observations of a peptide dependence to the TCR binding mode and structural compensations for altered interatomic interactions, in which lost TCR-peptide interactions are replaced with TCR-MHC interactions. The lack of a hard-coded physical distinction between peptide and MHC has implications not only for specificity and cross-reactivity but also the mechanisms underlying MHC restriction as well as attempts to modulate and control TCR recognition.
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Affiliation(s)
- Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, USA.
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56
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Limitations of time-resolved fluorescence suggested by molecular simulations: assessing the dynamics of T cell receptor binding loops. Biophys J 2012; 103:2532-40. [PMID: 23260055 DOI: 10.1016/j.bpj.2012.10.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/23/2012] [Accepted: 10/31/2012] [Indexed: 11/21/2022] Open
Abstract
Time-resolved fluorescence anisotropy (TRFA) has a rich history in evaluating protein dynamics. Yet as often employed, TRFA assumes that the motional properties of a covalently tethered fluorescent probe accurately portray the motional properties of the protein backbone at the probe attachment site. In an extensive survey using TRFA to study the dynamics of the binding loops of a αβ T cell receptor, we observed multiple discrepancies between the TRFA data and previously published results that led us to question this assumption. We thus simulated several of the experimentally probed systems using a protocol that permitted accurate determination of probe and protein time correlation functions. We found excellent agreement in the decays of the experimental and simulated correlation functions. However, the motional properties of the probe were poorly correlated with those of the backbone of both the labeled and unlabeled protein. Our results warrant caution in the interpretation of TRFA data and suggest further studies to ascertain the extent to which probe dynamics reflect those of the protein backbone. Meanwhile, the agreement between experiment and computation validates the use of molecular dynamics simulations as an accurate tool for exploring the molecular motion of T cell receptors and their binding loops.
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57
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Ferber M, Zoete V, Michielin O. T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions. PLoS One 2012; 7:e51943. [PMID: 23251658 PMCID: PMC3522592 DOI: 10.1371/journal.pone.0051943] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 11/08/2012] [Indexed: 11/19/2022] Open
Abstract
Crystallographic data about T-Cell Receptor - peptide - major histocompatibility complex class I (TCRpMHC) interaction have revealed extremely diverse TCR binding modes triggering antigen recognition. Understanding the molecular basis that governs TCR orientation over pMHC is still a considerable challenge. We present a simplified rigid approach applied on all non-redundant TCRpMHC crystal structures available. The CHARMM force field in combination with the FACTS implicit solvation model is used to study the role of long-distance interactions between the TCR and pMHC. We demonstrate that the sum of the coulomb interactions and the electrostatic solvation energies is sufficient to identify two orientations corresponding to energetic minima at 0° and 180° from the native orientation. Interestingly, these results are shown to be robust upon small structural variations of the TCR such as changes induced by Molecular Dynamics simulations, suggesting that shape complementarity is not required to obtain a reliable signal. Accurate energy minima are also identified by confronting unbound TCR crystal structures to pMHC. Furthermore, we decompose the electrostatic energy into residue contributions to estimate their role in the overall orientation. Results show that most of the driving force leading to the formation of the complex is defined by CDR1,2/MHC interactions. This long-distance contribution appears to be independent from the binding process itself, since it is reliably identified without considering neither short-range energy terms nor CDR induced fit upon binding. Ultimately, we present an attempt to predict the TCR/pMHC binding mode for a TCR structure obtained by homology modeling. The simplicity of the approach and the absence of any fitted parameters make it also easily applicable to other types of macromolecular protein complexes.
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Affiliation(s)
- Mathias Ferber
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (VZ); (OM)
| | - Olivier Michielin
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (VZ); (OM)
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58
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Dynamics of free versus complexed β2-microglobulin and the evolution of interfaces in MHC class I molecules. Immunogenetics 2012; 65:157-72. [PMID: 23229474 DOI: 10.1007/s00251-012-0667-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
In major histocompatibility complex (MHC) class I molecules, monomorphic β(2)-microglobulin (β(2)m) is non-covalently bound to a heavy chain (HC) exhibiting a variable degree of polymorphism. β(2)M can stabilize a wide variety of complexes ranging from classical peptide binding to nonclassical lipid presenting MHC class I molecules as well as to MHC class I-like molecules that do not bind small ligands. Here we aim to assess the dynamics of individual regions in free as well as complexed β(2)m and to understand the evolution of the interfaces between β(2)m and different HC. Using human β(2)m and the HLA-B*27:09 complex as a model system, a comparison of free and HC-bound β(2)m by nuclear magnetic resonance spectroscopy was initially carried out. Although some regions retain their flexibility also after complex formation, these studies reveal that most parts of β(2)m gain rigidity upon binding to the HC. Sequence analyses demonstrate that some of the residues exhibiting flexibility participate in evolutionarily conserved β(2)m-HC contacts which are detectable in diverse vertebrate species or characterize a particular group of MHC class I complexes such as peptide- or lipid-binding molecules. Therefore, the spectroscopic experiments and the interface analyses demonstrate that β(2)m fulfills its role of interacting with diverse MHC class I HC as well as effector cell receptors not only by engaging in conserved intermolecular contacts but also by falling back upon key interface residues that exhibit a high degree of flexibility.
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59
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Abstract
The bias of αβ T cells for MHC ligands has been proposed to be intrinsic to the T-cell receptor (TCR). Equally, the CD4 and CD8 coreceptors contribute to ligand restriction by colocalizing Lck with the TCR when MHC ligands are engaged. To determine the importance of intrinsic ligand bias, the germ-line TCR complementarity determining regions were extensively diversified in vivo. We show that engagement with MHC ligands during thymocyte selection and peripheral T-cell activation imposes remarkably little constraint over TCR structure. Such versatility is more consistent with an opportunist, rather than a predetermined, mode of interface formation. This hypothesis was experimentally confirmed by expressing a hybrid TCR containing TCR-γ chain germ-line complementarity determining regions, which engaged efficiently with MHC ligands.
