1
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Fasoulis R, Rigo MM, Lizée G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model 2024; 64:1730-1750. [PMID: 38415656 PMCID: PMC10936522 DOI: 10.1021/acs.jcim.3c01667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
The recognition of peptides bound to class I major histocompatibility complex (MHC-I) receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune response. While the exact molecular features that drive the TCR recognition are still unknown, studies have suggested that the geometry of the joint peptide-MHC (pMHC) structure plays an important role. As such, there is a definite need for methods and tools that accurately predict the structure of the peptide bound to the MHC-I receptor. In the past few years, many pMHC structural modeling tools have emerged that provide high-quality modeled structures in the general case. However, there are numerous instances of non-canonical cases in the immunopeptidome that the majority of pMHC modeling tools do not attend to, most notably, peptides that exhibit non-standard amino acids and post-translational modifications (PTMs) or peptides that assume non-canonical geometries in the MHC binding cleft. Such chemical and structural properties have been shown to be present in neoantigens; therefore, accurate structural modeling of these instances can be vital for cancer immunotherapy. To this end, we have developed APE-Gen2.0, a tool that improves upon its predecessor and other pMHC modeling tools, both in terms of modeling accuracy and the available modeling range of non-canonical peptide cases. Some of the improvements include (i) the ability to model peptides that have different types of PTMs such as phosphorylation, nitration, and citrullination; (ii) a new and improved anchor identification routine in order to identify and model peptides that exhibit a non-canonical anchor conformation; and (iii) a web server that provides a platform for easy and accessible pMHC modeling. We further show that structures predicted by APE-Gen2.0 can be used to assess the effects that PTMs have in binding affinity in a more accurate manner than just using solely the sequence of the peptide. APE-Gen2.0 is freely available at https://apegen.kavrakilab.org.
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Affiliation(s)
- Romanos Fasoulis
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Mauricio M. Rigo
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
| | - Gregory Lizée
- Department
of Melanoma Medical Oncology—Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Dinler A. Antunes
- Department
of Biology and Biochemistry, University
of Houston, Houston, Texas 77004, United States
| | - Lydia E. Kavraki
- Department
of Computer Science, Rice University, Houston, Texas 77005, United States
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2
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Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc Natl Acad Sci U S A 2023; 120:e2312057120. [PMID: 38085776 PMCID: PMC10742377 DOI: 10.1073/pnas.2312057120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.
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Affiliation(s)
- Jean M. Custodio
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Tatiana J. Rosales
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Chad A. Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Alyssa G. Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Lauren M. Landau
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Grant L. J. Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Pramod K. Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT06030
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
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3
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McShan AC, Flores-Solis D, Sun Y, Garfinkle SE, Toor JS, Young MC, Sgourakis NG. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nat Commun 2023; 14:8204. [PMID: 38081856 PMCID: PMC10713829 DOI: 10.1038/s41467-023-43654-9] [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: 08/28/2022] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational landscapes of peptide/human leucocyte antigen (pHLA) protein complexes encompassing tumor neoantigens provide a rationale for target selection towards autologous T cell, vaccine, and antibody-based therapeutic modalities. Here, using complementary biophysical and computational methods, we characterize recurrent RAS55-64 Q61 neoepitopes presented by the common HLA-A*01:01 allotype. We integrate sparse NMR restraints with Rosetta docking to determine the solution structure of NRASQ61K/HLA-A*01:01, which enables modeling of other common RAS55-64 neoepitopes. Hydrogen/deuterium exchange mass spectrometry experiments alongside molecular dynamics simulations reveal differences in solvent accessibility and conformational plasticity across a panel of common Q61 neoepitopes that are relevant for recognition by immunoreceptors. Finally, we predict binding and provide structural models of NRASQ61K antigens spanning the entire HLA allelic landscape, together with in vitro validation for HLA-A*01:191, HLA-B*15:01, and HLA-C*08:02. Our work provides a basis to delineate the solution surface features and immunogenicity of clinically relevant neoepitope/HLA targets for cancer therapy.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr NW, Atlanta, GA, 30318, USA
| | - David Flores-Solis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 37075, Göttingen, Germany
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel E Garfinkle
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, 48202, USA
| | - Michael C Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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4
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Gupta S, Nerli S, Kutti Kandy S, Mersky GL, Sgourakis NG. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. Nat Commun 2023; 14:6349. [PMID: 37816745 PMCID: PMC10564892 DOI: 10.1038/s41467-023-42163-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptides bound to the human MHC, HLA, has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within our curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer pHLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work may be applied towards predicting antigen immunogenicity, and receptor cross-reactivity.
