1
|
Srinivasan S, Zhu C, McShan AC. Structure, function, and immunomodulation of the CD8 co-receptor. Front Immunol 2024; 15:1412513. [PMID: 39253084 PMCID: PMC11381289 DOI: 10.3389/fimmu.2024.1412513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024] Open
Abstract
Expressed on the surface of CD8+ T cells, the CD8 co-receptor is a key component of the T cells that contributes to antigen recognition, immune cell maturation, and immune cell signaling. While CD8 is widely recognized as a co-stimulatory molecule for conventional CD8+ αβ T cells, recent reports highlight its multifaceted role in both adaptive and innate immune responses. In this review, we discuss the utility of CD8 in relation to its immunomodulatory properties. We outline the unique structure and function of different CD8 domains (ectodomain, hinge, transmembrane, cytoplasmic tail) in the context of the distinct properties of CD8αα homodimers and CD8αβ heterodimers. We discuss CD8 features commonly used to construct chimeric antigen receptors for immunotherapy. We describe the molecular interactions of CD8 with classical MHC-I, non-classical MHCs, and Lck partners involved in T cell signaling. Engineered and naturally occurring CD8 mutations that alter immune responses are discussed. The applications of anti-CD8 monoclonal antibodies (mABs) that target CD8 are summarized. Finally, we examine the unique structure and function of several CD8/mAB complexes. Collectively, these findings reveal the promising immunomodulatory properties of CD8 and CD8 binding partners, not only to uncover basic immune system function, but to advance efforts towards translational research for targeted immunotherapy.
Collapse
Affiliation(s)
- Shreyaa Srinivasan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, United States
| |
Collapse
|
2
|
Sun Y, Ma L, Li S, Wang Y, Xiao R, Yang J, Dijkstra JM, Xia C. Crystal Structure of a Classical MHC Class I Molecule in Dogs; Comparison of DLA-88*0 and DLA-88*5 Category Molecules. Cells 2023; 12:cells12071097. [PMID: 37048169 PMCID: PMC10093629 DOI: 10.3390/cells12071097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
DLA-88 is a classical major histocompatibility complex (MHC) class I gene in dogs, and allelic DLA-88 molecules have been divided into two categories named "DLA-88*0" and "DLA-88*5." The defining difference between the two categories concerns an LQW motif in the α2 domain helical region of the DLA-88*5 molecules that includes the insertion of an extra amino acid compared to MHC class I consensus length. We here show that this motif has been exchanged by recombination between different DLA-88 evolutionary lineages. Previously, with pDLA-88*508:01, the structure of a molecule of the DLA-88*5 category was elucidated. The present study is the first to elucidate a structure, using X-ray crystallography, of the DLA-88*0 category, namely DLA-88*001:04 complexed with β2m and a nonamer peptide derived from canine distemper virus (CDV). The LQW motif that distinguishes DLA-88*5 from DLA-88*0 causes a shallower peptide binding groove (PBG) and a leucine exposed at the top of the α2 domain helix expected to affect T cell selection. Peptide ligand amino acid substitution and pMHC-I complex formation and stability analyses revealed that P2 and P3 are the major anchor residue positions for binding to DLA-88*001:04. We speculate that the distribution pattern of the LQW motif among canine classical MHC class I alleles represents a strategy to enhance allogeneic rejection by T cells of transmissible cancers such as canine transmissible venereal tumor (CTVT).
Collapse
Affiliation(s)
- Yujiao Sun
- Yantai Institute of China Agricultural University, No. 2006, Binhai Mid-Rd, High-Tech Zone, Yantai City 264003, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China
| | - Shen Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yawen Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ruiqi Xiao
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Junqi Yang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Johannes M Dijkstra
- Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Chun Xia
- Yantai Institute of China Agricultural University, No. 2006, Binhai Mid-Rd, High-Tech Zone, Yantai City 264003, China
| |
Collapse
|
3
|
Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
Collapse
Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
4
|
TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
Collapse
|
5
|
Ott JA, Castro CD, Deiss TC, Ohta Y, Flajnik MF, Criscitiello MF. Somatic hypermutation of T cell receptor α chain contributes to selection in nurse shark thymus. eLife 2018; 7:28477. [PMID: 29664399 PMCID: PMC5931798 DOI: 10.7554/elife.28477] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 04/16/2018] [Indexed: 12/17/2022] Open
Abstract
Since the discovery of the T cell receptor (TcR), immunologists have assigned somatic hypermutation (SHM) as a mechanism employed solely by B cells to diversify their antigen receptors. Remarkably, we found SHM acting in the thymus on α chain locus of shark TcR. SHM in developing shark T cells likely is catalyzed by activation-induced cytidine deaminase (AID) and results in both point and tandem mutations that accumulate non-conservative amino acid replacements within complementarity-determining regions (CDRs). Mutation frequency at TcRα was as high as that seen at B cell receptor loci (BcR) in sharks and mammals, and the mechanism of SHM shares unique characteristics first detected at shark BcR loci. Additionally, fluorescence in situ hybridization showed the strongest AID expression in thymic corticomedullary junction and medulla. We suggest that TcRα utilizes SHM to broaden diversification of the primary αβ T cell repertoire in sharks, the first reported use in vertebrates.
Collapse
Affiliation(s)
- Jeannine A Ott
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Caitlin D Castro
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Thaddeus C Deiss
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland at Baltimore, Baltimore, United States
| | - Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Texas, United States.,Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, Texas, United States
| |
Collapse
|
6
|
Yang X, Chen G, Weng NP, Mariuzza RA. Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope. J Biol Chem 2017; 292:18618-18627. [PMID: 28931605 DOI: 10.1074/jbc.m117.810382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Influenza A virus (IAV) causes an acute infection in humans that is normally eliminated by CD8+ cytotoxic T lymphocytes. Individuals expressing the MHC class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T-cell receptors (TCRs) that recognize the immunodominant IAV epitope GILGFVFTL (GIL). Most GIL-specific TCRs utilize α/β chain pairs encoded by the TRAV27/TRBV19 gene combination to recognize this relatively featureless peptide epitope (canonical TCRs). However, ∼40% of GIL-specific TCRs express a wide variety of other TRAV/TRBV combinations (non-canonical TCRs). To investigate the structural underpinnings of this remarkable diversity, we determined the crystal structure of a non-canonical GIL-specific TCR (F50) expressing the TRAV13-1/TRBV27 gene combination bound to GIL-HLA-A2 to 1.7 Å resolution. Comparison of the F50-GIL-HLA-A2 complex with the previously published complex formed by a canonical TCR (JM22) revealed that F50 and JM22 engage GIL-HLA-A2 in markedly different orientations. These orientations are distinguished by crossing angles of TCR to peptide-MHC of 29° for F50 versus 69° for JM22 and by a focus by F50 on the C terminus rather than the center of the MHC α1 helix for JM22. In addition, F50, unlike JM22, uses a tryptophan instead of an arginine to fill a critical notch between GIL and the HLA-A2 α2 helix. The F50-GIL-HLA-A2 complex shows that there are multiple structurally distinct solutions to recognizing an identical peptide-MHC ligand with sufficient affinity to elicit a broad anti-IAV response that protects against viral escape and T-cell clonal loss.