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60
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Allerbring EB, Duru AD, Uchtenhagen H, Madhurantakam C, Tomek MB, Grimm S, Mazumdar PA, Friemann R, Uhlin M, Sandalova T, Nygren PÅ, Achour A. Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics. Eur J Immunol 2012; 42:2990-3000. [PMID: 22837158 DOI: 10.1002/eji.201242588] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/18/2012] [Accepted: 07/23/2012] [Indexed: 11/07/2022]
Abstract
The molecular basis underlying T-cell recognition of MHC molecules presenting altered peptide ligands is still not well-established. A hierarchy of T-cell activation by MHC class I-restricted altered peptide ligands has been defined using the T-cell receptor P14 specific for H-2D(b) in complex with the immunodominant lymphocytic choriomeningitis virus peptide gp33 (KAVYNFATM). While substitution of tyrosine to phenylalanine (Y4F) or serine (Y4S) abolished recognition by P14, the TCR unexpectedly recognized H-2D(b) in complex with the alanine-substituted semiagonist Y4A, which displayed the most significant structural modification. The observed functional hierarchy gp33 > Y4A > Y4S = Y4F was neither due to higher stabilization capacity nor to differences in structural conformation. However, thermodynamic analysis demonstrated that while recognition of the full agonist H-2D(b) /gp33 was strictly enthalpy driven, recognition of the weak agonist H-2D(b) /Y4A was instead entropy driven with a large reduction in the favorable enthalpy term. The fourfold larger negative heat capacity derived for the interaction of P14 with H-2D(b) /gp33 compared with H-2D(b) /Y4A can possibly be explained by higher water entrapment at the TCR/MHC interface, which is also consistent with the measured opposite entropy contributions for the interactions of P14 with both MHCs. In conclusion, this study demonstrates that P14 makes use of different strategies to adapt to structural modifications in the MHC/peptide complex.
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Affiliation(s)
- Eva B Allerbring
- Center for Infectious Medicine, Department of Medicine, Karolinska University Hospital Huddinge, Karolinska Institutet, Stockholm, Sweden
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61
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Lynch JN, Donermeyer DL, Weber KS, Kranz DM, Allen PM. Subtle changes in TCRα CDR1 profoundly increase the sensitivity of CD4 T cells. Mol Immunol 2012; 53:283-94. [PMID: 22982754 DOI: 10.1016/j.molimm.2012.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 08/15/2012] [Accepted: 08/18/2012] [Indexed: 10/27/2022]
Abstract
Changes in the peptide and MHC molecules have been extensively examined for how they alter T cell activation, but many fewer studies have examined the TCR. Structural studies of how TCR differences alter T cell specificity have focused on broad variation in the CDR3 loops. However, changes in the CDR1 and 2 loops can also alter TCR recognition of pMHC. In this study we focus on two mutations in the CDR1α loop of the TCR that increased the affinity of a TCR for agonist Hb(64-76)/I-E(k) by increasing the on-rate of the reaction. These same mutations also conferred broader recognition of altered peptide ligands. TCR transgenic mice expressing the CDR1α mutations had altered thymic selection, as most of the T cells were negatively selected compared to T cells expressing the wildtype TCR. The few T cells that escaped negative selection and were found in the periphery were rendered anergic, thereby avoiding autoimmunity. T cells with the CDR1α mutations were completely deleted in the presence of Hb(64-76) as an endogenous peptide. Interestingly, the wildtype T cells were not eliminated, identifying a threshold affinity for negative selection where a 3-fold increase in affinity is the difference between incomplete and complete deletion. Overall, these studies highlight how small changes in the TCR can increase the affinity of TCR:pMHC but with the consequences of skewing selection and producing an unresponsive T cell.
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Affiliation(s)
- Jennifer N Lynch
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, United States
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62
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Holland CJ, Rizkallah PJ, Vollers S, Calvo-Calle JM, Madura F, Fuller A, Sewell AK, Stern LJ, Godkin A, Cole DK. Minimal conformational plasticity enables TCR cross-reactivity to different MHC class II heterodimers. Sci Rep 2012; 2:629. [PMID: 22953050 PMCID: PMC3432979 DOI: 10.1038/srep00629] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 08/17/2012] [Indexed: 01/11/2023] Open
Abstract
Successful immunity requires that a limited pool of αβ T-cell receptors (TCRs) provide cover for a vast number of potential foreign peptide antigens presented by 'self' major histocompatibility complex (pMHC) molecules. Structures of unligated and ligated MHC class-I-restricted TCRs with different ligands, supplemented with biophysical analyses, have revealed a number of important mechanisms that govern TCR mediated antigen recognition. HA1.7 TCR binding to the influenza hemagglutinin antigen (HA(306-318)) presented by HLA-DR1 or HLA-DR4 represents an ideal system for interrogating pMHC-II antigen recognition. Accordingly, we solved the structure of the unligated HA1.7 TCR and compared it to both complex structures. Despite a relatively rigid binding mode, HA1.7 T-cells could tolerate mutations in key contact residues within the peptide epitope. Thermodynamic analysis revealed that limited plasticity and extreme favorable entropy underpinned the ability of the HA1.7 T-cell clone to cross-react with HA(306-318) presented by multiple MHC-II alleles.
