1
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Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Front Immunol 2024; 15:1345368. [PMID: 38545094 PMCID: PMC10967027 DOI: 10.3389/fimmu.2024.1345368] [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: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.
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Affiliation(s)
- Aaron M. Rosenberg
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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2
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Roca-Martinez J, Lazar T, Gavalda-Garcia J, Bickel D, Pancsa R, Dixit B, Tzavella K, Ramasamy P, Sanchez-Fornaris M, Grau I, Vranken WF. Challenges in describing the conformation and dynamics of proteins with ambiguous behavior. Front Mol Biosci 2022; 9:959956. [PMID: 35992270 PMCID: PMC9382080 DOI: 10.3389/fmolb.2022.959956] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Traditionally, our understanding of how proteins operate and how evolution shapes them is based on two main data sources: the overall protein fold and the protein amino acid sequence. However, a significant part of the proteome shows highly dynamic and/or structurally ambiguous behavior, which cannot be correctly represented by the traditional fixed set of static coordinates. Representing such protein behaviors remains challenging and necessarily involves a complex interpretation of conformational states, including probabilistic descriptions. Relating protein dynamics and multiple conformations to their function as well as their physiological context (e.g., post-translational modifications and subcellular localization), therefore, remains elusive for much of the proteome, with studies to investigate the effect of protein dynamics relying heavily on computational models. We here investigate the possibility of delineating three classes of protein conformational behavior: order, disorder, and ambiguity. These definitions are explored based on three different datasets, using interpretable machine learning from a set of features, from AlphaFold2 to sequence-based predictions, to understand the overlap and differences between these datasets. This forms the basis for a discussion on the current limitations in describing the behavior of dynamic and ambiguous proteins.
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Affiliation(s)
- Joel Roca-Martinez
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Tamas Lazar
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, Brussels, Belgium
| | - Jose Gavalda-Garcia
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - David Bickel
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Rita Pancsa
- Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | - Bhawna Dixit
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- IBiTech-Biommeda, Universiteit Gent, Gent, Belgium
| | - Konstantina Tzavella
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
| | - Pathmanaban Ramasamy
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- VIB-UGent Center for Medical Biotechnology, Universiteit Gent, Gent, Belgium
| | - Maite Sanchez-Fornaris
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- Department of Computer Sciences, University of Camagüey, Camagüey, Cuba
| | - Isel Grau
- Information Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Wim F. Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, VUB/ULB, Brussels, Belgium
- *Correspondence: Wim F. Vranken,
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3
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Tomasiak L, Karch R, Schreiner W. Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations. BMC Immunol 2022; 23:36. [PMID: 35902791 PMCID: PMC9335952 DOI: 10.1186/s12865-022-00510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Major histocompatibility complexes (MHCs) play a crucial role in the cell-mediated adaptive immune response as they present antigenic peptides (p) which are recognized by host T cells through a complex formation of the T cell receptor (TCR) with pMHC. In the present study, we report on changes in conformational flexibility within a pMHC molecule upon TCR binding by looking at molecular dynamics (MD) simulations of the free and the TCR-bound pMHC-I protein of the LC13-HLA-B*44:05-pEEYLQAFTY complex. Results We performed long-term MD simulations with a total simulation time of 8 µs, employing 10 independent 400 ns replicas for the free and the TCR-bound pMHC system. Upon TCR ligation, we observed a reduced dynamic flexibility in the central residues of the peptide and the MHC α1-helix, altered occurrences of hydrogen bonds between the peptide and the MHC, a reduced conformational entropy of the peptide-binding groove, as well as a decreased solvent accessible surface area. Conclusions In summary, our results from 8 µs MD simulations indicate a restricted conformational space of the MHC peptide-binding groove upon TCR ligation and suggest a minimum simulation time of approximately 100 ns for biomolecules of comparable complexity to draw meaningful conclusions. Given the relatively long total simulation time, our results contribute to a more detailed view on conformational flexibility properties of the investigated free and TCR-bound pMHC-I system. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-022-00510-7.
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Affiliation(s)
- Lisa Tomasiak
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Rudolf Karch
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
| | - Wolfgang Schreiner
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
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4
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Erausquin E, Serra P, Parras D, Santamaria P, López-Sagaseta J. Structural plasticity in I-Ag7 links autoreactivity to hybrid insulin peptides in type I diabetes. Front Immunol 2022; 13:924311. [PMID: 35967292 PMCID: PMC9365947 DOI: 10.3389/fimmu.2022.924311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-Ag7-restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-Ag7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-Ag7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR’s complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-Ag7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-Ag7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-Ag7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.
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Affiliation(s)
- Elena Erausquin
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
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5
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Riedel F, Aparicio-Soto M, Curato C, Thierse HJ, Siewert K, Luch A. Immunological Mechanisms of Metal Allergies and the Nickel-Specific TCR-pMHC Interface. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10867. [PMID: 34682608 PMCID: PMC8535423 DOI: 10.3390/ijerph182010867] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
Besides having physiological functions and general toxic effects, many metal ions can cause allergic reactions in humans. We here review the immune events involved in the mediation of metal allergies. We focus on nickel (Ni), cobalt (Co) and palladium (Pd), because these allergens are among the most prevalent sensitizers (Ni, Co) and immediate neighbors in the periodic table of the chemical elements. Co-sensitization between Ni and the other two metals is frequent while the knowledge on a possible immunological cross-reactivity using in vivo and in vitro approaches remains limited. At the center of an allergic reaction lies the capability of a metal allergen to form T cell epitopes that are recognized by specific T cell receptors (TCR). Technological advances such as activation-induced marker assays and TCR high-throughput sequencing recently provided new insights into the interaction of Ni2+ with the αβ TCR-peptide-major histocompatibility complex (pMHC) interface. Ni2+ functionally binds to the TCR gene segment TRAV9-2 or a histidine in the complementarity determining region 3 (CDR3), the main antigen binding region. Thus, we overview known, newly identified and hypothesized mechanisms of metal-specific T cell activation and discuss current knowledge on cross-reactivity.
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Affiliation(s)
- Franziska Riedel
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
| | - Marina Aparicio-Soto
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Caterina Curato
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Hermann-Josef Thierse
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Katherina Siewert
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Andreas Luch
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
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6
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Abstract
T cell activation is a critical event in the adaptive immune response, indispensable for cell-mediated and humoral immunity as well as for immune regulation. Recent years have witnessed an emerging trend emphasizing the essential role that physical force and mechanical properties play at the T cell interface. In this review, we integrate current knowledge of T cell antigen recognition and the different models of T cell activation from the perspective of mechanobiology, focusing on the interaction between the T cell receptor (TCR) and the peptide-major histocompatibility complex (pMHC) antigen. We address the shortcomings of TCR affinity alone in explaining T cell functional outcomes and the rising status of force-regulated TCR bond lifetimes, most notably the TCR catch bond. Ultimately, T cell activation and the ensuing physiological responses result from mechanical interaction between TCRs and the pMHC. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Baoyu Liu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Elizabeth M Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Brian D Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
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7
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Ronayne EK, Peters SC, Gish JS, Wilson C, Spencer HT, Doering CB, Lollar P, Spiegel PC, Childers KC. Structure of Blood Coagulation Factor VIII in Complex With an Anti-C2 Domain Non-Classical, Pathogenic Antibody Inhibitor. Front Immunol 2021; 12:697602. [PMID: 34177966 PMCID: PMC8223065 DOI: 10.3389/fimmu.2021.697602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 01/19/2023] Open
Abstract
Factor VIII (fVIII) is a procoagulant protein that binds to activated factor IX (fIXa) on platelet surfaces to form the intrinsic tenase complex. Due to the high immunogenicity of fVIII, generation of antibody inhibitors is a common occurrence in patients during hemophilia A treatment and spontaneously occurs in acquired hemophilia A patients. Non-classical antibody inhibitors, which block fVIII activation by thrombin and formation of the tenase complex, are the most common anti-C2 domain pathogenic inhibitors in hemophilia A murine models and have been identified in patient plasmas. In this study, we report on the X-ray crystal structure of a B domain-deleted bioengineered fVIII bound to the non-classical antibody inhibitor, G99. While binding to G99 does not disrupt the overall domain architecture of fVIII, the C2 domain undergoes an ~8 Å translocation that is concomitant with breaking multiple domain-domain interactions. Analysis of normalized B-factor values revealed several solvent-exposed loops in the C1 and C2 domains which experience a decrease in thermal motion in the presence of inhibitory antibodies. These results enhance our understanding on the structural nature of binding non-classical inhibitors and provide a structural dynamics-based rationale for cooperativity between anti-C1 and anti-C2 domain inhibitors.