Collapse
Affiliation(s)
- Xinbo Yang
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850.,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
| | - Guobing Chen
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Nan-Ping Weng
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Roy A Mariuzza
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, .,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
| |
Collapse
|
7
|
Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8 + T cell epitope. Nat Struct Mol Biol 2017; 24:395-406. [PMID: 28250417 PMCID: PMC5383516 DOI: 10.1038/nsmb.3383] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022]
Abstract
A keystone of antiviral immunity is CD8 T-cell recognition of viral peptides bound to MHC-I proteins. The recognition mode of individual T cell receptors (TCRs) has been studied in some detail, but how TCR variation functions in providing a robust response to viral antigen is unclear. The influenza M1 epitope is an immunodominant target of CD8 T cells helping to control influenza in HLA-A2+ individuals. Here, we show that many distinct TCRs are used by CD8 T cells to recognize HLA-A2/M1, encoding different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen. The vast majority of responding TCRs target small clefts between peptide and MHC. These broad repertoires lead to plasticity in antigen recognition and protection against T cell clonal loss and viral escape.
Collapse
|
8
|
Mahendran R, Jeyabaskar S, Sitharaman G, Michael RD, Paul AV. Computer-aided vaccine designing approach against fish pathogens Edwardsiella tarda and Flavobacterium columnare using bioinformatics softwares. Drug Des Devel Ther 2016; 10:1703-14. [PMID: 27284239 PMCID: PMC4883809 DOI: 10.2147/dddt.s95691] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Edwardsiella tarda and Flavobacterium columnare are two important intracellular pathogenic bacteria that cause the infectious diseases edwardsiellosis and columnaris in wild and cultured fish. Prediction of major histocompatibility complex (MHC) binding is an important issue in T-cell epitope prediction. In a healthy immune system, the T-cells must recognize epitopes and induce the immune response. In this study, T-cell epitopes were predicted by using in silico immunoinformatics approach with the help of bioinformatics tools that are less expensive and are not time consuming. Such identification of binding interaction between peptides and MHC alleles aids in the discovery of new peptide vaccines. We have reported the potential peptides chosen from the outer membrane proteins (OMPs) of E. tarda and F. columnare, which interact well with MHC class I alleles. OMPs from E. tarda and F. columnare were selected and analyzed based on their antigenic and immunogenic properties. The OMPs of the genes TolC and FCOL_04620, respectively, from E. tarda and F. columnare were taken for study. Finally, two epitopes from the OMP of E. tarda exhibited excellent protein-peptide interaction when docked with MHC class I alleles. Five epitopes from the OMP of F. columnare had good protein-peptide interaction when docked with MHC class I alleles. Further in vitro studies can aid in the development of potential peptide vaccines using the predicted peptides.
Collapse
Affiliation(s)
- Radha Mahendran
- Department of Bioinformatics, School of Life Sciences, Vels University, Pallavaram, Chennai, Tamil Nadu, India
| | - Suganya Jeyabaskar
- Department of Bioinformatics, School of Life Sciences, Vels University, Pallavaram, Chennai, Tamil Nadu, India
| | - Gayathri Sitharaman
- Department of Bioinformatics, School of Life Sciences, Vels University, Pallavaram, Chennai, Tamil Nadu, India
| | - Rajamani Dinakaran Michael
- Centre for Fish Immunology, School of Life Sciences, Vels University, Pallavaram, Chennai, Tamil Nadu, India
| | - Agnal Vincent Paul
- Department of Bioinformatics, School of Life Sciences, Vels University, Pallavaram, Chennai, Tamil Nadu, India
| |
Collapse
|
9
|
How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc Natl Acad Sci U S A 2016; 113:E1276-85. [PMID: 26884163 DOI: 10.1073/pnas.1522069113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
Collapse
|
10
|
Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
Collapse
Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| |
Collapse
|
11
|
Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33:169-200. [PMID: 25493333 DOI: 10.1146/annurev-immunol-032414-112334] [Citation(s) in RCA: 508] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Major Histocompatibility Complex (MHC) locus encodes classical MHC class I and MHC class II molecules and nonclassical MHC-I molecules. The architecture of these molecules is ideally suited to capture and present an array of peptide antigens (Ags). In addition, the CD1 family members and MR1 are MHC class I-like molecules that bind lipid-based Ags and vitamin B precursors, respectively. These Ag-bound molecules are subsequently recognized by T cell antigen receptors (TCRs) expressed on the surface of T lymphocytes. Structural and associated functional studies have been highly informative in providing insight into these interactions, which are crucial to immunity, and how they can lead to aberrant T cell reactivity. Investigators have determined over thirty unique TCR-peptide-MHC-I complex structures and twenty unique TCR-peptide-MHC-II complex structures. These investigations have shown a broad consensus in docking geometry and provided insight into MHC restriction. Structural studies on TCR-mediated recognition of lipid and metabolite Ags have been mostly confined to TCRs from innate-like natural killer T cells and mucosal-associated invariant T cells, respectively. These studies revealed clear differences between TCR-lipid-CD1, TCR-metabolite-MR1, and TCR-peptide-MHC recognition. Accordingly, TCRs show remarkable structural and biological versatility in engaging different classes of Ag that are presented by polymorphic and monomorphic Ag-presenting molecules of the immune system.
Collapse
Affiliation(s)
- Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; ,
| | | | | | | | | | | |
Collapse
|
12
|
Rangarajan S, Mariuzza RA. T cell receptor bias for MHC: co-evolution or co-receptors? Cell Mol Life Sci 2014; 71:3059-68. [PMID: 24633202 PMCID: PMC11113676 DOI: 10.1007/s00018-014-1600-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/06/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
In contrast to antibodies, which recognize antigens in native form, αβ T cell receptors (TCRs) only recognize antigens as peptide fragments bound to MHC molecules, a feature known as MHC restriction. The mechanism by which MHC restriction is imposed on the TCR repertoire is an unsolved problem that has generated considerable debate. Two principal models have been advanced to explain TCR bias for MHC. According to the germline model, MHC restriction is intrinsic to TCR structure because TCR and MHC molecules have co-evolved to conserve germline-encoded TCR sequences with the ability to bind MHC, while eliminating TCR sequences lacking MHC reactivity. According to the selection model, MHC restriction is not intrinsic to TCR structure, but is imposed by the CD4 and CD8 co-receptors that promote signaling by delivering the Src tyrosine kinase Lck to TCR-MHC complexes through co-receptor binding to MHC during positive selection. Here, we review the evidence for and against each model and conclude that both contribute to determining TCR specificity, although their relative contributions remain to be defined. Thus, TCR bias for MHC reflects not only germline-encoded TCR-MHC interactions but also the requirement to form a ternary complex with the CD4 or CD8 co-receptor that is geometrically competent to deliver a maturation signal to double-positive thymocytes during T cell selection.
Collapse
Affiliation(s)
- Sneha Rangarajan
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850 USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Roy A. Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850 USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| |
Collapse
|
13
|
Abstract
CD8αβ plays crucial roles in the thymic selection, differentiation, and activation of some, but not all, CD8(+) T cells, whereas CD8αα does not. To investigate these roles, we produced mice that expressed transgene P14 T-cell receptor β (TCRβ) chain and CD8β or did not (WT and KO mice, respectively). The primary CD8(+) T-cell response to acute lymphocytic choriomeningitis virus (LCMV) infection was predominantly D(b)/GP33 specific and CD8 independent in KO mice and was mostly CD8 dependent in WT mice. Cytotoxic T lymphocytes (CTL) from KO mice failed to mobilize intracellular Ca(2+) and to kill via perforin/granzyme. Their strong Fas/FasL-mediated cytotoxicity and IFN-γ response were signaled via a Ca(2+)-independent, PI3K-dependent pathway. This was also true for 15-20% of CD8-independent CTL found in WT mice. Conversely, the perforin/granzyme-mediated killing and IFN-γ response of CD8-dependent CTL were signaled via a Ca(2+), p56(lck), and nuclear factor of activated T cells-dependent pathway. Deep sequencing of millions of TCRα chain transcripts revealed that the TCR repertoires of preimmune CD8(+) T cells were highly diverse, but those of LCMV D(b)/GP33-specific CTL, especially from KO mice, were narrow. The immune repertoires exhibited biased use of Vα segments that encoded different complementary-determining region 1α (CDR1α) and CDR2α sequences. We suggest that TCR from WT CD8-independent T cells may engage MHC-peptide complexes in a manner unfavorable for efficient CD8 engagement and Ca(2+) signaling but permissive for Ca(2+)-independent, PI3K-dependent signaling. This duality of the CD8 compartment may provide organisms with broader protective immunity.