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MESH Headings
- Amino Acid Sequence
- Cells, Cultured
- Cross Reactions
- Crystallography, X-Ray
- Epitopes/chemistry
- Epitopes/immunology
- HLA-DR1 Antigen/chemistry
- HLA-DR1 Antigen/immunology
- HLA-DR4 Antigen/chemistry
- HLA-DR4 Antigen/immunology
- Humans
- Hydrogen Bonding
- Hydrophobic and Hydrophilic Interactions
- Lymphocyte Activation
- Models, Molecular
- Protein Binding
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocytes/immunology
- T-Lymphocytes/physiology
- Thermodynamics
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Affiliation(s)
- Christopher J. Holland
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
| | - Pierre J. Rizkallah
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
| | - Sabrina Vollers
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655
| | - J. Mauricio Calvo-Calle
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Florian Madura
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
| | - Anna Fuller
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
| | - Andrew K. Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
| | - Lawrence J. Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Andrew Godkin
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
- Department of Integrated Medicine, University Hospital of Wales, Cardiff, CF14 4XW, United Kingdom
- These authors contributed equally
| | - David K. Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff, CF14 4XN, United Kingdom
- These authors contributed equally
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63
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Abstract
Clonal selection theory proposed that individual T cells are specific for a single peptide-MHC antigen. However, the repertoire of αβ T cell receptors (TCRs) is dwarfed by the vast array of potential foreign peptide-MHC complexes, and a comprehensive system requires each T cell to recognize numerous peptides and thus be cross-reactive. This compromise on specificity has profound implications because the chance of any natural peptide-MHC ligand being an optimal fit for its cognate TCR is small, as there will almost always be more-potent agonists. Furthermore, any TCR raised against a specific peptide-MHC complex in vivo can only be the best available solution from the naive T cell pool and is unlikely to be the best possible solution from the substantially greater number of TCRs that could theoretically be produced. This 'systems view' of TCR recognition provides a plausible cause for autoimmune disease and substantial scope for multiple therapeutic interventions.
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Affiliation(s)
- Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
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64
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Reboul CF, Meyer GR, Porebski BT, Borg NA, Buckle AM. Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex. PLoS Comput Biol 2012; 8:e1002404. [PMID: 22412359 PMCID: PMC3297556 DOI: 10.1371/journal.pcbi.1002404] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 01/11/2012] [Indexed: 11/25/2022] Open
Abstract
The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent ‘snapshots’ and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6–9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into ‘scanning’ mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography. When pathogens replicate within a host cell, their proteins are degraded into peptides, which are captured by the major histocompatibility complex (MHC) and brought to the cell surface. The peptide-MHC (pMHC) is surveyed by T cell receptors (TCRs) expressed on the surface of T cells. If the peptide is foreign, the peptide-MHC-TCR interaction initiates an immune response to eliminate the pathogen. However, the combinations of pMHC and TCRs are diverse. We ask how TCRs discriminate between structurally similar pMHCs? We address this by focusing on two MHC molecules that differ by a single change, both bind the same peptide but only one instigates a dominant immune response. Intriguingly, the single difference between the two MHCs does not alter the peptide shape nor does it contact the peptide or TCR. We examined the flexibility of the pMHC-TCR interface using molecular dynamics simulations. We observed differences in the peptide and TCR flexibilities that could explain their contrasting physiologies, as well as clues to how the TCR moves atop the MHC in order to ‘scan’ it. Our analysis provides insight into a particular pMHC-TCR interaction not accessible using crystallographic methods, and indicate dynamics may play an influential and perhaps under-appreciated role in other pMHC-TCR systems.
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Affiliation(s)
- Cyril F. Reboul
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Victoria, Australia
| | - Grischa R. Meyer
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- Monash eResearch Centre, Monash University, Victoria, Australia
| | - Benjamin T. Porebski
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
| | - Natalie A. Borg
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- * E-mail: (NAB); (AMB)
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
- * E-mail: (NAB); (AMB)
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65
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Bridgeman JS, Sewell AK, Miles JJ, Price DA, Cole DK. Structural and biophysical determinants of αβ T-cell antigen recognition. Immunology 2012; 135:9-18. [PMID: 22044041 DOI: 10.1111/j.1365-2567.2011.03515.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The molecular rules that govern MHC restriction, and allow T-cells to differentiate between peptides derived from healthy cells and those from diseased cells, remain poorly understood. Here we provide an overview of the structural constraints that enable the T-cell receptor (TCR) to discriminate between self and non-self peptides, and summarize studies that have attempted to correlate the biophysical parameters of TCR/peptide-major histocompatibility complex (pMHC) binding with T-cell activation. We further review how the antigenic origin of peptide epitopes affects TCR binding parameters and the 'quality' of a T-cell response. Understanding the principles that govern pMHC recognition by T-cells will unlock pathways to the rational development of immunotherapeutic approaches for the treatment of infectious disease, cancer and autoimmunity.
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Affiliation(s)
- John S Bridgeman
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, UK
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66
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Bulek AM, Cole DK, Skowera A, Dolton G, Gras S, Madura F, Fuller A, Miles JJ, Gostick E, Price DA, Drijfhout JW, Knight RR, Huang GC, Lissin N, Molloy PE, Wooldridge L, Jakobsen BK, Rossjohn J, Peakman M, Rizkallah PJ, Sewell AK. Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes. Nat Immunol 2012; 13:283-9. [PMID: 22245737 PMCID: PMC3378510 DOI: 10.1038/ni.2206] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/06/2011] [Indexed: 12/11/2022]
Abstract
The structural characteristics of the engagement of major histocompatibility complex (MHC) class II-restricted self antigens by autoreactive T cell antigen receptors (TCRs) is established, but how autoimmune TCRs interact with complexes of self peptide and MHC class I has been unclear. Here we examined how CD8(+) T cells kill human islet beta cells in type 1 diabetes via recognition of a human leukocyte antigen HLA-A*0201-restricted glucose-sensitive preproinsulin peptide by the autoreactive TCR 1E6. Rigid 'lock-and-key' binding underpinned the 1E6-HLA-A*0201-peptide interaction, whereby 1E6 docked similarly to most MHC class I-restricted TCRs. However, this interaction was extraordinarily weak because of limited contacts with MHC class I. TCR binding was highly peptide centric, dominated by two residues of the complementarity-determining region 3 (CDR3) loops that acted as an 'aromatic-cap' over the complex of peptide and MHC class I (pMHCI). Thus, highly focused peptide-centric interactions associated with suboptimal TCR-pMHCI binding affinities might lead to thymic escape and potential CD8(+) T cell-mediated autoreactivity.