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Affiliation(s)
- Estelle K Ronayne
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - Shaun C Peters
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - Joseph S Gish
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - Celena Wilson
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - H Trent Spencer
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, United States
| | - Christopher B Doering
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, United States
| | - Pete Lollar
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, Atlanta, GA, United States
| | - P Clint Spiegel
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
| | - Kenneth C Childers
- Department of Chemistry, Western Washington University, Bellingham, WA, United States
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8
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Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD. Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2021; 60:859-872. [PMID: 33689297 DOI: 10.1021/acs.biochem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of the T cell receptor (TCR) to its cognate, peptide antigen-loaded major histocompatibility complex (pMHC) is a key interaction for triggering T cell activation and ultimately elimination of the target cell. Despite the importance of this interaction for cellular immunity, a comprehensive molecular understanding of TCR specificity and affinity is lacking. We conducted hydrogen/deuterium exchange mass spectrometry (HDX-MS) analyses of individual affinity-enhanced TCR variants and clinically relevant pMHC class I molecules (HLA-A*0201/NY-ESO-1157-165) to investigate the causality between increased binding affinity and conformational dynamics in TCR-pMHC complexes. Differential HDX-MS analyses of TCR variants revealed that mutations for affinity enhancement in TCR CDRs altered the conformational response of TCR to pMHC ligation. Improved pMHC binding affinity was in general observed to correlate with greater differences in HDX upon pMHC binding in modified TCR CDR loops, thereby providing new insights into the TCR-pMHC interaction. Furthermore, a specific point mutation in the β-CDR3 loop of the NY-ESO-1 TCR associated with a substantial increase in binding affinity resulted in a substantial change in pMHC binding kinetics (i.e., very slow kon, revealed by the detection of EX1 HDX kinetics), thus providing experimental evidence for a slow induced-fit binding mode. We also examined the conformational impact of pMHC binding on an unrelated TRAV12-2 gene-encoded TCR directed against the immunodominant MART-126-35 cancer antigen restricted by HLA-A*0201. Our findings provide a molecular basis for the observed TRAV12-2 gene bias in natural CD8+ T cell-based immune responses against the MART-1 antigen, with potential implications for general ligand discrimination and TCR cross-reactivity processes.
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MESH Headings
- Humans
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- HLA-A2 Antigen/genetics
- Protein Conformation
- Hydrogen Deuterium Exchange-Mass Spectrometry
- Protein Binding
- Peptides/chemistry
- Peptides/metabolism
- Peptides/immunology
- Major Histocompatibility Complex
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/genetics
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Deuterium Exchange Measurement
- Mutation
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Affiliation(s)
- Patrick S Merkle
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esben Trabjerg
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Hongjian
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Immanuel Luescher
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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9
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Heikkilä N, Sormunen S, Mattila J, Härkönen T, Knip M, Ihantola EL, Kinnunen T, Mattila IP, Saramäki J, Arstila TP. Generation of self-reactive, shared T-cell receptor α chains in the human thymus. J Autoimmun 2021; 119:102616. [PMID: 33652347 DOI: 10.1016/j.jaut.2021.102616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 11/26/2022]
Abstract
The T-cell receptor (TCR) repertoire is generated in a semistochastic process of gene recombination and pairing of TCRα to TCRβ chains with the estimated total TCR diversity of >108. Despite this high diversity, similar or identical TCR chains are found to recur in immune responses. Here, we analyzed the thymic generation of TCR sequences previously associated with recognition of self- and nonself-antigens, represented by sequences associated with autoimmune diabetes and HIV, respectively. Unexpectedly, in the CD4+ compartment TCRα chains associated with the recognition of self-antigens were generated in significantly higher numbers than TCRα chains associated with the recognition of nonself-antigens. The analysis of the circulating repertoire further showed that these chains are not lost in negative selection nor predominantly converted to the regulatory T-cell lineage. The high abundance of self-reactive TCRα chains in multiple individuals suggests that the human thymus has a predilection to generate self-reactive TCRα chains independently of the HLA-type and that the individual risk of autoimmunity may be modulated by the TCRβ repertoire associated with these chains.
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Affiliation(s)
- Nelli Heikkilä
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland.
| | - Silja Sormunen
- Department of Computer Science, Aalto University, Konemiehenkatu 2, 02150, Espoo, Finland
| | - Joonatan Mattila
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland; Folkhälsan Research Center, Topeliuksenkatu 25, 00250, Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, Elämänaukio 2, 33520, Tampere, Finland
| | - Emmi-Leena Ihantola
- Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland
| | - Tuure Kinnunen
- Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland; Eastern Finland Laboratory Centre (ISLAB), Puijonlaaksontie 2, 70210, Kuopio, Finland
| | - Ilkka P Mattila
- Department of Pediatric Cardiac and Transplantation Surgery, Hospital for Children and Adolescents, Helsinki University Central Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland
| | - Jari Saramäki
- Department of Computer Science, Aalto University, Konemiehenkatu 2, 02150, Espoo, Finland
| | - T Petteri Arstila
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
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10
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Coles CH, McMurran C, Lloyd A, Hock M, Hibbert L, Raman MCC, Hayes C, Lupardus P, Cole DK, Harper S. T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4. J Biol Chem 2020; 295:11486-11494. [PMID: 32532817 PMCID: PMC7450119 DOI: 10.1074/jbc.ra120.014016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound pHLA in a position shifted toward the peptide's N terminus. This enabled the TCR to achieve peptide selectivity via an indirect mechanism, whereby the TCR sensed the first residue of the peptide through HLA residue Trp-167, which acted as a tunable gateway. Amino acid substitutions at peptide position 1 predicted to alter the HLA Trp-167 side-chain conformation abrogated TCR binding, indicating that this indirect binding mechanism is essential for peptide recognition. These findings extend our understanding of the molecular rules that underpin antigen recognition by TCRs and have important implications for the development of TCR-based therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David K Cole
- Immunocore Ltd., Abingdon, United Kingdom .,Cardiff University School of Medicine, Cardiff, United Kingdom
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11
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Hopkins JR, Crean RM, Catici DAM, Sewell AK, Arcus VL, Van der Kamp MW, Cole DK, Pudney CR. Peptide cargo tunes a network of correlated motions in human leucocyte antigens. FEBS J 2020; 287:3777-3793. [PMID: 32134551 PMCID: PMC8651013 DOI: 10.1111/febs.15278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Rory M Crean
- Department of Biology and Biochemistry, University of Bath, UK.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | | | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath, UK.,Centre for Therapeutic Innovation, University of Bath, UK
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12
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Loll B, Rückert C, Uchanska-Ziegler B, Ziegler A. Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Front Immunol 2020; 11:179. [PMID: 32117305 PMCID: PMC7027375 DOI: 10.3389/fimmu.2020.00179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 01/07/2023] Open
Abstract
The development of autoimmune disorders is incompletely understood. Inefficient thymic T cell selection against self-peptides presented by major histocompatibility antigens (HLA in humans) may contribute to the emergence of auto-reactive effector cells, and molecular mimicry between foreign and self-peptides could promote T cell cross-reactivity. A pair of class I subtypes, HLA-B2705 and HLA-B2709, have previously been intensely studied, because they are distinguished from each other only by a single amino acid exchange at the floor of the peptide-binding groove, yet are differentially associated with the autoinflammatory disorder ankylosing spondylitis. Using X-ray crystallography in combination with ensemble refinement, we find that the non-disease-associated subtype HLA-B2709, when presenting the self-peptide pGR (RRRWHRWRL), exhibits elevated conformational dynamics, and the complex can also be recognized by T cells. Both features are not observed in case of the sequence-related self-peptide pVIPR (RRKWRRWHL) in complex with this subtype, and T cell cross-reactivity between pGR, pVIPR, and the viral peptide pLMP2 (RRRWRRLTV) is only rarely observed. The disease-associated subtype HLA-B2705, however, exhibits extensive conformational flexibility in case of the three complexes, all of which are also recognized by frequently occurring cross-reactive T cells. A comparison of the structural and dynamic properties of the six HLA-B27 complexes, together with their individual ability to interact with T cells, permits us to correlate the flexibility of HLA-B27 complexes with effector cell reactivity. The results suggest the existence of an inverse relationship between conformational plasticity of peptide-HLA-B27 complexes and the efficiency of negative selection of self-reactive cells within the thymus.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Berlin, Germany,*Correspondence: Bernhard Loll
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany,Ziegler Biosolutions, Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Waldshut-Tiengen, Germany,Andreas Ziegler
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13
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Trowitzsch S, Tampé R. Multifunctional Chaperone and Quality Control Complexes in Adaptive Immunity. Annu Rev Biophys 2020; 49:135-161. [PMID: 32004089 DOI: 10.1146/annurev-biophys-121219-081643] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fundamental process of adaptive immunity relies on the differentiation of self from nonself. Nucleated cells are continuously monitored by effector cells of the immune system, which police the peptide status presented via cell surface molecules. Recent integrative structural approaches have provided insights toward our understanding of how sophisticated cellular machineries shape such hierarchical immune surveillance. Biophysical and structural achievements were invaluable for defining the interconnection of many key factors during antigen processing and presentation, and helped to solve several conundrums that persisted for many years. In this review, we illuminate the numerous quality control machineries involved in different steps during the maturation of major histocompatibility complex class I (MHC I) proteins, from their synthesis in the endoplasmic reticulum to folding and trafficking via the secretory pathway, optimization of antigenic cargo, final release to the cell surface, and engagement with their cognate receptors on cytotoxic T lymphocytes.