Collapse
|
14
|
Bhati M, Cole DK, McCluskey J, Sewell AK, Rossjohn J. The versatility of the αβ T-cell antigen receptor. Protein Sci 2014; 23:260-72. [PMID: 24375592 DOI: 10.1002/pro.2412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 02/06/2023]
Abstract
The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
Collapse
Affiliation(s)
- Mugdha Bhati
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
| | | | | | | | | |
Collapse
|
15
|
Abstract
Background The adaptive immune response is antigen-specific and triggered by pathogen recognition through T cells. Although the interactions and mechanisms of TCR-peptide-MHC (TCR-pMHC) have been studied over three decades, the biological basis for these processes remains controversial. As an increasing number of high-throughput binding epitopes and available TCR-pMHC complex structures, a fast genome-wide structural modelling of TCR-pMHC interactions is an emergent task for understanding immune interactions and developing peptide vaccines. Results We first constructed the PPI matrices and iMatrix, using 621 non-redundant PPI interfaces and 398 non-redundant antigen-antibody interfaces, respectively, for modelling the MHC-peptide and TCR-peptide interfaces, respectively. The iMatrix consists of four knowledge-based scoring matrices to evaluate the hydrogen bonds and van der Waals forces between sidechains or backbones, respectively. The predicted energies of iMatrix are high correlated (Pearson's correlation coefficient is 0.6) to 70 experimental free energies on antigen-antibody interfaces. To further investigate iMatrix and PPI matrices, we inferred the 701,897 potential peptide antigens with significant statistic from 389 pathogen genomes and modelled the TCR-pMHC interactions using available TCR-pMHC complex structures. These identified peptide antigens keep hydrogen-bond energies and consensus interactions and our TCR-pMHC models can provide detailed interacting models and crucial binding regions. Conclusions Experimental results demonstrate that our method can achieve high precision for predicting binding affinity and potential peptide antigens. We believe that iMatrix and our template-based method can be useful for the binding mechanisms of TCR-pMHC complexes and peptide vaccine designs.
Collapse
|
16
|
Li Y, Yin Y, Mariuzza RA. Structural and biophysical insights into the role of CD4 and CD8 in T cell activation. Front Immunol 2013; 4:206. [PMID: 23885256 PMCID: PMC3717711 DOI: 10.3389/fimmu.2013.00206] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022] Open
Abstract
T cell receptors (TCRs) recognize peptides presented by MHC molecules (pMHC) on an antigen-presenting cell (APC) to discriminate foreign from self-antigens and initiate adaptive immune responses. In addition, T cell activation generally requires binding of this same pMHC to a CD4 or CD8 co-receptor, resulting in assembly of a TCR–pMHC–CD4 or TCR–pMHC–CD8 complex and recruitment of Lck via its association with the co-receptor. Here we review structural and biophysical studies of CD4 and CD8 interactions with MHC molecules and TCR–pMHC complexes. Crystal structures have been determined of CD8αα and CD8αβ in complex with MHC class I, of CD4 bound to MHC class II, and of a complete TCR–pMHC–CD4 ternary complex. Additionally, the binding of these co-receptors to pMHC and TCR–pMHC ligands has been investigated both in solution and in situ at the T cell–APC interface. Together, these studies have provided key insights into the role of CD4 and CD8 in T cell activation, and into how these co-receptors focus TCR on MHC to guide TCR docking on pMHC during thymic T cell selection.
Collapse
Affiliation(s)
- Yili Li
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD , USA ; Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD , USA
| | | | | |
Collapse
|
17
|
Patronov A, Doytchinova I. T-cell epitope vaccine design by immunoinformatics. Open Biol 2013; 3:120139. [PMID: 23303307 PMCID: PMC3603454 DOI: 10.1098/rsob.120139] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 12/11/2012] [Indexed: 01/08/2023] Open
Abstract
Vaccination is generally considered to be the most effective method of preventing infectious diseases. All vaccinations work by presenting a foreign antigen to the immune system in order to evoke an immune response. The active agent of a vaccine may be intact but inactivated ('attenuated') forms of the causative pathogens (bacteria or viruses), or purified components of the pathogen that have been found to be highly immunogenic. The increased understanding of antigen recognition at molecular level has resulted in the development of rationally designed peptide vaccines. The concept of peptide vaccines is based on identification and chemical synthesis of B-cell and T-cell epitopes which are immunodominant and can induce specific immune responses. The accelerating growth of bioinformatics techniques and applications along with the substantial amount of experimental data has given rise to a new field, called immunoinformatics. Immunoinformatics is a branch of bioinformatics dealing with in silico analysis and modelling of immunological data and problems. Different sequence- and structure-based immunoinformatics methods are reviewed in the paper.
Collapse
Affiliation(s)
| | - Irini Doytchinova
- Department of Chemistry, Faculty of Pharmacy, Medical University of Sofia, Sofia, Bulgaria
| |
Collapse
|
18
|
Cole DK, Laugel B, Clement M, Price DA, Wooldridge L, Sewell AK. The molecular determinants of CD8 co-receptor function. Immunology 2012; 137:139-48. [PMID: 22804746 DOI: 10.1111/j.1365-2567.2012.03625.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
CD8(+) T cells respond to signals mediated through a specific interaction between the T-cell receptor (TCR) and a composite antigen in the form of an epitopic peptide bound between the polymorphic α1 and α2 helices of an MHC class I (MHCI) molecule. The CD8 glycoprotein 'co-receives' antigen by binding to an invariant region of the MHCI molecule and can enhance ligand recognition by up to 1 million-fold. In recent years, a number of structural and biophysical investigations have shed light on the role of the CD8 co-receptor during T-cell antigen recognition. Here, we provide a collated resource for these data, and discuss how the structural and biophysical parameters governing CD8 co-receptor function further our understanding of T-cell cross-reactivity and the productive engagement of low-affinity antigenic ligands.
Collapse
Affiliation(s)
- David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.
| | | | | | | | | | | |
Collapse
|
19
|
Gras S, Burrows SR, Turner SJ, Sewell AK, McCluskey J, Rossjohn J. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev 2012; 250:61-81. [DOI: 10.1111/j.1600-065x.2012.01159.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephanie Gras
- Department of Biochemistry and Molecular Biology; School of Biomedical Sciences; Monash University; Clayton; Australia
| | - Scott R. Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development; Brisbane; Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | - Andrew K. Sewell
- Institute of Infection and Immunity; Cardiff University School of Medicine; Cardiff; UK
| | - James McCluskey
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | | |
Collapse
|
20
|
Garcia KC. Reconciling views on T cell receptor germline bias for MHC. Trends Immunol 2012; 33:429-36. [PMID: 22771140 PMCID: PMC3983780 DOI: 10.1016/j.it.2012.05.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/13/2012] [Accepted: 05/13/2012] [Indexed: 01/25/2023]
Abstract
Whether MHC restriction by the T cell receptor (TCR) is a product of evolutionary pressures leading to germline-encoded 'rules of engagement' remains avidly debated. Structural results derived from analysis of TCR-peptide-MHC complexes appear to support a model of physical specificity between TCR germline V regions and MHC. Yet, some recent evidence suggests that thymic selection, and co-receptors may have misled us into thinking the TCR is exclusively MHC-specific, when in fact, TCRs can robustly engage non-MHC ligands when given the chance. Here, I propose that seemingly contradictory data and hypotheses for, and against, germline bias are, in fact, compatible and can be reconciled into a unifying model.