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Affiliation(s)
- Anna M Bulek
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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67
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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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68
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69
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Leimgruber A, Ferber M, Irving M, Hussain-Kahn H, Wieckowski S, Derré L, Rufer N, Zoete V, Michielin O. TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires. PLoS One 2011; 6:e26301. [PMID: 22053188 PMCID: PMC3203878 DOI: 10.1371/journal.pone.0026301] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.
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Affiliation(s)
- Antoine Leimgruber
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
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70
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Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism. J Mol Biol 2011; 414:385-400. [PMID: 22019736 DOI: 10.1016/j.jmb.2011.10.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 11/21/2022]
Abstract
αβ T-cell receptors (TCRs) recognize multiple antigenic peptides bound and presented by major histocompatibility complex molecules. TCR cross-reactivity has been attributed in part to the flexibility of TCR complementarity-determining region (CDR) loops, yet there have been limited direct studies of loop dynamics to determine the extent of its role. Here we studied the flexibility of the binding loops of the αβ TCR A6 using crystallographic, spectroscopic, and computational methods. A significant role for flexibility in binding and cross-reactivity was indicated only for the CDR3α and CDR3β hypervariable loops. Examination of the energy landscapes of these two loops indicated that CDR3β possesses a broad, smooth energy landscape, leading to rapid sampling in the free TCR of a range of conformations compatible with different ligands. The landscape for CDR3α is more rugged, resulting in more limited conformational sampling that leads to specificity for a reduced set of peptides as well as the major histocompatibility complex protein. In addition to informing on the mechanisms of cross-reactivity and specificity, the energy landscapes of the two loops indicate a complex mechanism for TCR binding, incorporating elements of both conformational selection and induced fit in a manner that blends features of popular models for TCR recognition.
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71
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Cuendet MA, Zoete V, Michielin O. How T cell receptors interact with peptide-MHCs: A multiple steered molecular dynamics study. Proteins 2011; 79:3007-24. [DOI: 10.1002/prot.23104] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 05/18/2011] [Accepted: 05/20/2011] [Indexed: 12/11/2022]
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72
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T-Cell Clones Expressing Different T-Cell Receptors Accumulate in the Brains of Dying and Surviving Mice After Peripheral Infection with Far Eastern Strain of Tick-Borne Encephalitis Virus. Viral Immunol 2011; 24:291-302. [DOI: 10.1089/vim.2011.0017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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73
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Borbulevych OY, Santhanagopolan SM, Hossain M, Baker BM. TCRs used in cancer gene therapy cross-react with MART-1/Melan-A tumor antigens via distinct mechanisms. THE JOURNAL OF IMMUNOLOGY 2011; 187:2453-63. [PMID: 21795600 DOI: 10.4049/jimmunol.1101268] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
T cells engineered to express TCRs specific for tumor Ags can drive cancer regression. The first TCRs used in cancer gene therapy, DMF4 and DMF5, recognize two structurally distinct peptide epitopes of the melanoma-associated MART-1/Melan-A protein, both presented by the class I MHC protein HLA-A*0201. To help understand the mechanisms of TCR cross-reactivity and provide a foundation for the further development of immunotherapy, we determined the crystallographic structures of DMF4 and DMF5 in complex with both of the MART-1/Melan-A epitopes. The two TCRs use different mechanisms to accommodate the two ligands. Although DMF4 binds the two with a different orientation, altering its position over the peptide/MHC, DMF5 binds them both identically. The simpler mode of cross-reactivity by DMF5 is associated with higher affinity toward both ligands, consistent with the superior functional avidity of DMF5. More generally, the observation of two diverging mechanisms of cross-reactivity with the same Ags and the finding that TCR-binding orientation can be determined by peptide alone extend our understanding of the mechanisms underlying TCR cross-reactivity.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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74
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Wolfson MY, Nam K, Chakraborty AK. The effect of mutations on the alloreactive T cell receptor/peptide-MHC interface structure: a molecular dynamics study. J Phys Chem B 2011; 115:8317-27. [PMID: 21651302 PMCID: PMC3131071 DOI: 10.1021/jp202471d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
T cells orchestrate adaptive, pathogen-specific immune responses. T cells have a surface receptor (called TCR) whose ligands are complexes (pMHCs) of peptides (derived from pathogens or host proteins) and major histocompatibility complex proteins (MHCs). MHC proteins vary between hosts. During organ transplants, host TCRs interact with peptides present in complex with genetically different MHCs. This usually causes a vigorous immune response: alloreactivity. Studies of alloreactive protein interactions have yielded results that present a puzzle. Some crystallographic studies concluded that the alloreactive TCR/MHC interface is essentially unaffected by changing the TCR peptide-binding region, suggesting that the peptide does not influence the interface. Another biochemical study concluded from mutation data that different peptides can alter the binding interface with the same TCR. To explore the origin of this puzzle, we used molecular dynamics simulations to study the dependence of the TCR/pMHC interface on changes in both the peptide and the TCR. Our simulations show that the footprint of the TCR on the pMHC is insensitive to mutations of the TCR peptide-binding loops, but peptide mutations can make multiple local changes to TCR/pMHC contacts. Therefore, our results demonstrate that the structural and mutation data do not conflict and reveal how subtle, but important, characteristics of the alloreactive TCR/pMHC interface are influenced by the TCR and the peptide.