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Affiliation(s)
- Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
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14
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Tripathi SK, Salunke DM. Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition. J Biomol Struct Dyn 2020; 39:188-201. [PMID: 31870204 DOI: 10.1080/07391102.2019.1708795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar Tripathi
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dinakar M Salunke
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.,Structural Immunology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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15
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Pradana KA, Widjaya MA, Wahjudi M. Indonesians Human Leukocyte Antigen (HLA) Distributions and Correlations with Global Diseases. Immunol Invest 2019; 49:333-363. [PMID: 31648579 DOI: 10.1080/08820139.2019.1673771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In Human, Major Histocompatibility Complex known as Human Leukocyte Antigen (HLA). The HLA grouped into three subclasses regions: the class I region, the class II region, and the class III region. There are thousands of polymorphic HLAs, many of them are proven to have correlations with diseases. Indonesia consists of diverse ethnicity people and populations. It carries a unique genetic diversity between one and another geographical positions. This paper aims to extract Indonesians HLA allele data, mapping the data, and correlating them with global diseases. From the study, it is found that global diseases, like Crohn's disease, rheumatoid arthritis, Graves' disease, gelatin allergy, T1D, HIV, systemic lupus erythematosus, juvenile chronic arthritis, and Mycobacterial disease (tuberculosis and leprosy) suspected associated with the Indonesian HLA profiles.
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Affiliation(s)
- Krisnawan Andy Pradana
- Faculty of Biotechnology, University of Surabaya, Surabaya City, Indonesia.,Department of Anatomy and Histology Faculty of Medicine, Airlangga University, Tambaksari, Surabaya City, Indonesia
| | | | - Mariana Wahjudi
- Faculty of Biotechnology, University of Surabaya, Surabaya City, Indonesia
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16
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Duro N, Varma S. Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase. Structure 2019; 27:1601-1611.e2. [DOI: 10.1016/j.str.2019.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/29/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022]
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17
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Karch R, Stocsits C, Ilieva N, Schreiner W. Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study. Cells 2019; 8:cells8070720. [PMID: 31337065 PMCID: PMC6678086 DOI: 10.3390/cells8070720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the distances and mutual orientations of these domains. In comparison to unbound states, we found decreased inter-domain movements in the simulations of bound states. Moreover, increased conformational flexibility was observed for the MHC α2-helix, the peptide, and for the complementary determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.
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Affiliation(s)
- Rudolf Karch
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Claudia Stocsits
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Nevena Ilieva
- Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria
- CERN-TH, Esplanade des Particules 1, 1211 Geneva, Switzerland
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria.
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18
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Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK. TCR-induced alteration of primary MHC peptide anchor residue. Eur J Immunol 2019; 49:1052-1066. [PMID: 31091334 PMCID: PMC6618058 DOI: 10.1002/eji.201948085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide-MHC anchoring. This "flexing" at the TCR-peptide-MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.
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Affiliation(s)
| | | | | | | | - Anna Fuller
- School of MedicineCardiff UniversityCardiffUK
| | - Anna Bulek
- School of MedicineCardiff UniversityCardiffUK
| | | | | | | | | | | | - John J. Miles
- School of MedicineCardiff UniversityCardiffUK
- Centre for Biodiscovery and Molecular Development of TherapeuticsAustralian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | | | - Yi Li
- Immunocore Ltd.AbingdonUK
| | | | | | - E. Joel Loveridge
- School of ChemistryCardiff UniversityCardiffUK
- Department of ChemistrySwansea UniversitySwanseaUK
| | - David K. Cole
- School of MedicineCardiff UniversityCardiffUK
- Immunocore Ltd.AbingdonUK
| | - Andrew K. Sewell
- School of MedicineCardiff UniversityCardiffUK
- Systems Immunity Research InstituteCardiff UniversityCardiffUK
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19
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Moura J, Madureira P, Leal EC, Fonseca AC, Carvalho E. Immune aging in diabetes and its implications in wound healing. Clin Immunol 2019; 200:43-54. [PMID: 30735729 PMCID: PMC7322932 DOI: 10.1016/j.clim.2019.02.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 02/06/2023]
Abstract
Immune systems have evolved to recognize and eliminate pathogens and damaged cells. In humans, it is estimated to recognize 109 epitopes and natural selection ensures that clonally expanded cells replace unstimulated cells and overall immune cell numbers remain stationary. But, with age, it faces continuous repertoire restriction and concomitant accumulation of primed cells. Changes shaping the aging immune system have bitter consequences because, as inflammatory responses gain intensity and duration, tissue-damaging immunity and inflammatory disease arise. During inflammation, the glycolytic flux cannot cope with increasing ATP demands, limiting the immune response's extent. In diabetes, higher glucose availability stretches the glycolytic limit, dysregulating proteostasis and increasing T-cell expansion. Long-term hyperglycemia exerts an accumulating effect, leading to higher inflammatory cytokine levels and increased cytotoxic mediator secretion upon infection, a phenomenon known as diabetic chronic inflammation. Here we review the etiology of diabetic chronic inflammation and its consequences on wound healing.
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Affiliation(s)
- J Moura
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; INEB - Instituto Nacional de Engenharia Biomédica, University of Porto, Porto, Portugal; i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
| | - P Madureira
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal; IBMC - Instituto de Biologia Celular e Molecular, University of Porto, Porto, Portugal; Immunethep, Biocant Park, Cantanhede, Portugal
| | - E C Leal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - A C Fonseca
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - E Carvalho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Instituto de Investigação Interdisciplinar, University of Coimbra, Coimbra, Portugal; Department of Geriatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, United States
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20
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Peripheral T cell receptor beta immune repertoire is promptly reconstituted after acute myocardial infarction. J Transl Med 2019; 17:40. [PMID: 30728066 PMCID: PMC6366076 DOI: 10.1186/s12967-019-1788-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Acute myocardial infarction (AMI) is characterized by an inflammatory process in which T cell plays a key role. However, the profile of immune microenvironment in AMI is still uncertain. High-throughput sequencing of T cell receptor (TCR) provides deep insight into monitoring the immune microenvironment. METHODS 30 patients with AMI were enrolled and 30 healthy individuals were recruited as controls. Flow cytometer were used to analyze the distribution of αβ T cells and their CD69 expression from peripheral leukomonocytes. TCRβ repertoire library was amplified by two-round multiplex PCR and detected by next-generation sequencing (NGS). RESULTS The percentage of αβ T cells in AMI patients were significantly restricted than those in healthy controls, while the highly activated αβ T cells along with distinguishing usage of variable (V), diversity (D) and joining (J) gene segments were also found in AMI patients. In addition, AMI induced a significantly restricted CDR3 amino acid (AA) diversity and remarkably reconstituted TCR immune repertoires. Finally, we identified several AMI-associated tendency of CDR3 AAs expression after AMI. CONCLUSIONS Our work suggests that the aberrant αβ T cells distribution and activation may associated with the pathogenesis of AMI and demonstrates a reconstitution of TCRβ immune repertoire after AMI.