Collapse
Affiliation(s)
- K Christopher Garcia
- Howard Hughes Medical Institute, Department of Molecular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
21
|
Structural insights into the editing of germ-line-encoded interactions between T-cell receptor and MHC class II by Vα CDR3. Proc Natl Acad Sci U S A 2012; 109:14960-5. [PMID: 22930819 DOI: 10.1073/pnas.1207186109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conserved diagonal docking mode observed in structures of T-cell receptors (TCRs) bound to peptide-MHC ligands is believed to reflect coevolution of TCR and MHC genes. This coevolution is supported by the conservation of certain interactions between the germ-line-encoded complementarity-determining region (CDR)1 and CDR2 loops of TCR and MHC. However, the rules governing these interactions are not straightforward, even when the same variable (V) region recognizes the same MHC molecule. Here, we demonstrate that the somatically generated CDR3 loops can markedly alter evolutionarily selected contacts between TCR and MHC ("CDR3 editing"). To understand CDR3 editing at the atomic level, we determined the structure of a human melanoma-specific TCR (G4) bound to the MHC class II molecule HLA-DR1 and an epitope from mutant triose phosphate isomerase (mutTPI). A comparison of the G4-mutTPI-DR1 complex with a complex involving a TCR (E8) that uses the same Vα region to recognize the same mutTPI-DR1 ligand as G4 revealed that CDR1α adopts markedly different conformations in the two TCRs, resulting in an almost entirely different set of contacts with MHC. Based on the structures of unbound G4 and E8, the distinct conformations of CDR1α in these TCRs are not induced by binding to mutTPI-DR1 but result from differences in the length and sequence of CDR3α that are transmitted to CDR1α. The editing of germ-line-encoded TCR-MHC interactions by CDR3 demonstrates that these interactions possess sufficient intrinsic flexibility to accommodate large structural variations in CDR3 and, consequently, in the TCR-binding site.
Collapse
|
22
|
Anikeeva N, Gakamsky D, Schøller J, Sykulev Y. Evidence that the density of self peptide-MHC ligands regulates T-cell receptor signaling. PLoS One 2012; 7:e41466. [PMID: 22870225 PMCID: PMC3411518 DOI: 10.1371/journal.pone.0041466] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/21/2012] [Indexed: 11/24/2022] Open
Abstract
Noncognate or self peptide-MHC (pMHC) ligands productively interact with T-cell receptor (TCR) and are always in a large access over the cognate pMHC on the surface of antigen presenting cells. We assembled soluble cognate and noncognate pMHC class I (pMHC-I) ligands at designated ratios on various scaffolds into oligomers that mimic pMHC clustering and examined how multivalency and density of the pMHCs in model clusters influences the binding to live CD8 T cells and the kinetics of TCR signaling. Our data demonstrate that the density of self pMHC-I proteins promotes their interaction with CD8 co-receptor, which plays a critical role in recognition of a small number of cognate pMHC-I ligands. This suggests that MHC clustering on live target cells could be utilized as a sensitive mechanism to regulate T cell responsiveness.
Collapse
Affiliation(s)
- Nadia Anikeeva
- Department of Microbiology and Immunology and Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | | | | | - Yuri Sykulev
- Department of Microbiology and Immunology and Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
23
|
Yin Y, Wang XX, Mariuzza RA. Crystal structure of a complete ternary complex of T-cell receptor, peptide-MHC, and CD4. Proc Natl Acad Sci U S A 2012; 109:5405-10. [PMID: 22431638 PMCID: PMC3325661 DOI: 10.1073/pnas.1118801109] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adaptive immunity depends on specific recognition by a T-cell receptor (TCR) of an antigenic peptide bound to a major histocompatibility complex (pMHC) molecule on an antigen-presenting cell (APC). In addition, T-cell activation generally requires binding of this same pMHC to a CD4 or CD8 coreceptor. Here, we report the structure of a complete TCR-pMHC-CD4 ternary complex involving a human autoimmune TCR, a myelin-derived self-peptide bound to HLA-DR4, and CD4. The complex resembles a pointed arch in which TCR and CD4 are each tilted ∼65° relative to the T-cell membrane. By precluding direct contacts between TCR and CD4, the structure explains how TCR and CD4 on the T cell can simultaneously, yet independently, engage the same pMHC on the APC. The structure, in conjunction with previous mutagenesis data, places TCR-associated CD3εγ and CD3εδ subunits, which transmit activation signals to the T cell, inside the TCR-pMHC-CD4 arch, facing CD4. By establishing anchor points for TCR and CD4 on the T-cell membrane, the complex provides a basis for understanding how the CD4 coreceptor focuses TCR on MHC to guide TCR docking on pMHC during thymic T-cell selection.
Collapse
Affiliation(s)
- Yiyuan Yin
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850; and
- Program in Molecular and Cell Biology and
| | - Xin Xiang Wang
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850; and
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Roy A. Mariuzza
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850; and
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| |
Collapse
|
24
|
Calis JJA, de Boer RJ, Keşmir C. Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol 2012; 8:e1002412. [PMID: 22396638 PMCID: PMC3291541 DOI: 10.1371/journal.pcbi.1002412] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 01/18/2012] [Indexed: 11/18/2022] Open
Abstract
The cellular immune system screens peptides presented by host cells on MHC molecules to assess if the cells are infected. In this study we examined whether the presented peptides contain enough information for a proper self/nonself assessment by comparing the presented human (self) and bacterial or viral (nonself) peptides on a large number of MHC molecules. For all MHC molecules tested, only a small fraction of the presented nonself peptides from 174 species of bacteria and 1000 viral proteomes ([Formula: see text]0.2%) is shown to be identical to a presented self peptide. Next, we use available data on T-cell receptor-peptide-MHC interactions to estimate how well T-cells distinguish between similar peptides. The recognition of a peptide-MHC by the T-cell receptor is flexible, and as a result, about one-third of the presented nonself peptides is expected to be indistinguishable (by T-cells) from presented self peptides. This suggests that T-cells are expected to remain tolerant for a large fraction of the presented nonself peptides, which provides an explanation for the "holes in the T-cell repertoire" that are found for a large fraction of foreign epitopes. Additionally, this overlap with self increases the need for efficient self tolerance, as many self-similar nonself peptides could initiate an autoimmune response. Degenerate recognition of peptide-MHC-I complexes by T-cells thus creates large and potentially dangerous overlaps between self and nonself.