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Affiliation(s)
| | - Kwangho Nam
- To whom correspondence should be addressed: ; , Phone: +1 617 495 8997; +1 617 253 3890. Fax: +1 617 495 8755; +1 617 253 2272
| | - Arup K. Chakraborty
- To whom correspondence should be addressed: ; , Phone: +1 617 495 8997; +1 617 253 3890. Fax: +1 617 495 8755; +1 617 253 2272
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75
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Newell EW, Ely LK, Kruse AC, Reay PA, Rodriguez SN, Lin AE, Kuhns MS, Garcia KC, Davis MM. Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k). JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:5823-32. [PMID: 21490152 PMCID: PMC3754796 DOI: 10.4049/jimmunol.1100197] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures for the well-studied 2B4 TCR, as well as a naturally occurring variant of the 5c.c7 TCR, 226, which is cross-reactive with more than half of possible substitutions at all three TCR-sensitive residues on the peptide Ag. These structures alone and in complex with peptide-MHC ligands allow us to reassess many prior mutagenesis results. In addition, the structure of 226 bound to one peptide variant, p5E, shows major changes in the CDR3 contacts compared with wild-type, yet the TCR V-region contacts with MHC are conserved. These and other data illustrate the ability of TCRs to accommodate large variations in CDR3 structure and peptide contacts within the constraints of highly conserved TCR-MHC interactions.
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Affiliation(s)
- Evan W. Newell
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Lauren K. Ely
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Andrew C. Kruse
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Philip A. Reay
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Stephanie N. Rodriguez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Aaron E. Lin
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Michael S. Kuhns
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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76
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Abstract
This essay provides an analysis of the inadequacy of the current view of restrictive recognition of peptide by the T-cell antigen receptor. A competing model is developed, and the experimental evidence for the prevailing model is reinterpreted in the new framework. The goal is to contrast the two models with respect to their consistency, coverage of the data, explanatory power, and predictability.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute For Biological Studies, La Jolla, CA 92037, USA.
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77
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Khan JM, Ranganathan S. Understanding TR binding to pMHC complexes: how does a TR scan many pMHC complexes yet preferentially bind to one. PLoS One 2011; 6:e17194. [PMID: 21364947 PMCID: PMC3043089 DOI: 10.1371/journal.pone.0017194] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 01/22/2011] [Indexed: 01/08/2023] Open
Abstract
Understanding the basis of the binding of a T cell receptor (TR) to the peptide-MHC (pMHC) complex is essential due to the vital role it plays in adaptive immune response. We describe the use of computed binding (free) energy (BE), TR paratope, pMHC epitope, molecular surface electrostatic potential (MSEP) and calculated TR docking angle (θ) to analyse 61 TR/pMHC crystallographic structures to comprehend TR/pMHC interaction. In doing so, we have successfully demonstrated a novel/rational approach for θ calculation, obtained a linear correlation between BE and θ without any “codon” or amino acid preference, provided an explanation for TR ability to scan many pMHC ligands yet specifically bind one, proposed a mechanism for pMHC recognition by TR leading to T cell activation and illustrated the importance of the peptide in determining TR specificity, challenging the “germline bias” theory.
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MESH Headings
- Animals
- Comprehension/physiology
- Energy Metabolism/physiology
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Humans
- Lymphocyte Activation/immunology
- Mice
- Models, Biological
- Models, Molecular
- Multiprotein Complexes/chemistry
- Multiprotein Complexes/immunology
- Multiprotein Complexes/metabolism
- Protein Binding/physiology
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Receptors, Antigen, T-Cell/agonists
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Substrate Specificity/immunology
- T-Cell Antigen Receptor Specificity/immunology
- T-Cell Antigen Receptor Specificity/physiology
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Affiliation(s)
- Javed Mohammed Khan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
| | - Shoba Ranganathan
- Department of Chemistry and Biomolecular Sciences and ARC Centre of Excellence in Bioinformatics, Macquarie University, Sydney, Australia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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78
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Borbulevych OY, Piepenbrink KH, Baker BM. Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics. THE JOURNAL OF IMMUNOLOGY 2011; 186:2950-8. [PMID: 21282516 DOI: 10.4049/jimmunol.1003150] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The αβ TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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79
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Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations. Cell Biochem Biophys 2011; 60:283-95. [DOI: 10.1007/s12013-011-9151-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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80
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Erijman A, Aizner Y, Shifman JM. Multispecific Recognition: Mechanism, Evolution, and Design. Biochemistry 2011; 50:602-11. [DOI: 10.1021/bi101563v] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ariel Erijman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yonatan Aizner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Julia M. Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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81
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Sethi DK, Schubert DA, Anders AK, Heroux A, Bonsor DA, Thomas CP, Sundberg EJ, Pyrdol J, Wucherpfennig KW. A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC. ACTA ACUST UNITED AC 2011; 208:91-102. [PMID: 21199956 PMCID: PMC3023130 DOI: 10.1084/jem.20100725] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A TCR derived from a patient with relapsing-remitting multiple sclerosis engages the self-peptide myelin basic protein in the context of HLA-DQ1 in a very unusual way. Self-reactive T cells that escape elimination in the thymus can cause autoimmune pathology, and it is therefore important to understand the structural mechanisms of self-antigen recognition. We report the crystal structure of a T cell receptor (TCR) from a patient with relapsing-remitting multiple sclerosis that engages its self-peptide–major histocompatibility complex (pMHC) ligand in an unusual manner. The TCR is bound in a highly tilted orientation that prevents interaction of the TCR-α chain with the MHC class II β chain helix. In this structure, only a single germline-encoded TCR loop engages the MHC protein, whereas in most other TCR-pMHC structures all four germline-encoded TCR loops bind to the MHC helices. The tilted binding mode also prevents peptide contacts by the short complementarity-determining region (CDR) 3β loop, and interactions that contribute to peptide side chain specificity are focused on the CDR3α loop. This structure is the first example in which only a single germline-encoded TCR loop contacts the MHC helices. Furthermore, the reduced interaction surface with the peptide may facilitate TCR cross-reactivity. The structural alterations in the trimolecular complex are distinct from previously characterized self-reactive TCRs, indicating that there are multiple unusual ways for self-reactive TCRs to bind their pMHC ligand.