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21
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Marks C, Shi J, Deane CM. Predicting loop conformational ensembles. Bioinformatics 2018; 34:949-956. [PMID: 29136084 DOI: 10.1093/bioinformatics/btx718] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/09/2017] [Indexed: 12/23/2022] Open
Abstract
Motivation Protein function is often facilitated by the existence of multiple stable conformations. Structure prediction algorithms need to be able to model these different conformations accurately and produce an ensemble of structures that represent a target's conformational diversity rather than just a single state. Here, we investigate whether current loop prediction algorithms are capable of this. We use the algorithms to predict the structures of loops with multiple experimentally determined conformations, and the structures of loops with only one conformation, and assess their ability to generate and select decoys that are close to any, or all, of the observed structures. Results We find that while loops with only one known conformation are predicted well, conformationally diverse loops are modelled poorly, and in most cases the predictions returned by the methods do not resemble any of the known conformers. Our results contradict the often-held assumption that multiple native conformations will be present in the decoy set, making the production of accurate conformational ensembles impossible, and hence indicating that current methodologies are not well suited to prediction of conformationally diverse, often functionally important protein regions. Contact marks@stats.ox.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Jiye Shi
- Department of Chemistry, UCB Pharma, Slough SL1 3WE, UK
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22
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Ogunshola F, Anmole G, Miller RL, Goering E, Nkosi T, Muema D, Mann J, Ismail N, Chopera D, Ndung'u T, Brockman MA, Ndhlovu ZM. Dual HLA B*42 and B*81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants. Nat Commun 2018; 9:5023. [PMID: 30479346 PMCID: PMC6258674 DOI: 10.1038/s41467-018-07209-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8+ T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML180–188) in the context of the protective allele B*81:01 and the less protective allele B*42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B*81:01 and B*42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B*42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation. Closely related HLA alleles presenting similar HIV-1 epitopes can be associated with variable clinical outcome. Here the authors report their findings on CD8+ T cell responses to the HIV-1 Gag-p24 TL9 immunodominant epitope in the context of closely related protective and less protective HLA alleles, and their differential effect on viral control
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Affiliation(s)
- Funsho Ogunshola
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Rachel L Miller
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Emily Goering
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Thandeka Nkosi
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel Muema
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Nasreen Ismail
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Denis Chopera
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Mark A Brockman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada. .,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, V6Z 1Y6, Canada.
| | - Zaza M Ndhlovu
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa. .,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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23
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Riley TP, Hellman LM, Gee MH, Mendoza JL, Alonso JA, Foley KC, Nishimura MI, Vander Kooi CW, Garcia KC, Baker BM. T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability. Nat Chem Biol 2018; 14:934-942. [PMID: 30224695 PMCID: PMC6371774 DOI: 10.1038/s41589-018-0130-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022]
Abstract
T cell receptor cross-reactivity allows a fixed T cell repertoire to respond to a much larger universe of potential antigens. Recent work has emphasized the importance of peptide structural and chemical homology, as opposed to sequence similarity, in T cell receptor cross-reactivity. Surprisingly though, T cell receptors can also cross-react between ligands with little physiochemical commonalities. Studying the clinically relevant receptor DMF5, we demonstrate that cross-recognition of such divergent antigens can occur through mechanisms that involve heretofore unanticipated rearrangements in the peptide and presenting MHC protein, including binding-induced peptide register shifts and extensions from MHC peptide binding grooves. Moreover, cross-reactivity can proceed even when such dramatic rearrangements do not translate into structural or chemical molecular mimicry. Beyond demonstrating new principles of T cell receptor cross-reactivity, our results have implications for efforts to predict and control T cell specificity and cross-reactivity, and highlight challenges associated with predicting T cell reactivities.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Marvin H Gee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesus A Alonso
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kendra C Foley
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA. .,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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24
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Cuendet MA, Margul DT, Schneider E, Vogt-Maranto L, Tuckerman ME. Endpoint-restricted adiabatic free energy dynamics approach for the exploration of biomolecular conformational equilibria. J Chem Phys 2018; 149:072316. [DOI: 10.1063/1.5027479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Michel A. Cuendet
- Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL Sorge, 1015 Lausanne, Switzerland
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York 10065, USA
| | - Daniel T. Margul
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Elia Schneider
- Department of Chemistry, New York University, New York, New York 10003, USA
| | | | - Mark E. Tuckerman
- Department of Chemistry, New York University, New York, New York 10003, USA
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062, China
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25
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Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro. Proc Natl Acad Sci U S A 2018; 115:E7369-E7378. [PMID: 30021852 DOI: 10.1073/pnas.1802746115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity (Kd ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed "velcro," between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities. This additional interaction was generated through an eight-amino acid peptide library covalently linked to the N terminus of the MHC-bound peptide. Velcro was selected through an affinity-based isolation and was subsequently shown to enhance the cognate TCR/pMHC affinity in a peptide-dependent manner by ∼10-fold. This was sufficient to convert a nonstimulatory ultra-low-affinity ligand into a stimulatory ligand. An X-ray crystallographic structure revealed how velcro interacts with the TCR. To probe TCR cross-reactivity, we screened TCRs against yeast-displayed pMHC libraries with and without velcro, and found that the peptide cross-reactivity profiles of low-affinity (Kd > 100 μM) and high-affinity (Kd ∼ μM) TCR/pMHC interactions are remarkably similar. The conservation of recognition of the TCR for pMHC across affinities reveals the nature of low-affinity ligands for which there are important biological functions and has implications for understanding the specificities of affinity-matured TCRs.
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26
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Holland CJ, MacLachlan BJ, Bianchi V, Hesketh SJ, Morgan R, Vickery O, Bulek AM, Fuller A, Godkin A, Sewell AK, Rizkallah PJ, Wells S, Cole DK. In Silico and Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility. Front Immunol 2018; 9:674. [PMID: 29696015 PMCID: PMC5904202 DOI: 10.3389/fimmu.2018.00674] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
T-cell immunity is controlled by T cell receptor (TCR) binding to peptide major histocompatibility complexes (pMHCs). The nature of the interaction between these two proteins has been the subject of many investigations because of its central role in immunity against pathogens, cancer, in autoimmunity, and during organ transplant rejection. Crystal structures comparing unbound and pMHC-bound TCRs have revealed flexibility at the interaction interface, particularly from the perspective of the TCR. However, crystal structures represent only a snapshot of protein conformation that could be influenced through biologically irrelevant crystal lattice contacts and other factors. Here, we solved the structures of three unbound TCRs from multiple crystals. Superposition of identical TCR structures from different crystals revealed some conformation differences of up to 5 Å in individual complementarity determining region (CDR) loops that are similar to those that have previously been attributed to antigen engagement. We then used a combination of rigidity analysis and simulations of protein motion to reveal the theoretical potential of TCR CDR loop flexibility in unbound state. These simulations of protein motion support the notion that crystal structures may only offer an artifactual indication of TCR flexibility, influenced by crystallization conditions and crystal packing that is inconsistent with the theoretical potential of intrinsic TCR motions.
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Affiliation(s)
- Christopher J Holland
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore, Abingdon, United Kingdom
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Sophie J Hesketh
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Richard Morgan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Owen Vickery
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna M Bulek
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew Godkin
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephen Wells
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Immunocore, Abingdon, United Kingdom
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27
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Dendrou CA, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol 2018; 18:325-339. [PMID: 29292391 DOI: 10.1038/nri.2017.143] [Citation(s) in RCA: 405] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fifty years since the first description of an association between HLA and human disease, HLA molecules have proven to be central to physiology, protective immunity and deleterious, disease-causing autoimmune reactivity. Technological advances have enabled pivotal progress in the determination of the molecular mechanisms that underpin the association between HLA genetics and functional outcome. Here, we review our current understanding of HLA molecules as the fundamental platform for immune surveillance and responsiveness in health and disease. We evaluate the scope for personalized antigen-specific disease prevention, whereby harnessing HLA-ligand interactions for clinical benefit is becoming a realistic prospect.