Collapse
Affiliation(s)
- Jorg J A Calis
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.
| | | | | |
Collapse
|
25
|
Adams JJ, Narayanan S, Liu B, Birnbaum ME, Kruse AC, Bowerman NA, Chen W, Levin AM, Connolly JM, Zhu C, Kranz DM, Garcia KC. T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. Immunity 2012; 35:681-93. [PMID: 22101157 DOI: 10.1016/j.immuni.2011.09.013] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/16/2011] [Accepted: 09/02/2011] [Indexed: 02/04/2023]
Abstract
T cell receptor (TCR) engagement of peptide-major histocompatibility complex (pMHC) is essential to adaptive immunity, but it is unknown whether TCR signaling responses are influenced by the binding topology of the TCR-peptide-MHC complex. We developed yeast-displayed pMHC libraries that enabled us to identify new peptide sequences reactive with a single TCR. Structural analysis showed that four peptides bound to the TCR with distinct 3D and 2D affinities using entirely different binding chemistries. Three of the peptides that shared a common docking mode, where key TCR-MHC germline interactions are preserved, induced TCR signaling. The fourth peptide failed to induce signaling and was recognized in a substantially different TCR-MHC binding mode that apparently exceeded geometric tolerances compatible with signaling. We suggest that the stereotypical TCR-MHC docking paradigm evolved from productive signaling geometries and that TCR signaling can be modulated by peptides that are recognized in alternative TCR-pMHC binding orientations.
Collapse
MESH Headings
- Amino Acid Motifs/immunology
- Amino Acid Sequence
- Animals
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Histocompatibility Antigens Class I/chemistry
- Humans
- Lymphocyte Activation/immunology
- Mice
- Models, Molecular
- Peptide Library
- Peptides/chemistry
- Peptides/immunology
- Peptides/metabolism
- Protein Binding/immunology
- Protein Conformation
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Reproducibility of Results
- Sequence Alignment
- Signal Transduction
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
Collapse
Affiliation(s)
- Jarrett J Adams
- Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- Antoine Leimgruber
- Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Scott-Browne JP, Crawford F, Young MH, Kappler JW, Marrack P, Gapin L. Evolutionarily conserved features contribute to αβ T cell receptor specificity. Immunity 2011; 35:526-35. [PMID: 21962492 DOI: 10.1016/j.immuni.2011.09.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 08/02/2011] [Accepted: 09/06/2011] [Indexed: 11/17/2022]
Abstract
αβ T cell receptors (TCRs) bind specifically to foreign antigens presented by major histocompatibility complex proteins (MHC) or MHC-like molecules. Accumulating evidence indicates that the germline-encoded TCR segments have features that promote binding to MHC and MHC-like molecules, suggesting coevolution between TCR and MHC molecules. Here, we assess directly the evolutionary conservation of αβ TCR specificity for MHC. Sequence comparisons showed that some Vβs from distantly related jawed vertebrates share amino acids in their complementarity determining region 2 (CDR2). Chimeric TCRs containing amphibian, bony fish, or cartilaginous fish Vβs can recognize antigens presented by mouse MHC class II and CD1d (an MHC-like protein), and this recognition is dependent upon the shared CDR2 amino acids. These results indicate that features of the TCR that control specificity for MHC and MHC-like molecules were selected early in evolution and maintained between species that last shared a common ancestor more than 400 million years ago.
Collapse
Affiliation(s)
- James P Scott-Browne
- Integrated Department of Immunology, National Jewish Health and University of Colorado School of Medicine, Denver, CO 80206, USA
| | | | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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
Collapse
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:
| |
Collapse
|
29
|
Roomp K, Domingues FS. Predicting interactions between T cell receptors and MHC-peptide complexes. Mol Immunol 2010; 48:553-62. [PMID: 21106246 DOI: 10.1016/j.molimm.2010.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 10/24/2010] [Indexed: 12/30/2022]
Abstract
Conserved interactions between T cell receptors (TCRs) and major histocompatibility complex (MHC) proteins with bound peptide antigens are not well understood. In order to gain a better understanding of the interaction modes of human TCR variable (V) regions, we have performed a structural analysis of the TCRs bound to their MHC-peptide ligands in human, using the available structural models determined by X-ray crystallography. We identified important differences to previous studies in which such interactions were evaluated. Based on the interactions found in the actual experimental structures we developed the first rule-based approach for predicting the ability of TCR residues in the complementarity-determining region (CDR) 1, CDR2, and CDR3 loops to interact with the MHC-peptide antigen complex. Two relatively simple algorithms show good performance under cross validation.
Collapse
Affiliation(s)
- Kirsten Roomp
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbruecken, Germany.
| | | |
Collapse
|
30
|
Wang H, Fang Z, Morita CT. Vgamma2Vdelta2 T Cell Receptor recognition of prenyl pyrophosphates is dependent on all CDRs. THE JOURNAL OF IMMUNOLOGY 2010; 184:6209-22. [PMID: 20483784 DOI: 10.4049/jimmunol.1000231] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
gammadelta T cells differ from alphabeta T cells in the Ags they recognize and their functions in immunity. Although most alphabeta TCRs recognize peptides presented by MHC class I or II, human gammadelta T cells expressing Vgamma2Vdelta2 TCRs recognize nonpeptide prenyl pyrophosphates. To define the molecular basis for this recognition, the effect of mutations in the TCR CDR was assessed. Mutations in all CDR loops altered recognition and cover a large footprint. Unlike murine gammadelta TCR recognition of the MHC class Ib T22 protein, there was no CDR3delta motif required for recognition because only one residue is required. Instead, the length and sequence of CDR3gamma was key. Although a prenyl pyrophosphate-binding site was defined by Lys109 in Jgamma1.2 and Arg51 in CDR2delta, the area outlined by critical mutations is much larger. These results show that prenyl pyrophosphate recognition is primarily by germline-encoded regions of the gammadelta TCR, allowing a high proportion of Vgamma2Vdelta2 TCRs to respond. This underscores its parallels to innate immune receptors. Our results also provide strong evidence for the existence of an Ag-presenting molecule for prenyl pyrophosphates.
Collapse
Affiliation(s)
- Hong Wang
- Division of Rheumatology, Department of Internal Medicine, Interdisciplinary Graduate Program in Immunology, University of Iowa College of Medicine, Iowa City, IA 52242, USA
| | | | | |
Collapse
|
31
|
Piepenbrink KH, Gloor BE, Armstrong KM, Baker BM. Methods for quantifying T cell receptor binding affinities and thermodynamics. Methods Enzymol 2009; 466:359-81. [PMID: 21609868 DOI: 10.1016/s0076-6879(09)66015-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
αβ T cell receptors (TCRs) recognize peptide antigens bound and presented by class I or class II major histocompatibility complex (MHC) proteins. Recognition of a peptide/MHC complex is required for initiation and propagation of a cellular immune response, as well as the development and maintenance of the T cell repertoire. Here, we discuss methods to quantify the affinities and thermodynamics of interactions between soluble ectodomains of TCRs and their peptide/MHC ligands, focusing on titration calorimetry, surface plasmon resonance, and fluorescence anisotropy. As TCRs typically bind ligand with weak-to-moderate affinities, we focus the discussion on means to enhance the accuracy and precision of low-affinity measurements. In addition to further elucidating the biology of the T cell mediated immune response, more reliable low-affinity measurements will aid with more probing studies with mutants or altered peptides that can help illuminate the physical underpinnings of how TCRs achieve their remarkable recognition properties.