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Affiliation(s)
- Sagar Gupta
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Santrupti Nerli
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sreeja Kutti Kandy
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Glenn L Mersky
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Ayres CM, Corcelli SA, Baker BM. The Energetic Landscape of Catch Bonds in TCR Interfaces. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:325-332. [PMID: 37459192 PMCID: PMC10361606 DOI: 10.4049/jimmunol.2300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Steve A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
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6
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Gupta S, Nerli S, Kandy SK, Mersky GL, Sgourakis NG. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533510. [PMID: 36993660 PMCID: PMC10055217 DOI: 10.1101/2023.03.20.533510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptide/HLA (pHLA, the human MHC) structures has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within a curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these representative backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer peptide/HLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in terms of structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work provide a framework for linking conformational diversity with antigen immunogenicity and receptor cross-reactivity.
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7
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Li L, Peng X, Batliwala M, Bouvier M. Unusual crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing in antigen presentation. RESEARCH SQUARE 2023:rs.3.rs-2500847. [PMID: 36747752 PMCID: PMC9901037 DOI: 10.21203/rs.3.rs-2500847/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between conformational states as they sample peptides for potential ligands. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. We present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show significant conformational heterogeneity at the N-terminus of the groove. Long stretches of N-terminal residues were missing in the electron density maps creating an unstructured and widely open-ended groove. Our structures also revealed highly unusual features in MHC I and peptide conformations, and in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations showed that the complexes have varying degrees of flexibility in a manner consistent with the structures. We suggest that our structures represent transient substates explored by MHC I molecules during peptide editing. The visualization of peptide-dependent conformational flexibility in MHC I groove is a major step forward in our conceptual understanding of peptide repertoire development in antigen presentation. Our study also raises questions about the role of the N-terminus of the groove in peptide editing.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
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8
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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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9
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Ayres CM, Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity. Curr Opin Immunol 2022; 76:102184. [PMID: 35550277 PMCID: PMC10052791 DOI: 10.1016/j.coi.2022.102184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
T cell receptors (TCRs) and other receptors of the immune system recognize peptides presented by class I or class II major histocompatibility complex (MHC) proteins. Although we generally distinguish between the MHC protein and its peptide, at an atomic level the two form a structural composite, which allows peptides to influence MHC properties and vice versa. One consequence is the peptide-dependent tuning of MHC structural dynamics, which contributes to protein structural adaptability and influences how receptors identify and bind targets. Peptide-dependent tuning of MHC protein dynamics can impact processes such as antigenicity, TCR cross-reactivity, and T cell repertoire selection. Motional tuning extends beyond the binding groove, influencing peptide selection and exchange, as well as interactions with other immune receptors. Here, we review recent findings showing how peptides can affect the dynamic and adaptable nature of MHC proteins. We highlight consequences for immunity and demonstrate how MHC proteins have evolved to be highly sensitive dynamic reporters, with broad immunological consequences.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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10
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Awad N, Mohamed RH, Ghoneim NI, Elmehrath AO, El-Badri N. Immunoinformatics approach of epitope prediction for SARS-CoV-2. J Genet Eng Biotechnol 2022; 20:60. [PMID: 35441904 PMCID: PMC9019534 DOI: 10.1186/s43141-022-00344-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide during an unprecedented pandemic. Identification of the candidate viral epitopes is the first step in the design of vaccines against the viral infection. Several immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes that bind specifically with the major histocompatibility molecules class I (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. These alleles were also found with high frequency in other populations worldwide. RESULTS Molecular docking approach showed that using the co-crystallized MHC-I and T cell receptor (TCR) instead of using MHC-I structure only, significantly enhanced docking scores and stabilized the conformation, as well as the binding affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein sequence. This prediction has been confirmed by published experimentally validated and in silico predicted spike epitope. On the other hand, we predicted novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and antigenicity response with both MHC-I and TCR. Moreover, antigenicity, allergenicity, toxicity, and physicochemical properties of the predicted SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, showing high efficacy of the proposed epitopes as a vaccine candidate. CONCLUSION Our predicted SARS-CoV-2 epitopes can facilitate vaccine development to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for further experimental validation. Our proposed molecular docking approach of exploiting both MHC and TCR structures can be used to identify potential epitopes for most microbial pathogens, provided the crystal structure of MHC co-crystallized with TCR.