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Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Medicine, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan Petersen
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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28
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Pereira SG, Moura J, Carvalho E, Empadinhas N. Microbiota of Chronic Diabetic Wounds: Ecology, Impact, and Potential for Innovative Treatment Strategies. Front Microbiol 2017; 8:1791. [PMID: 28983285 PMCID: PMC5613173 DOI: 10.3389/fmicb.2017.01791] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/05/2017] [Indexed: 12/24/2022] Open
Abstract
World Health Organization considered diabetes as one of the 20th century epidemics, estimating that over 10% of the world population is diabetic or at high risk. Self-assessment studies indicate that diabetic patients consider chronic wounds to affect their quality of life more dramatically than vision loss or renal failure. In addition to being the main reason for diabetic patients' hospitalization, the economic burden of diabetic chronic wounds is close to 1% of United Kingdom and United States health systems budgets, which exceeds the funds allocated to the treatment of some types of cancer in both countries. Among the factors preceding the emergence of chronic diabetic wounds, also designated diabetic foot ulcers (DFUs), hygiene and pressure in specific areas are under patient control, while others are still far from being understood. A triple impairment in the innervation, immune responses, and vascularization associated to DFU has been extensively studied by the scientific community. However, the skin natural microbiota has only recently emerged as having a tremendous impact on DFU emergence and evolution to chronicity. Despite the great inter- and intra-variability of microbial colonizers, ongoing efforts are now focused on deciphering the impact of commensal and pathogenic microbiota on DFU etiology, as well as the mechanisms of interkingdom microbial-host communication. This review summarizes recent work in this context and offers new microbiological perspectives that may hold potential in the prevention and treatment of chronic diabetic wounds.
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Affiliation(s)
- Sónia G. Pereira
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Polytechnic Institute of LeiriaLeiria, Portugal
| | - João Moura
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
| | - Eugénia Carvalho
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
- Department of Geriatrics, University of Arkansas for Medical Sciences, Little RockAR, United States
- Arkansas Children’s Hospital Research Institute, Little RockAR, United States
| | - Nuno Empadinhas
- Center for Neuroscience and Cell Biology, University of CoimbraCoimbra, Portugal
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29
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Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites. Biochemistry 2017; 56:3945-3961. [DOI: 10.1021/acs.biochem.7b00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Patrick S. Merkle
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Song Hongjian
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Kirsten Scholten
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - George Coukos
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A. Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Department
of Physiology and Biophysics, Weill Cornell Medical College, 1300
York Avenue, New York, New
York 10065, United States
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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30
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MacLachlan BJ, Greenshields-Watson A, Mason GH, Schauenburg AJ, Bianchi V, Rizkallah PJ, Sewell AK, Fuller A, Cole DK. Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens. J Vis Exp 2017:54991. [PMID: 28287509 PMCID: PMC5408581 DOI: 10.3791/54991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human CD8+ cytotoxic T lymphocytes (CTLs) are known to play an important role in tumor control. In order to carry out this function, the cell surface-expressed T-cell receptor (TCR) must functionally recognize human leukocyte antigen (HLA)-restricted tumor-derived peptides (pHLA). However, we and others have shown that most TCRs bind sub-optimally to tumor antigens. Uncovering the molecular mechanisms that define this poor recognition could aid in the development of new targeted therapies that circumnavigate these shortcomings. Indeed, present therapies that lack this molecular understanding have not been universally effective. Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between TCRs and pHLA governs T-cell functionality. These methods include the generation of soluble TCRs and pHLA and the use of these reagents for X-ray crystallography, biophysical analysis, and antigen-specific T-cell staining with pHLA multimers. Using these approaches and guided by structural analysis, it is possible to modify the interaction between TCRs and pHLA and to then test how these modifications impact T-cell antigen recognition. These findings have already helped to clarify the mechanism of T-cell recognition of a number of cancer antigens and could direct the development of altered peptides and modified TCRs for new cancer therapies.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | | | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrea J Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University; Department of Oncology, University Hospital of Lausanne (CHUV); Ludwig Insitutue for Cancer Research, Lausanne Branch, University of Lausanne
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University;
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31
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Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel 2016; 29:595-606. [PMID: 27624308 PMCID: PMC5181382 DOI: 10.1093/protein/gzw050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
T-cell receptors (TCRs) have emerged as a new class of therapeutics, most prominently for cancer where they are the key components of new cellular therapies as well as soluble biologics. Many studies have generated high affinity TCRs in order to enhance sensitivity. Recent outcomes, however, have suggested that fine manipulation of TCR binding, with an emphasis on specificity may be more valuable than large affinity increments. Structure-guided design is ideally suited for this role, and here we studied the generality of structure-guided design as applied to TCRs. We found that a previous approach, which successfully optimized the binding of a therapeutic TCR, had poor accuracy when applied to a broader set of TCR interfaces. We thus sought to develop a more general purpose TCR design framework. After assembling a large dataset of experimental data spanning multiple interfaces, we trained a new scoring function that accounted for unique features of each interface. Together with other improvements, such as explicit inclusion of molecular flexibility, this permitted the design new affinity-enhancing mutations in multiple TCRs, including those not used in training. Our approach also captured the impacts of mutations and substitutions in the peptide/MHC ligand, and recapitulated recent findings regarding TCR specificity, indicating utility in more general mutational scanning of TCR-pMHC interfaces.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Lance M Hellman
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Nishant K Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael Cosiano
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Jennifer M Cimons
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael J Anderson
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Kurt H Piepenbrink
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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32
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Attaf M, Holland SJ, Bartok I, Dyson J. αβ T cell receptor germline CDR regions moderate contact with MHC ligands and regulate peptide cross-reactivity. Sci Rep 2016; 6:35006. [PMID: 27775030 PMCID: PMC5075794 DOI: 10.1038/srep35006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/22/2016] [Indexed: 12/18/2022] Open
Abstract
αβ T cells respond to peptide epitopes presented by major histocompatibility complex (MHC) molecules. The role of T cell receptor (TCR) germline complementarity determining regions (CDR1 and 2) in MHC restriction is not well understood. Here, we examine T cell development, MHC restriction and antigen recognition where germline CDR loop structure has been modified by multiple glycine/alanine substitutions. Surprisingly, loss of germline structure increases TCR engagement with MHC ligands leading to excessive loss of immature thymocytes. MHC restriction is, however, strictly maintained. The peripheral T cell repertoire is affected similarly, exhibiting elevated cross-reactivity to foreign peptides. Our findings are consistent with germline TCR structure optimising T cell cross-reactivity and immunity by moderating engagement with MHC ligands. This strategy may operate alongside co-receptor imposed MHC restriction, freeing germline TCR structure to adopt this novel role in the TCR-MHC interface.
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Affiliation(s)
- Meriem Attaf
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Stephan J Holland
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Istvan Bartok
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Julian Dyson
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
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33
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Kohler AC, Chen LH, Hurlburt N, Salvucci A, Schwessinger B, Fisher AJ, Stergiopoulos I. Structural Analysis of an Avr4 Effector Ortholog Offers Insight into Chitin Binding and Recognition by the Cf-4 Receptor. THE PLANT CELL 2016; 28:1945-65. [PMID: 27401545 PMCID: PMC5006696 DOI: 10.1105/tpc.15.00893] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 06/08/2016] [Accepted: 07/07/2016] [Indexed: 05/18/2023]
Abstract
Chitin is a key component of fungal cell walls and a potent inducer of innate immune responses. Consequently, fungi may secrete chitin-binding lectins, such as the Cf-Avr4 effector protein from the tomato pathogen Cladosporium fulvum, to shield chitin from host-derived chitinases during infection. Homologs of Cf-Avr4 are found throughout Dothideomycetes, and despite their modest primary sequence identity, many are perceived by the cognate tomato immune receptor Cf-4. Here, we determined the x-ray crystal structure of Pf-Avr4 from the tomato pathogen Pseudocercospora fuligena, thus providing a three-dimensional model of an Avr4 effector protein. In addition, we explored structural, biochemical, and functional aspects of Pf-Avr4 and Cf-Avr4 to further define the biology of core effector proteins and outline a conceptual framework for their pleiotropic recognition by single immune receptors. We show that Cf-Avr4 and Pf-Avr4 share functional specificity in binding (GlcNAc)6 and in providing protection against plant- and microbial-derived chitinases, suggesting a broader role beyond deregulation of host immunity. Furthermore, structure-guided site-directed mutagenesis indicated that residues in Pf-Avr4 important for binding chitin do not directly influence recognition by Cf-4 and further suggested that the property of recognition is structurally separated or does not fully overlap with the virulence function of the effector.