Collapse
Affiliation(s)
- Kurt H Piepenbrink
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | | | | | | |
Collapse
|
32
|
Kumar P, Vahedi-Faridi A, Saenger W, Ziegler A, Uchanska-Ziegler B. Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity. Protein Sci 2009; 18:37-49. [PMID: 19177349 DOI: 10.1002/pro.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although there is X-ray crystallographic evidence that the interaction between major histocompatibility complex (MHC, in humans HLA) class I molecules and T cell receptors (TCR) or killer cell Ig-like receptors (KIR) may be accompanied by considerable changes in the conformation of selected residues or even entire loops within TCR or KIR, conformational changes between receptor-bound and -unbound MHC class I molecules of comparable magnitude have not been observed so far. We have previously determined the structure of the MHC class I molecule HLA-A1 bound to a melanoma antigen-encoding gene (MAGE)-A1-derived peptide in complex with a recombinant antibody fragment with TCR-like specificity, Fab-Hyb3. Here, we compare the X-ray structure of HLA-A1:MAGE-A1 with that complexed with Fab-Hyb3 to gain insight into structural changes of the MHC molecule that might be induced by the interaction with the antibody fragment. Apart from the expulsion of several water molecules from the interface, Fab-Hyb3 binding results in major rearrangements (up to 5.5 A) of heavy chain residues Arg65, Gln72, Arg145, and Lys146. Residue 65 is frequently and residues 72 and 146 are occasionally involved in TCR binding-induced conformational changes, as revealed by a comparison with MHC class I structures in TCR-liganded and -unliganded forms. On the other hand, residue 145 is subject to a reorientation following engagement of HLA-Cw4 and KIR2DL1. Therefore, conformational changes within the HLA-A1:MAGE-A1:Fab-Hyb3 complex include MHC residues that are also involved in reorientations in complexes with natural ligands, pointing to their central importance for the peptide-dependent recognition of MHC molecules.
Collapse
Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, Berlin 14195, Germany
| | | | | | | | | |
Collapse
|
33
|
Neumann F, Sturm C, Hülsmeyer M, Dauth N, Guillaume P, Luescher IF, Pfreundschuh M, Held G. Fab antibodies capable of blocking T cells by competitive binding have the identical specificity but a higher affinity to the MHC-peptide-complex than the T cell receptor. Immunol Lett 2009; 125:86-92. [DOI: 10.1016/j.imlet.2009.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 05/16/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
|
34
|
Collins EJ, Riddle DS. TCR-MHC docking orientation: natural selection, or thymic selection? Immunol Res 2009; 41:267-94. [PMID: 18726714 DOI: 10.1007/s12026-008-8040-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T cell receptors (TCR) dock on their peptide-major histocompatibility complex (pMHC) targets in a conserved orientation. Since amino acid sidechains are the foundation of specific protein-protein interactions, a simple explanation for the conserved docking orientation is that key amino acids encoded by the TCR and MHC genes have been selected and maintained through evolution in order to preserve TCR/pMHC binding. Expectations that follow from the hypothesis that TCR and MHC evolved to interact are discussed in light of the data that both support and refute them. Finally, an alternative and equally simple explanation for the driving force behind the conserved docking orientation is described.
Collapse
Affiliation(s)
- Edward J Collins
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, 804 Mary Ellen Jones Building, Chapel Hill, NC 27510, USA.
| | | |
Collapse
|
35
|
Garcia KC, Adams JJ, Feng D, Ely LK. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat Immunol 2009; 10:143-7. [PMID: 19148199 PMCID: PMC3982143 DOI: 10.1038/ni.f.219] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The elusive etiology of germline bias of the T cell receptor (TCR) for major histocompatibility complex (MHC) has been clarified by recent 'proof-of-concept' structural results demonstrating the conservation of specific TCR-MHC interfacial contacts in complexes bearing common variable segments and MHC allotypes. We suggest that each TCR variable-region gene product engages each type of MHC through a 'menu' of structurally coded recognition motifs that have arisen through coevolution. The requirement for MHC-restricted T cell recognition during thymic selection and peripheral surveillance has necessitated the existence of such a coded recognition system. Given these findings, a reconsideration of the TCR-peptide-MHC structural database shows that not only have the answers been there all along but also they were predictable by the first principles of physical chemistry.
Collapse
Affiliation(s)
- K Christopher Garcia
- Department of Molecular & Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.
| | | | | | | |
Collapse
|
36
|
Angelov GS, Guillaume P, Luescher IF. CD8β knockout mice mount normal anti-viral CD8+ T cell responses—but why? Int Immunol 2008; 21:123-35. [DOI: 10.1093/intimm/dxn130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
37
|
Armstrong K, Piepenbrink K, Baker B. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem J 2008; 415:183-96. [PMID: 18800968 PMCID: PMC2782316 DOI: 10.1042/bj20080850] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/23/2008] [Accepted: 07/09/2008] [Indexed: 01/07/2023]
Abstract
A necessary feature of the immune system, TCR (T-cell receptor) cross-reactivity has been implicated in numerous autoimmune pathologies and is an underlying cause of transplant rejection. Early studies of the interactions of alphabeta TCRs (T-cell receptors) with their peptide-MHC ligands suggested that conformational plasticity in the TCR CDR (complementarity determining region) loops is a dominant contributor to T-cell cross-reactivity. Since these initial studies, the database of TCRs whose structures have been solved both bound and free is now large enough to permit general conclusions to be drawn about the extent of TCR plasticity and the types and locations of motion that occur. In the present paper, we review the conformational differences between free and bound TCRs, quantifying the structural changes that occur and discussing their possible roles in specificity and cross-reactivity. We show that, rather than undergoing major structural alterations or 'folding' upon binding, the majority of TCR CDR loops shift by relatively small amounts. The structural changes that do occur are dominated by hinge-bending motions, with loop remodelling usually occurring near loop apexes. As predicted from previous studies, the largest changes are in the hypervariable CDR3alpha and CDR3beta loops, although in some cases the germline-encoded CDR1alpha and CDR2alpha loops shift in magnitudes that approximate those of the CDR3 loops. Intriguingly, the smallest shifts are in the germline-encoded loops of the beta-chain, consistent with recent suggestions that the TCR beta domain may drive ligand recognition.
Collapse
Affiliation(s)
- Kathryn M. Armstrong
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Kurt H. Piepenbrink
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Brian M. Baker
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
- †Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| |
Collapse
|
38
|
Armstrong KM, Insaidoo FK, Baker BM. Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities. J Mol Recognit 2008; 21:275-87. [PMID: 18496839 DOI: 10.1002/jmr.896] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
alphabeta T-cell receptors (TCRs) recognize peptide antigens presented by class I or class II major histocompatibility complex molecules (pMHC). Here we review the use of thermodynamic measurements in the study of TCR-pMHC interactions, with attention to the diversity in binding thermodynamics and how this is related to the variation in TCR-pMHC interfaces. We show that there is no enthalpic or entropic signature for TCR binding; rather, enthalpy and entropy changes vary in a compensatory manner that reflects a narrow free energy window for the interactions that have been characterized. Binding enthalpy and entropy changes do not correlate with structural features such as buried surface area or the number of hydrogen bonds within TCR-pMHC interfaces, possibly reflecting the myriad of contributors to binding thermodynamics, but likely also reflecting a reliance on van't Hoff over calorimetric measurements and the unaccounted influence of equilibria linked to binding. TCR-pMHC binding heat capacity changes likewise vary considerably. In some cases, the heat capacity changes are consistent with conformational differences between bound and free receptors, but there is little data indicating these conformational differences represent the need to organize disordered CDR loops. In this regard, we discuss how thermodynamics may provide additional insight into conformational changes occurring upon TCR binding. Finally, we highlight opportunities for the further use of thermodynamic measurements in the study of TCR-pMHC interactions, not only for understanding TCR binding in general, but also for understanding specifics of individual interactions and the engineering of TCRs with desired molecular recognition properties.