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Affiliation(s)
- Nourelislam Awad
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Center of Informatics Sciences, Nile University, Giza, Egypt
| | - Rania Hassan Mohamed
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nehal I Ghoneim
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed O Elmehrath
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.
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11
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Strand A, Shen ST, Tomchick D, Wang J, Wang CR, Deisenhofer J. Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides. J Biomol Struct Dyn 2022; 40:10300-10312. [PMID: 34176438 PMCID: PMC8722451 DOI: 10.1080/07391102.2021.1942214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Presentation of antigenic peptides to T-cell receptors is an essential step in the adaptive immune response. In the mouse the class Ib major histocompatibility complex molecule, H2-M3, presents bacterial- and mitochondrial-derived peptides to T-cell receptors on cytotoxic T cells. Four mitochondrial heptapeptides, differing only at residue 6, form complexes with H2-M3 which can be distinguished by T cells. No structures of relevant receptors are available. To investigate the structural basis for this distinction, crystal structures were determined and molecular dynamics simulations over one microsecond were done for each complex. In the crystal structures of the heptapeptide complexes with H2-M3, presented here, the side chains of the peptide residues at position 6 all point into the H2-M3 binding groove, and are thus inaccessible, so that the very similar structures do not suggest how recognition and initiation of responses by the T cells may occur. However, conformational differences, which could be crucial to T-cell discrimination, appear within one microsecond during molecular dynamics simulations of the four complexes. Specifically, the three C-terminal residues of peptide ligands with alanine or threonine at position 6 partially exit the binding groove; this does not occur in peptide ligands with isoleucine or valine at position 6. Structural changes associated with partial peptide exit from the binding groove, along with relevant peptide binding energetics and immunological results are discussed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arne Strand
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - San-Tai Shen
- AnTaimmu Biomed Co., Ltd., Zhubei City, Hsinchu County, Taiwan
| | - Diana Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chyung-Ru Wang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Johann Deisenhofer
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Corresponding author
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12
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Hadeler A, Saikia A, Zacharias M, Springer S. Rapid peptide exchange on MHC class I by small molecules elucidates dynamics of bound peptide. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:167-174. [PMID: 36042776 PMCID: PMC9420430 DOI: 10.1016/j.crimmu.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022] Open
Abstract
Complexes of peptides with recombinant major histocompatibility complex class I molecules (rpMHCs) are an important tool for T cell detection, isolation, and activation in cancer immunotherapy. The rapid preparation of rpMHCs is aided by peptide exchange, for which several technologies exist. Here, we show peptide exchange with small-molecule alcohols and demonstrate that they accelerate the dissociation of pre-bound peptides, creating a novel method for rapid production of rpMHCs and increasing the understanding of the conformational flexibility of the MHC-bound peptides. Small alcohols can catalyze peptide exchange on MHC-I. C-terminal peptide binding plays an important role in ethanol mediated exchange. MHC-I ethanol peptide exchange is allotype dependent.
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13
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Truong HV, Sgourakis NG. Dynamics of MHC-I molecules in the antigen processing and presentation pathway. Curr Opin Immunol 2021; 70:122-128. [PMID: 34153556 PMCID: PMC8622473 DOI: 10.1016/j.coi.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 01/07/2023]
Abstract
The endogenous antigen processing and presentation (APP) is a fundamental pathway found in jawed vertebrates, which allows for a set of epitope peptides sampled from the intracellular proteome to be assembled and displayed on class I proteins of the major histocompatibility complex (MHC-I). Peptide/MHC-I antigens enable different aspects of adaptive immunity to emerge, by providing a basis for recognition of self vs. non-self by T cells and Natural Killer (NK) cells. Pioneering studies of pMHC-I molecules and their higher-order protein complexes with molecular chaperones and membrane receptors have gleaned important insights into the peptide loading and antigen recognition mechanisms. While X-ray and cryoEM structures have provided us with static snapshots of different MHC-I assembly stages, complementary biophysical techniques have revealed that MHC-I molecules are highly mobile on a range of biologically relevant timescales, which bears importance for their assembly, peptide repertoire selection, membrane display and turnover. This review summarizes insights gained from experimental and simulation studies aimed at investigating MHC-I dynamics, and their functional implications.