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Affiliation(s)
- Dhruv K Sethi
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA
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82
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Abstract
Our goal is to provide a perspective on current understanding of the origins of specificity in immune reactions, a topic that has intrigued scientists for over a century. A fundamental property of adaptive immune responses is the ability to discriminate among an immense variety of substances by means of antibodies (Abs) and Ab-like receptors on T lymphocytes [T-cell receptors (TCRs)], each able to bind a particular chemical structure [the antigen (Ag)] and not, or only weakly, similar alternatives. Evidence has long existed, however, and has grown, especially recently, that while exhibiting remarkable specificity, many individual Abs and TCRs can also bind a variety of very different ligands. How can Ag recognition by these receptors exercise the great specificity for which they are renowned and yet react with a variety of different ligands (degeneracy)? We critically consider the mechanistic bases for this specificity/degeneracy enigma and also compare and contrast Ag recognition by Abs and TCRs.
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83
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Douat-Casassus C, Borbulevych O, Tarbe M, Gervois N, Jotereau F, Baker BM, Quideau S. Crystal structures of HLA-A*0201 complexed with Melan-A/MART-1(26(27L)-35) peptidomimetics reveal conformational heterogeneity and highlight degeneracy of T cell recognition. J Med Chem 2010; 53:7061-6. [PMID: 20806940 DOI: 10.1021/jm100683p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is growing interest in using tumor associated antigens presented by class I major histocompatibility complex (MHC-I) proteins as cancer vaccines. As native peptides are poorly stable in biological fluids, researchers have sought to engineer synthetic peptidomimetics with greater biostability. Here, we demonstrate that antigenic peptidomimetics of the Melan-A/MART-1(26(27L)-35) melanoma antigen adopt strikingly different conformations when bound to MHC-I, highlighting the degeneracy of T cell recognition and revealing the challenges associated with mimicking native peptide conformation.
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Affiliation(s)
- Céline Douat-Casassus
- Institut des Sciences Moléculaires (UMR-CNRS 5255) and Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux, 2 Rue Robert Escarpit, 33607 Pessac, France
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84
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Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry 2010; 49:7050-9. [PMID: 20681514 DOI: 10.1021/bi901969a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the energetic and structural response to multiple mutations in a protein-protein interface is a key aspect of rational protein design. Here we investigate the cooperativity of combinations of point mutations of a T cell receptor (TCR) that binds in vivo to HLA-A2 MHC and a viral peptide. The mutations were obtained from two sources: a structure-based design study on the TCR alpha chain (nine mutations) and an in vitro selection study on the TCR beta chain (four mutations). In addition to combining the highest-affinity variants from each chain, we tested other combinations of mutations within and among the chains, for a total of 23 TCR mutants that we measured for binding kinetics to the peptide and major histocompatibility complex. A wide range of binding affinities was observed, from 2- to 1000-fold binding improvement versus that of the wild type, with significant nonadditive effects observed within and between TCR chains. This included an amino acid-dependent cooperative interaction between CDR1 and CDR3 residues that are separated by more than 9 A in the wild-type complex. When analyzing the kinetics of the mutations, we found that the association rates were primarily responsible for the cooperativity, while the dissociation rates were responsible for the anticooperativity (less-than-additive energetics). On the basis of structural modeling of anticooperative mutants, we determined that side chain clash between proximal mutants likely led to nonadditive binding energies. These results highlight the complex nature of TCR association and binding and will be informative in future design efforts that combine multiple mutant residues.
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Affiliation(s)
- Brian G Pierce
- Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
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85
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Modeling the ternary complex TCR-Vbeta/CollagenII(261-273)/HLA-DR4 associated with rheumatoid arthritis. PLoS One 2010; 5:e11550. [PMID: 20644721 PMCID: PMC2904365 DOI: 10.1371/journal.pone.0011550] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 06/15/2010] [Indexed: 11/19/2022] Open
Abstract
Background It is known that genetic predisposition to rheumatoid arthritis (RA) is associated with the MHC class II allele HLA-DR4 and that residues 261–273 of type II collagen (huCollp261) represent an immunodominant T cell epitope restricted by the DR4 molecule. Despite recent advances in characterization of MHC and T cell receptor (TCR) contacts to this epitope, the atomic details of TCR/huCollp261/HLA-DR4 ternary complex are not known. Methodology/Principal Findings Here we have used computational modeling to get insight into this interaction. A three-dimensional model of the TCR Vβ domain from a DR4+ patient affected by RA has been derived by homology modeling techniques. Subsequently, the structure of the TCR Vβ domain in complex with huCollp261/HLA-DR4 was obtained from a docking approach in conjunction with a filtering procedure based on biochemical information. The best complex from the docking experiments was then refined by 20 ns of molecular dynamics simulation in explicit water. The predicted model is consistent with available experimental data. Our results indicate that residues 97–101 of CDR3β are critical for recognition of huCollp261/HLA-DR4 by TCR. We also show that TCR contacts on p/MHC surface affect the conformation of the shared epitope expressed by DR alleles associated with RA susceptibility. Conclusions/Significance This work presents a three-dimensional model for the ternary complex TCR-Vβ/collagenII(261–273)/HLA-DR4 associated with rheumatoid arthritis that can provide insights into the molecular mechanisms of self reactivity.