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Affiliation(s)
- Amanda C Kohler
- Department of Plant Pathology, University of California Davis, Davis, California 95616
| | - Li-Hung Chen
- Department of Plant Pathology, University of California Davis, Davis, California 95616
| | - Nicholas Hurlburt
- Department of Chemistry, University of California Davis, Davis, California 95616
| | - Anthony Salvucci
- Department of Plant Pathology, University of California Davis, Davis, California 95616
| | - Benjamin Schwessinger
- Department of Plant Pathology, University of California Davis, Davis, California 95616
| | - Andrew J Fisher
- Department of Chemistry, University of California Davis, Davis, California 95616 Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California 95616
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34
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Cole DK, Bulek AM, Dolton G, Schauenberg AJ, Szomolay B, Rittase W, Trimby A, Jothikumar P, Fuller A, Skowera A, Rossjohn J, Zhu C, Miles JJ, Peakman M, Wooldridge L, Rizkallah PJ, Sewell AK. Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. J Clin Invest 2016; 126:2191-204. [PMID: 27183389 PMCID: PMC4887163 DOI: 10.1172/jci85679] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/10/2016] [Indexed: 12/11/2022] Open
Abstract
The cross-reactivity of T cells with pathogen- and self-derived peptides has been implicated as a pathway involved in the development of autoimmunity. However, the mechanisms that allow the clonal T cell antigen receptor (TCR) to functionally engage multiple peptide–major histocompatibility complexes (pMHC) are unclear. Here, we studied multiligand discrimination by a human, preproinsulin reactive, MHC class-I–restricted CD8+ T cell clone (1E6) that can recognize over 1 million different peptides. We generated high-resolution structures of the 1E6 TCR bound to 7 altered peptide ligands, including a pathogen-derived peptide that was an order of magnitude more potent than the natural self-peptide. Evaluation of these structures demonstrated that binding was stabilized through a conserved lock-and-key–like minimal binding footprint that enables 1E6 TCR to tolerate vast numbers of substitutions outside of this so-called hotspot. Highly potent antigens of the 1E6 TCR engaged with a strong antipathogen-like binding affinity; this engagement was governed though an energetic switch from an enthalpically to entropically driven interaction compared with the natural autoimmune ligand. Together, these data highlight how T cell cross-reactivity with pathogen-derived antigens might break self-tolerance to induce autoimmune disease.
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Affiliation(s)
- David K. Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Anna M. Bulek
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrea J. Schauenberg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Barbara Szomolay
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - William Rittase
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Andrew Trimby
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Prithiviraj Jothikumar
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Ania Skowera
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Jamie Rossjohn
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Cheng Zhu
- Woodruff School of Mechanical Engineering and Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - John J. Miles
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark Peakman
- Department of Immunobiology, King’s College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, United Kingdom
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre J. Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Andrew K. Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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García-Guerrero E, Pérez-Simón JA, Sánchez-Abarca LI, Díaz-Moreno I, De la Rosa MA, Díaz-Quintana A. The Dynamics of the Human Leukocyte Antigen Head Domain Modulates Its Recognition by the T-Cell Receptor. PLoS One 2016; 11:e0154219. [PMID: 27124285 PMCID: PMC4849770 DOI: 10.1371/journal.pone.0154219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/11/2016] [Indexed: 01/13/2023] Open
Abstract
Generating the immune response requires the discrimination of peptides presented by the human leukocyte antigen complex (HLA) through the T-cell receptor (TCR). However, how a single amino acid substitution in the antigen bonded to HLA affects the response of T cells remains uncertain. Hence, we used molecular dynamics computations to analyze the molecular interactions between peptides, HLA and TCR. We compared immunologically reactive complexes with non-reactive and weakly reactive complexes. MD trajectories were produced to simulate the behavior of isolated components of the various p-HLA-TCR complexes. Analysis of the fluctuations showed that p-HLA binding barely restrains TCR motions, and mainly affects the CDR3 loops. Conversely, inactive p-HLA complexes displayed significant drop in their dynamics when compared with its free versus ternary forms (p-HLA-TCR). In agreement, the free non-reactive p-HLA complexes showed a lower amount of salt bridges than the responsive ones. This resulted in differences between the electrostatic potentials of reactive and inactive p-HLA species and larger vibrational entropies in non-elicitor complexes. Analysis of the ternary p-HLA-TCR complexes also revealed a larger number of salt bridges in the responsive complexes. To summarize, our computations indicate that the affinity of each p-HLA complex towards TCR is intimately linked to both, the dynamics of its free species and its ability to form specific intermolecular salt-bridges in the ternary complexes. Of outstanding interest is the emerging concept of antigen reactivity involving its interplay with the HLA head sidechain dynamics by rearranging its salt-bridges.
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Affiliation(s)
- Estefanía García-Guerrero
- Instituto de Biomedicina de Sevilla (IBIS)/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - José Antonio Pérez-Simón
- Instituto de Biomedicina de Sevilla (IBIS)/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- * E-mail: (ADQ); (JAPS)
| | | | - Irene Díaz-Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla—CSIC, Seville, Spain
| | - Miguel A. De la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla—CSIC, Seville, Spain
| | - Antonio Díaz-Quintana
- Instituto de Bioquímica Vegetal y Fotosíntesis, cicCartuja, Universidad de Sevilla—CSIC, Seville, Spain
- * E-mail: (ADQ); (JAPS)
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36
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Moura J, Rodrigues J, Gonçalves M, Amaral C, Lima M, Carvalho E. Impaired T-cell differentiation in diabetic foot ulceration. Cell Mol Immunol 2016; 14:758-769. [PMID: 26996067 DOI: 10.1038/cmi.2015.116] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 12/31/2022] Open
Abstract
Foot ulceration is one of the most debilitating complications associated with diabetes, but its cause remains poorly understood. Several studies have been undertaken to understand healing kinetics or find possible therapies to enhance healing. However, few studies have been directed at understanding the immunological alterations that could influence wound healing in diabetes. In this study, we analysed the T-cell receptor (TCR) repertoire diversity in TCR-αβ+ T cells. We also analysed the distribution and phenotype of T cells obtained from the peripheral blood of healthy controls and diabetic individuals with or without foot ulcers. Our results showed that diabetic individuals, especially those with foot ulcers, have a significantly lower naive T-cell number and a poorer TCR-Vβ repertoire diversity. We also showed that the reduced TCR-Vβ repertoire diversity in diabetic individuals was mainly owing to the accumulation of effector T cells, the major source of tumour necrosis factor-α production, which was even more pronounced in patients with acute foot ulceration. Moreover, the expression of several inflammatory chemokine receptors was significantly reduced in diabetic patients. In conclusion, effector T-cell accumulation and TCR repertoire diversity reduction appear to precede the development of foot ulcers. This finding may open new immunological therapeutic possibilities and provide a new prognostic tool in diabetic wound care.