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Affiliation(s)
- Hau V Truong
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3401 Civic Center Blvd., Philadelphia, PA 19104, USA.
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14
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Jantz-Naeem N, Springer S. Venus flytrap or pas de trois? The dynamics of MHC class I molecules. Curr Opin Immunol 2021; 70:82-89. [PMID: 33993034 DOI: 10.1016/j.coi.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
The peptide binding site of major histocompatibility complex (MHC) class I molecules is natively unfolded when devoid of peptides. Peptide binding stabilizes the structure and slows the dynamics, but peptide-specific and subtype-specific motions influence, and are influenced by, interaction with assembly chaperones, the T cell receptor, and other class I-binding proteins. The molecular mechanisms of cooperation between peptide, class I heavy chain, and beta-2 microglobulin are insufficiently known but are being elucidated by nuclear magnetic resonance and other modern methods. It appears that micropolymorphic clusters of charged amino acids, often hidden in the molecule interior, determine the dynamics and thus chaperone dependence, cellular fate, and disease association of class I.
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Affiliation(s)
- Nouria Jantz-Naeem
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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15
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Huang C, Chen J, Ding F, Yang L, Zhang S, Wang X, Shi Y, Zhu Y. Related parameters of affinity and stability prediction of HLA-A*2402 restricted antigen peptides based on molecular docking. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:673. [PMID: 33987371 PMCID: PMC8106073 DOI: 10.21037/atm-21-630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background Major histocompatibility complex class I (MHC-I) plays an important role in cell immune response, and stable interaction between polypeptides and MHC-I ensures efficient presentation of polypeptide-MHC-I (pMHC-I) molecular complexes to T cells. The aim of this study was to explore ways to improve the affinity and stability of the p-Human Leukocyte Antigen (HLA)-A*2402 complex. Methods The peptide sequences of the restricted antigen peptides for HLA-A*2402 and the results of the in vitro competitive binding test were retrieved from the literature. The affinity values were predicted using NetMHCpan v4.1 server, and the stability values were predicted using the NetMHCstab v1.0 server. Auto Vina was used to dock peptides to HLA-A*2402 protein in a flexible docking manner, while Flexpepdock was employed to optimize the docking morphology. Maestro was used to analyze the intermolecular forces and the binding affinity of the complex, while MM-GBSA was used to calculate the binding free energy values. Results The intermolecular interactions that maintained the affinity and stability of peptide-HLA-A*2402 complex relied mainly on HB, followed by pi stack. The binding affinity values of molecular docking were associated with the predicted values of affinity and stability, the binding affinity and the binding free energy, as well as the intermolecular force pi-stack. The pi stack had a significant negative correlation with binding affinity and binding free energy. The replacement of the residues of the polypeptides that did not form pi-stack interactions with HLA-A*2402 improved the affinity and/or stability compared to before replacement. Conclusions The generation and increase in the number of pi-stacks between peptides and HLA-A*2402 molecules may help improve the affinity and stability of p-HLA-A*2402 complexes. The prediction of intermolecular forces and binding affinity of peptide-HLA by means of molecular docking is a supplement to the current commonly used prediction databases.
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Affiliation(s)
- Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Fei Ding
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Lili Yang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Siyu Zhang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xuechun Wang
- Zhejiang Chinese Medical University 4th School of Clinical Medicine, Hangzhou, China
| | - Yanfei Shi
- Hangzhou Normal University School of Medicine, Hangzhou, China
| | - Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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16
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Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc Natl Acad Sci U S A 2021; 118:e2018125118. [PMID: 33468649 PMCID: PMC7848747 DOI: 10.1073/pnas.2018125118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.