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86
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A structural basis for antigen recognition by the T cell-like lymphocytes of sea lamprey. Proc Natl Acad Sci U S A 2010; 107:13408-13. [PMID: 20616002 DOI: 10.1073/pnas.1005475107] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive immunity in jawless vertebrates is mediated by leucine-rich repeat proteins called "variable lymphocyte receptors" (VLRs). Two types of VLR (A and B) are expressed by mutually exclusive lymphocyte populations in lamprey. VLRB lymphocytes resemble the B cells of jawed vertebrates; VLRA lymphocytes are similar to T cells. We determined the structure of a high-affinity VLRA isolated from lamprey immunized with hen egg white lysozyme (HEL) in unbound and antigen-bound forms. The VLRA-HEL complex demonstrates that certain VLRAs, like gammadelta T-cell receptors (TCRs) but unlike alphabeta TCRs, can recognize antigens directly, without a requirement for processing or antigen-presenting molecules. Thus, these VLRAs feature the nanomolar affinities of antibodies, the direct recognition of unprocessed antigens of both antibodies and gammadelta TCRs, and the exclusive expression on the lymphocyte surface that is unique to alphabeta and gammadelta TCRs.
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87
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T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility. Immunity 2010; 31:885-96. [PMID: 20064447 DOI: 10.1016/j.immuni.2009.11.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 09/21/2009] [Accepted: 11/04/2009] [Indexed: 11/22/2022]
Abstract
T cell-mediated immunity requires T cell receptor (TCR) cross-reactivity, the mechanisms behind which remain incompletely elucidated. The alphabeta TCR A6 recognizes both the Tax (LLFGYPVYV) and Tel1p (MLWGYLQYV) peptides presented by the human class I MHC molecule HLA-A2. Here we found that although the two ligands are ideal structural mimics, they form substantially different interfaces with A6, with conformational differences in the peptide, the TCR, and unexpectedly, the MHC molecule. The differences between the Tax and Tel1p ternary complexes could not be predicted from the free peptide-MHC structures and are inconsistent with a traditional induced-fit mechanism. Instead, the differences were attributable to peptide and MHC molecular motion present in Tel1p-HLA-A2 but absent in Tax-HLA-A2. Differential "tuning" of the dynamic properties of HLA-A2 by the Tax and Tel1p peptides thus facilitates cross-recognition and impacts how structural diversity can be presented to and accommodated by receptors of the immune system.
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88
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Ebert PJR, Li QJ, Huppa JB, Davis MM. Functional development of the T cell receptor for antigen. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 92:65-100. [PMID: 20800817 PMCID: PMC4887107 DOI: 10.1016/s1877-1173(10)92004-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
For over three decades now, the T cell receptor (TCR) for antigen has not ceased to challenge the imaginations of cellular and molecular immunologists alike. T cell antigen recognition transcends every aspect of adaptive immunity: it shapes the T cell repertoire in the thymus and directs T cell-mediated effector functions in the periphery, where it is also central to the induction of peripheral tolerance. Yet, despite its central position, there remain many questions unresolved: how can one TCR be specific for one particular peptide-major histocompatibility complex (pMHC) ligand while also binding other pMHC ligands with an immunologically relevant affinity? And how can a T cell's extreme specificity (alterations of single methyl groups in their ligand can abrogate a response) and sensitivity (single agonist ligands on a cell surface are sufficient to trigger a measurable response) emerge from TCR-ligand interactions that are so low in affinity? Solving these questions is intimately tied to a fundamental understanding of molecular recognition dynamics within the many different contexts of various T cell-antigen presenting cell (APC) contacts: from the thymic APCs that shape the TCR repertoire and guide functional differentiation of developing T cells to the peripheral APCs that support homeostasis and provoke antigen responses in naïve, effector, memory, and regulatory T cells. Here, we discuss our recent findings relating to T cell antigen recognition and how this leads to the thymic development of foreign-antigen-responsive alphabetaT cells.
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Affiliation(s)
- Peter J R Ebert
- The Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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89
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Insaidoo FK, Zajicek J, Baker BM. A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves. Biochemistry 2009; 48:9708-10. [PMID: 19772349 PMCID: PMC2762276 DOI: 10.1021/bi9008787] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
T-Cell receptor recognition of peptides bound by major histocompatibility complex (MHC) proteins initiates a cellular immune response. Dynamics of peptides within MHC binding grooves can influence TCR recognition, yet NMR studies which could address this rigorously have been hindered by the expense of isotopically labeled peptides and the large size of peptide-MHC complexes. Here we describe a methodology for characterizing peptide dynamics within MHC binding grooves via NMR, using a biosynthetic approach for producing labeled peptide. With the Tax(11-19) peptide bound to the human class I MHC HLA-A*0201, we demonstrate that peptide generated in this manner can be well characterized in MHC binding grooves by NMR, providing opportunities to more precisely study the role of peptide dynamics in TCR recognition. Demonstrating the utility of such studies, the data with the Tax(11-19) peptide indicate the presence of slow conformational exchange in the peptide, supporting an "induced-fit" style TCR binding mechanism.