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Affiliation(s)
- João Moura
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-517 Coimbra, Portugal
| | - João Rodrigues
- Hospital de Santo António (HSA), Centro Hospitalar do Porto (CHP), 4099-001 Porto, Portugal.,Unidade Multidisciplinar de Investigação Biomédica (UMIB/ICBAS/UP), Porto, Portugal
| | - Marta Gonçalves
- Hospital de Santo António (HSA), Centro Hospitalar do Porto (CHP), 4099-001 Porto, Portugal.,Unidade Multidisciplinar de Investigação Biomédica (UMIB/ICBAS/UP), Porto, Portugal
| | - Cláudia Amaral
- Hospital de Santo António (HSA), Centro Hospitalar do Porto (CHP), 4099-001 Porto, Portugal
| | - Margarida Lima
- Hospital de Santo António (HSA), Centro Hospitalar do Porto (CHP), 4099-001 Porto, Portugal.,Unidade Multidisciplinar de Investigação Biomédica (UMIB/ICBAS/UP), Porto, Portugal.,These authors contributed equally to this work
| | - Eugénia Carvalho
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-517 Coimbra, Portugal.,Department of Geriatrics, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR 72202, USA.,Arkansas Children's Hospital Research Institute (ACHRI), Little Rock, AR 72202, USA.,These authors contributed equally to this work
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37
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Bello M, Correa-Basurto J. Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex. MOLECULAR BIOSYSTEMS 2016; 12:1350-66. [PMID: 26926952 DOI: 10.1039/c6mb00058d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, CP: 11340, Mexico.
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Patarroyo ME, Bermúdez A, Alba MP, Vanegas M, Moreno-Vranich A, Poloche LA, Patarroyo MA. IMPIPS: the immune protection-inducing protein structure concept in the search for steric-electron and topochemical principles for complete fully-protective chemically synthesised vaccine development. PLoS One 2015; 10:e0123249. [PMID: 25879751 PMCID: PMC4400017 DOI: 10.1371/journal.pone.0123249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/28/2015] [Indexed: 01/14/2023] Open
Abstract
Determining immune protection-inducing protein structures (IMPIPS) involves defining the stereo-electron and topochemical characteristics which are essential in MHC-p-TCR complex formation. Modified high activity binding peptides (mHABP) were thus synthesised to produce a large panel of IMPIPS measuring 26.5 ±3.5Å between the farthest atoms fitting into Pockets 1 to 9 of HLA-DRβ1* structures. They displayed a polyproline II-like (PPIIL) structure with their backbone O and N atoms orientated to establish H-bonds with specific residues from HLA-DRβ1*-peptide binding regions (PBR). Residues having specific charge and gauche+ orientation regarding p3χ1, p5χ2, and p7χ1 angles determined appropriate rotamer orientation for perfectly fitting into the TCR to induce an appropriate immune response. Immunological assays in Aotus monkeys involving IMPIPS mixtures led to promising results; taken together with the aforementioned physicochemical principles, non-interfering, long-lasting, protection-inducing, multi-epitope, multistage, minimal subunit-based chemically-synthesised peptides can be designed against diseases scourging humankind.
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Affiliation(s)
- Manuel Elkin Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail:
| | - Adriana Bermúdez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | - Martha Patricia Alba
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | - Magnolia Vanegas
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
| | | | | | - Manuel Alfonso Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Universidad del Rosario, Bogotá, Colombia
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Løset GÅ, Berntzen G, Frigstad T, Pollmann S, Gunnarsen KS, Sandlie I. Phage Display Engineered T Cell Receptors as Tools for the Study of Tumor Peptide-MHC Interactions. Front Oncol 2015; 4:378. [PMID: 25629004 PMCID: PMC4290511 DOI: 10.3389/fonc.2014.00378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/17/2014] [Indexed: 11/13/2022] Open
Abstract
Cancer immunotherapy has finally come of age, demonstrated by recent progress in strategies that engage the endogenous adaptive immune response in tumor killing. Occasionally, significant and durable tumor regression has been achieved. A giant leap forward was the demonstration that the pre-existing polyclonal T cell repertoire could be re-directed by use of cloned T cell receptors (TCRs), to obtain a defined tumor-specific pool of T cells. However, the procedure must be performed with caution to avoid deleterious cross-reactivity. Here, the use of engineered soluble TCRs may represent a safer, yet powerful, alternative. There is also a need for deeper understanding of the processes that underlie antigen presentation in disease and homeostasis, how tumor-specific peptides are generated, and how epitope spreading evolves during tumor development. Due to its plasticity, the pivotal interaction where a TCR engages a peptide/MHC (pMHC) also requires closer attention. For this purpose, phage display as a tool to evolve cloned TCRs represents an attractive avenue to generate suitable reagents allowing the study of defined pMHC presentation, TCR engagement, as well as for the discovery of novel therapeutic leads. Here, we highlight important aspects of the current status in this field.
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Affiliation(s)
- Geir Åge Løset
- Nextera AS , Oslo , Norway ; Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway ; Department of Biosciences, University of Oslo , Oslo , Norway
| | | | | | | | - Kristin S Gunnarsen
- Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Inger Sandlie
- Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway ; Department of Biosciences, University of Oslo , Oslo , Norway
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40
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Understanding the structural dynamics of TCR-pMHC interactions. Trends Immunol 2014; 35:604-612. [DOI: 10.1016/j.it.2014.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022]
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41
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Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Sci 2014; 22:35-46. [PMID: 23109003 DOI: 10.1002/pro.2181] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/15/2012] [Indexed: 11/10/2022]
Abstract
T cell receptors (TCRs) are immune proteins that specifically bind to antigenic molecules, which are often foreign peptides presented by major histocompatibility complex proteins (pMHCs), playing a key role in the cellular immune response. To advance our understanding and modeling of this dynamic immunological event, we assembled a protein-protein docking benchmark consisting of 20 structures of crystallized TCR/pMHC complexes for which unbound structures exist for both TCR and pMHC. We used our benchmark to compare predictive performance using several flexible and rigid backbone TCR/pMHC docking protocols. Our flexible TCR docking algorithm, TCRFlexDock, improved predictive success over the fixed backbone protocol, leading to near-native predictions for 80% of the TCR/pMHC cases among the top 10 models, and 100% of the cases in the top 30 models. We then applied TCRFlexDock to predict the two distinct docking modes recently described for a single TCR bound to two different antigens, and tested several protein modeling scoring functions for prediction of TCR/pMHC binding affinities. This algorithm and benchmark should enable future efforts to predict, and design of uncharacterized TCR/pMHC complexes.
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Affiliation(s)
- Brian G Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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42
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Hawse WF, De S, Greenwood AI, Nicholson LK, Zajicek J, Kovrigin EL, Kranz DM, Garcia KC, Baker BM. TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 192:2885-91. [PMID: 24523505 PMCID: PMC3992338 DOI: 10.4049/jimmunol.1302953] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Although conformational changes in TCRs and peptide Ags presented by MHC protein (pMHC) molecules often occur upon binding, their relationship to intrinsic flexibility and role in ligand selectivity are poorly understood. In this study, we used nuclear magnetic resonance to study TCR-pMHC binding, examining recognition of the QL9/H-2L(d) complex by the 2C TCR. Although the majority of the CDR loops of the 2C TCR rigidify upon binding, the CDR3β loop remains mobile within the TCR-pMHC interface. Remarkably, the region of the QL9 peptide that interfaces with CDR3β is also mobile in the free pMHC and in the TCR-pMHC complex. Determination of conformational exchange kinetics revealed that the motions of CDR3β and QL9 are closely matched. The matching of conformational exchange in the free proteins and its persistence in the complex enhances the thermodynamic and kinetic stability of the TCR-pMHC complex and provides a mechanism for facile binding. We thus propose that matching of structural fluctuations is a component of how TCRs scan among potential ligands for those that can bind with sufficient stability to enable T cell signaling.
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Affiliation(s)
- William F. Hawse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Soumya De
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alex I. Greenwood
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Linda K. Nicholson
- Department of Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jaroslav Zajicek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
| | | | - David M. Kranz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana IL 61801, USA
| | - K. Christopher Garcia
- Departments of Molecular & Cellular Physiology and Structural Biology, Program in Immunology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46530, USA
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43
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Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol 2014; 10:e1003478. [PMID: 24550723 PMCID: PMC3923660 DOI: 10.1371/journal.pcbi.1003478] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/02/2014] [Indexed: 01/15/2023] Open
Abstract
T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.