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MESH Headings
- Allosteric Regulation
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Jurkat Cells
- Kinetics
- Models, Molecular
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Engineering
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Th2 Cells/cytology
- Th2 Cells/immunology
- Thermodynamics
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Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, NV 89002
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
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17
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Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics 2020; 36:5377-5385. [PMID: 33355667 PMCID: PMC8016493 DOI: 10.1093/bioinformatics/btaa1050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 11/23/2020] [Accepted: 12/08/2020] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION The binding of T cell receptors (TCRs) to their target peptide MHC (pMHC) ligands initializes the cell-mediated immune response. In autoimmune diseases such as multiple sclerosis, the TCR erroneously recognizes self-peptides as foreign and activates an immune response against healthy cells. Such responses can be triggered by cross-recognition of the autoreactive TCR with foreign peptides. Hence, it would be desirable to identify such foreign-antigen triggers to provide a mechanistic understanding of autoimmune diseases. However, the large sequence space of foreign antigens presents an obstacle in the identification of cross-reactive peptides. RESULTS Here, we present an in silico modeling and scoring method which exploits the structural properties of TCR-pMHC complexes to predict the binding of cross-reactive peptides. We analyzed three mouse TCRs and one human TCR isolated from a patient with multiple sclerosis. Cross-reactive peptides for these TCRs were previously identified via yeast display coupled with deep sequencing, providing a robust dataset for evaluating our method. Modeling query peptides in their associated TCR-pMHC crystal structures, our method accurately selected the top binding peptides from sets containing more than a hundred thousand unique peptides. AVAILABILITY AND IMPLEMENTATION Analyses were performed using custom Python and R scripts available at https://github.com/tborrman/antigen-predict. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 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
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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18
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Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b 214-222 by combinatorial peptide library screening. Mol Immunol 2020; 125:43-50. [PMID: 32645549 DOI: 10.1016/j.molimm.2020.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/27/2020] [Accepted: 06/24/2020] [Indexed: 11/22/2022]
Abstract
The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.
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19
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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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20
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Tarbe M, Miles JJ, Edwards ESJ, Miles KM, Sewell AK, Baker BM, Quideau S. Synthesis and Biological Evaluation of Hapten-Clicked Analogues of The Antigenic Peptide Melan-A/MART-1 26(27L)-35. ChemMedChem 2020; 15:799-807. [PMID: 32162475 PMCID: PMC7473458 DOI: 10.1002/cmdc.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Indexed: 11/12/2022]
Abstract
A click-chemistry-based approach was implemented to prepare peptidomimetics designed in silico and made from aromatic azides and a propargylated GIGI-mimicking platform derived from the altered Melan-A/MART-126(27L)-35 antigenic peptide ELAGIGILTV. The CuI -catalyzed Huisgen cycloaddition was carried out on solid support to generate rapidly a first series of peptidomimetics, which were evaluated for their capacity to dock at the interface between the major histocompatibility complex class-I (MHC-I) human leucocyte antigen (HLA)-A2 and T-cell receptors (TCRs). Despite being a weak HLA-A2 ligand, one of these 11 first synthetic compounds bearing a p-nitrobenzyl-triazole side chain was recognized by the receptor proteins of Melan-A/MART-1-specific T-cells. After modification of the N and C termini of this agonist, which was intended to enhance HLA-A2 binding, one of the resulting seven additional compounds triggered significant T-cell responses. Thus, these results highlight the capacity of naturally circulating human TCRs that are specific for the native Melan-A/MART-126-35 peptide to cross-react with peptidomimetics bearing organic motifs structurally different from the native central amino acids.