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Affiliation(s)
- Francis K. Insaidoo
- Department of Chemistry and Biochemistry and Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jaroslav Zajicek
- Department of Chemistry and Biochemistry and Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
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90
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Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner. Biochem J 2009; 423:353-61. [PMID: 19698083 DOI: 10.1042/bj20090732] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TCR (T-cell receptor) recognition of antigenic peptides bound and presented by MHC (major histocompatibility complex) molecules forms the basis of the cellular immune response to pathogens and cancer. TCRs bind peptide-MHC complexes weakly and with fast kinetics, features which have hindered detailed biophysical studies of these interactions. Modified peptides resulting in enhanced TCR binding could help overcome these challenges. Furthermore, there is considerable interest in using modified peptides with enhanced TCR binding as the basis for clinical vaccines. In the present study, we examined how fluorine substitutions in an antigenic peptide can selectively impact TCR recognition. Using a structure-guided design approach, we found that fluorination of the Tax peptide [HTLV (human T-cell lymphotropic virus)-1 Tax(11-19)] enhanced binding by the Tax-specific TCR A6, yet weakened binding by the Tax-specific TCR B7. The changes in affinity were consistent with crystallographic structures and fluorine chemistry, and with the A6 TCR independent of other substitutions in the interface. Peptide fluorination thus provides a means to selectively modulate TCR binding affinity without significantly perturbing peptide composition or structure. Lastly, we probed the mechanism of fluorine's effect on TCR binding and we conclude that our results were most consistent with a 'polar hydrophobicity' mechanism, rather than a purely hydrophobic- or electrostatic-based mechanism. This finding should have an impact on other attempts to alter molecular recognition with fluorine.
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91
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Cole DK, Yuan F, Rizkallah PJ, Miles JJ, Gostick E, Price DA, Gao GF, Jakobsen BK, Sewell AK. Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor. J Biol Chem 2009; 284:27281-9. [PMID: 19605354 PMCID: PMC2785656 DOI: 10.1074/jbc.m109.022509] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/18/2009] [Indexed: 11/06/2022] Open
Abstract
CD8(+) T-cells specific for MART-1-(26-35), a dominant melanoma epitope restricted by human leukocyte antigen (HLA)-A*0201, are exceptionally common in the naive T-cell repertoire. Remarkably, the TRAV12-2 gene is used to encode the T-cell receptor alpha (TCRalpha) chain in >87% of these T-cells. Here, the molecular basis for this genetic bias is revealed from the structural and thermodynamic properties of an archetypal TRAV12-2-encoded TCR complexed to the clinically relevant heteroclitic peptide, ELAGIGILTV, bound to HLA-A*0201 (A2-ELA). Unusually, the TRAV12-2 germ line-encoded regions of the TCR dominate the major atomic contacts with the peptide at the TCR/A2-ELA interface. This "innate" pattern of antigen recognition probably explains the unique characteristics and extraordinary frequencies of CD8(+) T-cell responses to this epitope.
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Affiliation(s)
- David K. Cole
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Fang Yuan
- the Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DU, United Kingdom
| | - Pierre J. Rizkallah
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
- the STFC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, United Kingdom
| | - John J. Miles
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
- the Cellular Immunology Laboratory, Queensland Institute of Medical Research, University of Queensland, Brisbane 4029, Australia
| | - Emma Gostick
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David A. Price
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - George F. Gao
- the **Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Bent K. Jakobsen
- Immunocore Limited, 57C Milton Park, Abingdon, Oxon OX14 4RX, United Kingdom
| | - Andrew K. Sewell
- From the Department of Infection, Immunity, and Biochemistry, Henry Wellcome Building, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
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92
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Jones LL, Colf LA, Bankovich AJ, Stone JD, Gao YG, Chan CM, Huang RH, Garcia KC, Kranz DM. Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors. Biochemistry 2009; 47:12398-408. [PMID: 18973345 DOI: 10.1021/bi801349g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
To understand the mechanisms that govern T cell receptor (TCR)-peptide MHC (pMHC) binding and the role that different regions of the TCR play in affinity and antigen specificity, we have studied the TCR from T cell clone 2C. High-affinity mutants of the 2C TCR that bind QL9-L(d) as a strong agonist were generated previously by site-directed mutagenesis of complementarity determining regions (CDRs) 1beta, 2alpha, 3alpha, or 3beta. We performed isothermal titration calorimetry to assess whether they use similar thermodynamic mechanisms to achieve high affinity for QL9-L(d). Four of the five TCRs examined bound to QL9-L(d) in an enthalpically driven, entropically unfavorable manner. In contrast, the high-affinity CDR1beta mutant resembled the wild-type 2C TCR interaction, with favorable entropy. To assess fine specificity, we measured the binding and kinetics of these mutants for both QL9-L(d) and a single amino acid peptide variant of QL9, called QL9-Y5-L(d). While 2C and most of the mutants had equal or higher affinity for the Y5 variant than for QL9, mutant CDR1beta exhibited 8-fold lower affinity for Y5 compared to QL9. To examine possible structural correlates of the thermodynamic and fine specificity signatures of the TCRs, the structure of unliganded QL9-L(d) was solved and compared to structures of the 2C TCR/QL9-L(d) complex and three high-affinity TCR/QL9-L(d) complexes. Our findings show that the QL9-L(d) complex does not undergo major conformational changes upon binding. Thus, subtle changes in individual CDRs account for the diverse thermodynamic and kinetic binding mechanisms and for the different peptide fine specificities.
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Affiliation(s)
- Lindsay L Jones
- Department of Biochemistry and School of Chemical Sciences Biocrystallization Service, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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