Collapse
Affiliation(s)
- Kathryn M Armstrong
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | | | | |
Collapse
|
39
|
Riddle DS, Miller PJ, Vincent BG, Kepler TB, Maile R, Frelinger JA, Collins EJ. Rescue of cytotoxic function in the CD8alpha knockout mouse by removal of MHC class II. Eur J Immunol 2008; 38:1511-21. [PMID: 18465769 DOI: 10.1002/eji.200737710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
CD8 plays an important role in the activity of cytolytic T cells (CTL). However, whether or not CD8 is required for the development of CTL has not been clearly determined. Cytotoxic activity in the CD8alpha knockout mouse is difficult to induce, and has only been demonstrated against allogenic MHC targets. The lack of cytotoxicity may result from impaired lineage commitment of CTL in the absence of CD8, or diminished competitiveness during selection against (unimpaired) development of CD4(+) T cells on MHC class II (MHC II). To differentiate between these possibilities, we have generated a double-knockout mouse (MHC II(-/-)CD8alpha(-/-)). In MHC II(-/-)CD8alpha(-/-) mice, developing MHC class I (MHC I)-reactive thymocytes cannot rely upon CD8 for selection, but they also cannot be overwhelmed by efficient selection of MHC II-reactive thymocytes. In this mouse, a large, heterogeneous population of peripheral coreceptor double-negative (DN) and CD4(+) T cells develops. Peripheral DN T cells are fully functional CTL. They display cytolytic activity against allogeneic MHC, and against syngeneic MHC following lymphocytic choriomeningitis virus (LCMV) infection. Cells from LCMV-infected mice bind more MHC I tetramer at lower concentrations than their wild-type CTL counterparts. These results demonstrate unequivocally that CD8 is not required for commitment of thymocytes to the CTL lineage.
Collapse
Affiliation(s)
- David S Riddle
- University of North Carolina at Chapel Hill, Department of Microbiology and Immunology, Chapel Hill, NC 27599-7290, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
Gil D, Schrum AG, Daniels MA, Palmer E. A role for CD8 in the developmental tuning of antigen recognition and CD3 conformational change. THE JOURNAL OF IMMUNOLOGY 2008; 180:3900-9. [PMID: 18322198 DOI: 10.4049/jimmunol.180.6.3900] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
TCR engagement by peptide-MHC class I (pMHC) ligands induces a conformational change (Deltac) in CD3 (CD3Deltac) that contributes to T cell signaling. We found that when this interaction took place between primary T lineage cells and APCs, the CD8 coreceptor was required to generate CD3Deltac. Interestingly, neither enhancement of Ag binding strength nor Src kinase signaling explained this coreceptor activity. Furthermore, Ag-induced CD3Deltac was developmentally attenuated by the increase in sialylation that accompanies T cell maturation and limits CD8 activity. Thus, both weak and strong ligands induced CD3Deltac in preselection thymocytes, but only strong ligands were effective in mature T cells. We propose that CD8 participation in the TCR/pMHC interaction can physically regulate CD3Deltac induction by "translating" productive Ag encounter from the TCR to the CD3 complex. This suggests one mechanism by which the developmentally regulated variation in CD8 sialylation may contribute to the developmental tuning of T cell sensitivity.
Collapse
Affiliation(s)
- Diana Gil
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | |
Collapse
|
41
|
Marrack P, Rubtsova K, Scott-Browne J, Kappler JW. T cell receptor specificity for major histocompatibility complex proteins. Curr Opin Immunol 2008; 20:203-7. [PMID: 18456484 DOI: 10.1016/j.coi.2008.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
Abstract
The ligands for alpha beta T cell receptors (alphabetaTCRs) are usually major histocompatibility complex (MHC) proteins bound to peptides. Although there is evidence that T cell receptor variable regions have been selected evolutionarily to bind MHC, the rules governing this interaction have not previously been apparent. However, recent solved structures of T cell receptors with related variable regions bound to MHC plus peptides suggest that some amino acids in variable region CDR1 and CDR2s almost always react in a consistent way with MHC. These amino acids may therefore have been selected evolutionarily to predispose T cell receptors toward recognition of MHC ligands.
Collapse
Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, Colorado 80206, USA.
| | | | | | | |
Collapse
|
42
|
Dai S, Huseby ES, Rubtsova K, Scott-Browne J, Crawford F, Macdonald WA, Kappler JW, Marrack P. Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules. Immunity 2008; 28:324-34. [PMID: 18308592 PMCID: PMC2287197 DOI: 10.1016/j.immuni.2008.01.008] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 01/15/2008] [Indexed: 01/11/2023]
Abstract
To test whether highly crossreactive alphabeta T cell receptors (TCRs) produced during limited negative selection best illustrate evolutionarily conserved interactions between TCR and major histocompatibility complex (MHC) molecules, we solved the structures of three TCRs bound to the same MHC II peptide (IAb-3K). The TCRs had similar affinities for IAb-3K but varied from noncrossreactive to extremely crossreactive with other peptides and MHCs. Crossreactivity correlated with a shrinking, increasingly hydrophobic TCR-ligand interface, involving fewer TCR amino acids. A few CDR1 and CDR2 amino acids dominated the most crossreactive TCR interface with MHC, including Vbeta8 48Y and 54E and Valpha4 29Y, arranged to impose the familiar diagonal orientation of TCR on MHC. These interactions contribute to MHC binding by other TCRs using related V regions, but not usually so dominantly. These data show that crossreactive TCRs can spotlight the evolutionarily conserved features of TCR-MHC interactions and that these interactions impose the diagonal docking of TCRs on MHC.
Collapse
Affiliation(s)
- Shaodong Dai
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
| | - Eric S. Huseby
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
| | - Kira Rubtsova
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
| | - James Scott-Browne
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
| | - Frances Crawford
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
| | | | - John W. Kappler
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Program in Biomolecular Structure, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045 USA
| | - Philippa Marrack
- Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Integrated Department of Immunology, National Jewish Medical and Research Center, Denver, CO 80206 USA
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Aurora, CO 80045
| |
Collapse
|
43
|
|
44
|
Cole DK, Dunn SM, Sami M, Boulter JM, Jakobsen BK, Sewell AK. T cell receptor engagement of peptide-major histocompatibility complex class I does not modify CD8 binding. Mol Immunol 2008; 45:2700-9. [PMID: 18243322 DOI: 10.1016/j.molimm.2007.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 12/14/2007] [Indexed: 11/30/2022]
Abstract
Activation of cytotoxic T cells is initiated by engagement of the T-cell receptor (TCR) with peptide-major histocompatibility class I complexes (pMHCI). The CD8 co-receptor also binds to pMHCI, but at a distinct site, and allows the potential for tripartite TCR/pMHCI/CD8 interactions, which can increase T cell antigen sensitivity. There has been a substantial interest in the effect of the pMHCI/CD8 interaction upon TCR/pMHCI engagement, and several conflicting studies have examined this event, using the soluble extracellular domains of CD8 and the TCR, by surface plasmon resonance. However, the evidence to date suggests that the TCR engages cognate pMHCI before CD8 recruitment, so the question of whether TCR engagement alters CD8 binding is likely to be more relevant to the biological order of T cell antigen encounter. Here, we have examined the binding of CD8 to several variants of the HLA A2-restricted telomerase(540-548) antigen (ILAKFLHWL) and the HLA A2-restricted NY-ESO-1(157-165) antigen (SLLMWITQC) that bind to their cognate TCRs with distinct affinities and kinetics. These interactions represent a range of agonists that exhibit different CD8 dependency for activation of their respective T cells. By using engineered affinity enhanced TCRs to these ligands, which have extended off-rates of approximately 1h compared to seconds for the wildtype TCRs, we have examined pMHCI/CD8 binding before and during TCR-engagement. Here we show that the binding of the extracellular domain of the TCR to pMHCI does not transmit structural changes to the pMHCI-CD8 binding site that would alter the subsequent pMHCI/CD8 interaction.