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Affiliation(s)
- Marion Tarbe
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - John J Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Emily S J Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
- Department of Immunology and Pathology, Central Clinical School, Monash University, Level 6, 89 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Kim M Miles
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Brian M Baker
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Stéphane Quideau
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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21
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Duru AD, Sun R, Allerbring EB, Chadderton J, Kadri N, Han X, Peqini K, Uchtenhagen H, Madhurantakam C, Pellegrino S, Sandalova T, Nygren PÅ, Turner SJ, Achour A. Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination. PLoS Pathog 2020; 16:e1008244. [PMID: 32365082 PMCID: PMC7224568 DOI: 10.1371/journal.ppat.1008244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/14/2020] [Accepted: 04/11/2020] [Indexed: 12/16/2022] Open
Abstract
Viral escape from CD8+ cytotoxic T lymphocyte responses correlates with disease progression and represents a significant challenge for vaccination. Here, we demonstrate that CD8+ T cell recognition of the naturally occurring MHC-I-restricted LCMV-associated immune escape variant Y4F is restored following vaccination with a proline-altered peptide ligand (APL). The APL increases MHC/peptide (pMHC) complex stability, rigidifies the peptide and facilitates T cell receptor (TCR) recognition through reduced entropy costs. Structural analyses of pMHC complexes before and after TCR binding, combined with biophysical analyses, revealed that although the TCR binds similarly to all complexes, the p3P modification alters the conformations of a very limited amount of specific MHC and peptide residues, facilitating efficient TCR recognition. This approach can be easily introduced in peptides restricted to other MHC alleles, and can be combined with currently available and future vaccination protocols in order to prevent viral immune escape.
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Affiliation(s)
- Adil Doganay Duru
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- NSU Cell Therapy Institute & Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Eva B. Allerbring
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jesseka Chadderton
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Nadir Kadri
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Kaliroi Peqini
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Hannes Uchtenhagen
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Chaithanya Madhurantakam
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI, School of Advanced Studies, New Delhi, India
| | - Sara Pellegrino
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Stephen J. Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- * E-mail:
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22
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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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23
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Coles CH, Mulvaney RM, Malla S, Walker A, Smith KJ, Lloyd A, Lowe KL, McCully ML, Martinez Hague R, Aleksic M, Harper J, Paston SJ, Donnellan Z, Chester F, Wiederhold K, Robinson RA, Knox A, Stacey AR, Dukes J, Baston E, Griffin S, Jakobsen BK, Vuidepot A, Harper S. TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1943-1953. [PMID: 32102902 DOI: 10.4049/jimmunol.1900915] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.
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Affiliation(s)
- Charlotte H Coles
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Rachel M Mulvaney
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sunir Malla
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Walker
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kathrine J Smith
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Angharad Lloyd
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kate L Lowe
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | | | | | - Milos Aleksic
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Jane Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Samantha J Paston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Zoe Donnellan
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Fiona Chester
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Katrin Wiederhold
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Ross A Robinson
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Knox
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrea R Stacey
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Joseph Dukes
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Emma Baston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sue Griffin
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bent K Jakobsen
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Annelise Vuidepot
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Stephen Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
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24
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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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25
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Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proc Natl Acad Sci U S A 2019; 116:25602-25613. [PMID: 31796585 PMCID: PMC6926029 DOI: 10.1073/pnas.1915562116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The interplay between a highly polymorphic set of MHC-I alleles and molecular chaperones shapes the repertoire of peptide antigens displayed on the cell surface for T cell surveillance. Here, we demonstrate that the molecular chaperone TAP-binding protein related (TAPBPR) associates with a broad range of partially folded MHC-I species inside the cell. Bimolecular fluorescence complementation and deep mutational scanning reveal that TAPBPR recognition is polarized toward the α2 domain of the peptide-binding groove, and depends on the formation of a conserved MHC-I disulfide epitope in the α2 domain. Conversely, thermodynamic measurements of TAPBPR binding for a representative set of properly conformed, peptide-loaded molecules suggest a narrower MHC-I specificity range. Using solution NMR, we find that the extent of dynamics at "hotspot" surfaces confers TAPBPR recognition of a sparsely populated MHC-I state attained through a global conformational change. Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfide bond between the α1/α2 helices abrogates TAPBPR binding, both in solution and on a cellular membrane, while intracellular binding is tolerant of many destabilizing MHC-I substitutions. Our data support parallel TAPBPR functions of 1) chaperoning unstable MHC-I molecules with broad allele-specificity at early stages of their folding process, and 2) editing the peptide cargo of properly conformed MHC-I molecules en route to the surface, which demonstrates a narrower specificity. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize discrete conformational states sampled by MHC-I alleles, toward editing the repertoire of displayed antigens.