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Affiliation(s)
- Brian G. Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lance M. Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Moushumi Hossain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, United States of America
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The basis for limited specificity and MHC restriction in a T cell receptor interface. Nat Commun 2013; 4:1948. [PMID: 23736024 PMCID: PMC3708045 DOI: 10.1038/ncomms2948] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 04/30/2013] [Indexed: 02/03/2023] Open
Abstract
αβ T cell receptors (TCRs) recognize peptides presented by major histocompatibility complex (MHC) proteins using multiple complementarity determining region (CDR) loops. TCRs display an array of poorly understood recognition properties, including specificity, cross-reactivity, and MHC restriction. Here we report a comprehensive thermodynamic deconstruction of the interaction between the A6 TCR and the Tax peptide presented by the class I MHC HLA-A*0201, uncovering the physical basis for the receptor's recognition properties. Broadly, our findings are in conflict with widely-held generalities regarding TCR recognition, such as the relative contributions of central and peripheral peptide residues and the roles of the hypervariable and germline CDR loops in engaging peptide and MHC. Instead we find that the recognition properties of the receptor emerge from the need to engage the composite peptide/MHC surface, with the receptor utilizing its CDR loops in a cooperative fashion such that specificity, cross-reactivity, and MHC restriction are inextricably linked.
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45
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Sulfamethoxazole induces a switch mechanism in T cell receptors containing TCRVβ20-1, altering pHLA recognition. PLoS One 2013; 8:e76211. [PMID: 24116097 PMCID: PMC3792127 DOI: 10.1371/journal.pone.0076211] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/21/2013] [Indexed: 11/19/2022] Open
Abstract
T cell receptors (TCR) containing Vβ20-1 have been implicated in a wide range of T cell mediated disease and allergic reactions, making it a target for understanding these. Mechanics of T cell receptors are largely unexplained by static structures available from x-ray crystallographic studies. A small number of molecular dynamic simulations have been conducted on TCR, however are currently lacking either portions of the receptor or explanations for differences between binding and non-binding TCR recognition of respective peptide-HLA. We performed molecular dynamic simulations of a TCR containing variable domain Vβ20-1, sequenced from drug responsive T cells. These were initially from a patient showing maculopapular eruptions in response to the sulfanilamide-antibiotic sulfamethoxazole (SMX). The CDR2β domain of this TCR was found to dock SMX with high affinity. Using this compound as a perturbation, overall mechanisms involved in responses mediated by this receptor were explored, showing a chemical action on the TCR free from HLA or peptide interaction. Our simulations show two completely separate modes of binding cognate peptide-HLA complexes, with an increased affinity induced by SMX bound to the Vβ20-1. Overall binding of the TCR is mediated through a primary recognition by either the variable β or α domain, and a switch in recognition within these across TCR loops contacting the peptide and HLA occurs when SMX is present in the CDR2β loop. Large binding affinity differences are induced by summed small amino acid changes primarily by SMX modifying only three critical CDR2β loop amino acid positions. These residues, TYRβ57, ASPβ64, and LYSβ65 initially hold hydrogen bonds from the CDR2β to adjacent CDR loops. Effects from SMX binding are amplified and traverse longer distances through internal TCR hydrogen bonding networks, controlling the overall TCR conformation. Thus, the CDR2β of Vβ20-1 acts as a ligand controlled switch affecting overall TCR binding affinity.
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46
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NMR spectroscopy on domain dynamics in biomacromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 112:58-117. [DOI: 10.1016/j.pbiomolbio.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022]
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47
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Yin Q, Tan H, Chen S, Yang L, Ye J, Li Y. Characterization of conserved CDR3 sequence of TCRα- andβ-chain genes in peripheral blood T-cells from patients with diffuse large B-cell lymphoma. Hematology 2013; 15:48-57. [PMID: 20132663 DOI: 10.1179/102453310x12583347009694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- Qingsong Yin
- Institute of HematologyMedical College, Jinan University, Guangzhou, China
| | - Huo Tan
- Center of Oncology and Hematologythe First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Shaohua Chen
- Institute of HematologyMedical College, Jinan University, Guangzhou, China
| | - Lijian Yang
- Institute of HematologyMedical College, Jinan University, Guangzhou, China
| | - Jingmei Ye
- Center of Oncology and Hematologythe First Affiliated Hospital of Guangzhou Medical College, Guangzhou, China
| | - Yangqiu Li
- Institute of HematologyMedical College, Jinan University, Guangzhou, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
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48
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Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, Baker BM. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. J Biol Chem 2013; 288:24372-81. [PMID: 23836912 DOI: 10.1074/jbc.m113.490664] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
T cells use the αβ T cell receptor (TCR) to recognize antigenic peptides presented by class I major histocompatibility complex proteins (pMHCs) on the surfaces of antigen-presenting cells. Flexibility in both TCRs and peptides plays an important role in antigen recognition and discrimination. Less clear is the role of flexibility in the MHC protein; although recent observations have indicated that mobility in the MHC can impact TCR recognition in a peptide-dependent fashion, the extent of this behavior is unknown. Here, using hydrogen/deuterium exchange, fluorescence anisotropy, and structural analyses, we show that the flexibility of the peptide binding groove of the class I MHC protein HLA-A*0201 varies significantly with different peptides. The variations extend throughout the binding groove, impacting regions contacted by TCRs as well as other activating and inhibitory receptors of the immune system. Our results are consistent with statistical mechanical models of protein structure and dynamics, in which the binding of different peptides alters the populations and exchange kinetics of substates in the MHC conformational ensemble. Altered MHC flexibility will influence receptor engagement, impacting conformational adaptations, entropic penalties associated with receptor recognition, and the populations of binding-competent states. Our results highlight a previously unrecognized aspect of the "altered self" mechanism of immune recognition and have implications for specificity, cross-reactivity, and antigenicity in cellular immunity.
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Affiliation(s)
- William F Hawse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Cole DK, Sami M, Scott DR, Rizkallah PJ, Borbulevych OY, Todorov PT, Moysey RK, Jakobsen BK, Boulter JM, Baker BM, Yi Li. Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode. Front Immunol 2013; 4:168. [PMID: 23805144 PMCID: PMC3693486 DOI: 10.3389/fimmu.2013.00168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/12/2013] [Indexed: 12/15/2022] Open
Abstract
Natural T cell receptors (TCRs) generally bind to their cognate pMHC molecules with weak affinity and fast kinetics, limiting their use as therapeutic agents. Using phage display, we have engineered a high affinity version of the A6 wild-type TCR (A6wt), specific for the human leukocyte antigen (HLA-A∗0201) complexed with human T cell lymphotropic virus type 111–19 peptide (A2-Tax). Mutations in just 4 residues in the CDR3β loop region of the A6wt TCR were selected that improved binding to A2-Tax by nearly 1000-fold. Biophysical measurements of this mutant TCR (A6c134) demonstrated that the enhanced binding was derived through favorable enthalpy and a slower off-rate. The structure of the free A6c134 TCR and the A6c134/A2-Tax complex revealed a native binding mode, similar to the A6wt/A2-Tax complex. However, concordant with the more favorable binding enthalpy, the A6c134 TCR made increased contacts with the Tax peptide compared with the A6wt/A2-Tax complex, demonstrating a peptide-focused mechanism for the enhanced affinity that directly involved the mutated residues in the A6c134 TCR CDR3β loop. This peptide-focused enhanced TCR binding may represent an important approach for developing antigen specific high affinity TCR reagents for use in T cell based therapies.
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, Heath Park , Cardiff , UK
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Eckle SBG, Rossjohn J, McCluskey J. Alloreactivity. Methods Mol Biol 2013; 1034:3-39. [PMID: 23775729 DOI: 10.1007/978-1-62703-493-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The alloimmune response between individuals genetically disparate for antigens encoded within the major histocompatibility complex (MHC) remains a substantial barrier to transplantation of solid organs, tissues, and hematopoietic stem cells. Alloreactivity has been an immunological paradox because of its apparent contradiction to the requirement of MHC restriction for the induction of normal T lymphocyte mediated immune responses. Through crystallographic analyses and experimental systems utilizing murine CD8(+) cytolytic T cell clones, major advances have been achieved in understanding the molecular and structural basis of T cell receptor recognition of MHC-peptide complexes and the basis of T cell mediated alloreactivity. These studies have further provided an explanation for the relatively high frequencies of alloreactive T cells compared to the frequencies of T cells for microbial derived antigens.
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Affiliation(s)
- Sidonia B G Eckle
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC, Australia
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