Collapse
Affiliation(s)
- David K Cole
- Department of Medical Biochemistry & Immunology, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
| | | | | | | | | | | |
Collapse
|
45
|
A permissive geometry model for TCR–CD3 activation. Trends Biochem Sci 2008; 33:51-7. [DOI: 10.1016/j.tibs.2007.10.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 10/09/2007] [Accepted: 10/19/2007] [Indexed: 01/23/2023]
|
46
|
|
47
|
Tian S, Maile R, Collins EJ, Frelinger JA. CD8+ T cell activation is governed by TCR-peptide/MHC affinity, not dissociation rate. THE JOURNAL OF IMMUNOLOGY 2007; 179:2952-60. [PMID: 17709510 DOI: 10.4049/jimmunol.179.5.2952] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Binding of peptide/MHC (pMHC) complexes by TCR initiates T cell activation. Despite long interest, the exact relationship between the biochemistry of TCR/pMHC interaction (particularly TCR affinity or ligand off-rate) and T cell responses remains unresolved, because the number of complexes examined in each independent system has been too small to draw a definitive conclusion. To test the current models of T cell activation, we have analyzed the interactions between the mouse P14 TCR and a set of altered peptides based on the lymphocytic choriomeningitis virus epitope gp33-41 sequence bound to mouse class I MHC D(b). pMHC binding, TCR-binding characteristics, CD8+ T cell cytotoxicity, and IFN-gamma production were measured for the peptides. We found affinity correlated well with both cytotoxicity and IFN-gamma production. In contrast, no correlation was observed between any kinetic parameter of TCR-pMHC interaction and cytotoxicity or IFN-gamma production. This study strongly argues for an affinity threshold model of T cell activation.
Collapse
Affiliation(s)
- Shaomin Tian
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | | | | |
Collapse
|
48
|
Miller PJ, Pazy Y, Conti B, Riddle D, Appella E, Collins EJ. Single MHC mutation eliminates enthalpy associated with T cell receptor binding. J Mol Biol 2007; 373:315-27. [PMID: 17825839 PMCID: PMC2065754 DOI: 10.1016/j.jmb.2007.07.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 07/07/2007] [Accepted: 07/10/2007] [Indexed: 01/23/2023]
Abstract
The keystone of the adaptive immune response is T cell receptor (TCR) recognition of peptide presented by major histocompatibility complex (pMHC) molecules. The crystal structure of AHIII TCR bound to MHC, HLA-A2, showed a large interface with an atypical binding orientation. MHC mutations in the interface of the proteins were tested for changes in TCR recognition. From the range of responses observed, three representative HLA-A2 mutants, T163A, W167A, and K66A, were selected for further study. Binding constants and co-crystal structures of the AHIII TCR and the three mutants were determined. K66 in HLA-A2 makes contacts with both peptide and TCR, and has been identified as a critical residue for recognition by numerous TCR. The K66A mutation resulted in the lowest AHIII T cell response and the lowest binding affinity, which suggests that the T cell response may correlate with affinity. Importantly, the K66A mutation does not affect the conformation of the peptide. The change in affinity appears to be due to a loss in hydrogen bonds in the interface as a result of a conformational change in the TCR complementarity-determining region 3 (CDR3) loop. Isothermal titration calorimetry confirmed the loss of hydrogen bonding by a large loss in enthalpy. Our findings are inconsistent with the notion that the CDR1 and CDR2 loops of the TCR are responsible for MHC restriction, while the CDR3 loops interact solely with the peptide. Instead, we present here an MHC mutation that does not change the conformation of the peptide, yet results in an altered conformation of a CDR3.
Collapse
Affiliation(s)
- Peter J Miller
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | | |
Collapse
|
49
|
McNicol AM, Bendle G, Holler A, Matjeka T, Dalton E, Rettig L, Zamoyska R, Uckert W, Xue SA, Stauss HJ. CD8alpha/alpha homodimers fail to function as co-receptor for a CD8-dependent TCR. Eur J Immunol 2007; 37:1634-41. [PMID: 17506031 DOI: 10.1002/eji.200636900] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study, we have started to dissect the molecular basis of CD8 dependence of a high and low avidity CTL clone specific for the same peptide epitope. Using anti-CD8alpha and anti-CD8beta antibodies, we found that cytotoxicity and IFN-gamma production by high but not by low avidity CTL was strongly CD8 dependent. We isolated the TCR genes of both types of CTL clones and used retroviral gene transfer to analyse the function of these TCR in primary T cells of wild-type and CD8beta-deficient mice. Both TCR triggered antigen-specific killing in wild-type T cells, and blocking experiments showed that CD8 dependence/independence co-transferred with the TCR into primary T cells, indicating that it was dictated by the TCR itself. Gene transfer experiments into CD8beta-deficient T cells revealed that only the TCR derived from the CD8-independent CTL clone elicited antigen-specific cytotoxicity, while the CD8-dependent TCR was non-functional in the absence of the CD8beta-chain. These data indicate a striking difference between CD8alpha/beta heterodimers and CD8alpha/alpha homodimers as only the former were able to provide co-receptor function for the CD8-dependent TCR.
Collapse
MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/pharmacology
- CD3 Complex/immunology
- CD8 Antigens/genetics
- CD8 Antigens/immunology
- Cell Line, Tumor
- Cytotoxicity, Immunologic/drug effects
- Cytotoxicity, Immunologic/immunology
- Interferon-gamma/metabolism
- Interleukin-4/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Peptides/immunology
- Protein Subunits/immunology
- Protein Subunits/metabolism
- Proto-Oncogene Proteins c-mdm2/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Spleen/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Transfection
Collapse
Affiliation(s)
- Anne-Marie McNicol
- Department of Immunology and Molecular Pathology, University College London, London, UK
| | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Feng D, Bond CJ, Ely LK, Maynard J, Garcia KC. Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'. Nat Immunol 2007; 8:975-83. [PMID: 17694060 DOI: 10.1038/ni1502] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/17/2007] [Indexed: 11/09/2022]
Abstract
All complexes of T cell receptors (TCRs) bound to peptide-major histocompatibility complex (pMHC) molecules assume a stereotyped binding 'polarity', despite wide variations in TCR-pMHC docking angles. However, existing TCR-pMHC crystal structures have failed to show broadly conserved pairwise interaction motifs. Here we determined the crystal structures of two TCRs encoded by the variable beta-chain 8.2 (V(beta)8.2), each bound to the MHC class II molecule I-A(u), and did energetic mapping of V(alpha) and V(beta) contacts with I-A(u). Together with two previously solved structures of V(beta)8.2-containing TCR-MHC complexes, we found four TCR-I-A complexes with structurally superimposable interactions between the V(beta) loops and the I-A alpha-helix. This examination of a narrow 'slice' of the TCR-MHC repertoire demonstrates what is probably one of many germline-derived TCR-MHC interaction 'codons'.
Collapse
Affiliation(s)
- Dan Feng
- Howard Hughes Medical Institute, Department of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|