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26
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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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27
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Salutari I, Martin R, Caflisch A. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins 2019; 88:31-46. [PMID: 31237711 DOI: 10.1002/prot.25764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 11/11/2022]
Abstract
T-cell receptor (TCR) recognition of the myelin basic protein (MBP) peptide presented by major histocompatibility complex (MHC) protein HLA-DR2a, one of the MHC class II alleles associated with multiple sclerosis, is highly variable. Interactions in the trimolecular complex between the TCR of the MBP83-99-specific T cell clone 3A6 with the MBP-peptide/HLA-DR2a (abbreviated TCR/pMHC) lead to substantially different proliferative responses when comparing the wild-type decapeptide MBP90-99 and a superagonist peptide, which differs mainly in the residues that point toward the TCR. Here, we investigate the influence of the peptide sequence on the interface and intrinsic plasticity of the TCR/pMHC trimolecular and pMHC bimolecular complexes by molecular dynamics simulations. The intermolecular contacts at the TCR/pMHC interface are similar for the complexes with the superagonist and the MBP self-peptide. The orientation angle between TCR and pMHC fluctuates less in the complex with the superagonist peptide. Thus, the higher structural stability of the TCR/pMHC tripartite complex with the superagonist peptide, rather than a major difference in binding mode with respect to the self-peptide, seems to be responsible for the stronger proliferative response.
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Affiliation(s)
- Ilaria Salutari
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Roland Martin
- Department of Neurology, University Hospital Zürich, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
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28
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Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Front Immunol 2019; 10:966. [PMID: 31130956 PMCID: PMC6509175 DOI: 10.3389/fimmu.2019.00966] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 11/21/2022] Open
Abstract
T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible. These include MHC protein motions, or dynamics, which are believed to influence interactions with a variety of MHC-binding proteins, including not only TCRs, but other activating and inhibitory receptors as well as components of the peptide loading machinery. Here, we investigated the mechanisms by which peptides tune the dynamics of the common class I MHC protein HLA-A2. By examining more than 50 lengthy molecular dynamics simulations of HLA-A2 presenting different peptides, we identified regions susceptible to dynamic tuning, including regions in the peptide binding domain as well as the distal α3 domain. Further analyses of the simulations illuminated mechanisms by which the influences of different peptides are communicated throughout the protein, and involve regions of the peptide binding groove, the β2-microglobulin subunit, and the α3 domain. Overall, our results demonstrate that the class I MHC protein is a highly tunable peptide sensor whose physical properties vary considerably with bound peptide. Our data provides insight into the underlying principles and suggest a role for dynamically driven allostery in the immunological function of MHC proteins.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Alistair Bailey
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Christian Abraham
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Tim Elliott
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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29
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Buckle AM, Borg NA. Integrating Experiment and Theory to Understand TCR-pMHC Dynamics. Front Immunol 2018; 9:2898. [PMID: 30581442 PMCID: PMC6293202 DOI: 10.3389/fimmu.2018.02898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
The conformational dynamism of proteins is well established. Rather than having a single structure, proteins are more accurately described as a conformational ensemble that exists across a rugged energy landscape, where different conformational sub-states interconvert. The interaction between αβ T cell receptors (TCR) and cognate peptide-MHC (pMHC) is no exception, and is a dynamic process that involves substantial conformational change. This review focuses on technological advances that have begun to establish the role of conformational dynamics and dynamic allostery in TCR recognition of the pMHC and the early stages of signaling. We discuss how the marriage of molecular dynamics (MD) simulations with experimental techniques provides us with new ways to dissect and interpret the process of TCR ligation. Notably, application of simulation techniques lags behind other fields, but is predicted to make substantial contributions. Finally, we highlight integrated approaches that are being used to shed light on some of the key outstanding questions in the early events leading to TCR signaling.
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Affiliation(s)
- Ashley M Buckle
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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30
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Blaha DT, Anderson SD, Yoakum DM, Hager MV, Zha Y, Gajewski TF, Kranz DM. High-Throughput Stability Screening of Neoantigen/HLA Complexes Improves Immunogenicity Predictions. Cancer Immunol Res 2018; 7:50-61. [PMID: 30425106 DOI: 10.1158/2326-6066.cir-18-0395] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/31/2018] [Accepted: 11/09/2018] [Indexed: 12/30/2022]
Abstract
Mutated peptides (neoantigens) from a patient's cancer genome can serve as targets for T-cell immunity, but identifying which peptides can be presented by an MHC molecule and elicit T cells has been difficult. Although algorithms that predict MHC binding exist, they are not yet able to distinguish experimental differences in half-lives of the complexes (an immunologically relevant parameter, referred to here as kinetic stability). Improvement in determining actual neoantigen peptide/MHC stability could be important, as only a small fraction of peptides in most current vaccines are capable of eliciting CD8+ T-cell responses. Here, we used a rapid, high-throughput method to experimentally determine peptide/HLA thermal stability on a scale that will be necessary for analysis of neoantigens from thousands of patients. The method combined the use of UV-cleavable peptide/HLA class I complexes and differential scanning fluorimetry to determine the Tm values of neoantigen complexes. Measured Tm values were accurate and reproducible and were directly proportional to the half-lives of the complexes. Analysis of known HLA-A2-restricted immunogenic peptides showed that Tm values better correlated with immunogenicity than algorithm-predicted binding affinities. We propose that temperature stability information can be used as a guide for the selection of neoantigens in cancer vaccines in order to focus attention on those mutated peptides with the highest probability of being expressed on the cell surface.
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Affiliation(s)
- Dylan T Blaha
- Department of Biochemistry, University of Illinois, Urbana, Illinois
| | - Scott D Anderson
- Department of Biochemistry, University of Illinois, Urbana, Illinois
| | - Daniel M Yoakum
- Department of Biochemistry, University of Illinois, Urbana, Illinois
| | - Marlies V Hager
- Department of Biochemistry, University of Illinois, Urbana, Illinois
| | - Yuanyuan Zha
- Department of Pathology, Department of Medicine, and the Ben May Department of Cancer, University of Chicago, Chicago, Illinois
| | - Thomas F Gajewski
- Department of Pathology, Department of Medicine, and the Ben May Department of Cancer, University of Chicago, Chicago, Illinois
| | - David M Kranz
- Department of Biochemistry, University of Illinois, Urbana, Illinois.
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31
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Ochoa R, Soler MA, Laio A, Cossio P. Assessing the capability of in silico mutation protocols for predicting the finite temperature conformation of amino acids. Phys Chem Chem Phys 2018; 20:25901-25909. [PMID: 30289133 DOI: 10.1039/c8cp03826k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mutation protocols are a key tool in computational biophysics for modelling unknown side chain conformations. In particular, these protocols are used to generate the starting structures for molecular dynamics simulations. The accuracy of the initial side chain and backbone placement is crucial to obtain a stable and quickly converging simulation. In this work, we assessed the performance of several mutation protocols in predicting the most probable conformer observed in finite temperature molecular dynamics simulations for a set of protein-peptide crystals differing only by single-point mutations in the peptide sequence. Our results show that several programs which predict well the crystal conformations fail to predict the most probable finite temperature configuration. Methods relying on backbone-dependent rotamer libraries have, in general, a better performance, but even the best protocol fails in predicting approximately 30% of the mutations.
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Affiliation(s)
- Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia, Medellin, Colombia.
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32
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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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33
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Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax A, Margulies DH. The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling. Front Immunol 2018; 9:1657. [PMID: 30065727 PMCID: PMC6056622 DOI: 10.3389/fimmu.2018.01657] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023] Open
Abstract
Antigen presentation is a cellular process that involves a number of steps, beginning with the production of peptides by proteolysis or aberrant synthesis and the delivery of peptides to cellular compartments where they are loaded on MHC class I (MHC-I) or MHC class II (MHC-II) molecules. The selective loading and editing of high-affinity immunodominant antigens is orchestrated by molecular chaperones: tapasin/TAP-binding protein, related for MHC-I and HLA-DM for MHC-II. Once peptide/MHC (pMHC) complexes are assembled, following various steps of quality control, they are delivered to the cell surface, where they are available for identification by αβ receptors on CD8+ or CD4+ T lymphocytes. In addition, recognition of cell surface peptide/MHC-I complexes by natural killer cell receptors plays a regulatory role in some aspects of the innate immune response. Many of the components of the pathways of antigen processing and presentation and of T cell receptor (TCR)-mediated signaling have been studied extensively by biochemical, genetic, immunological, and structural approaches over the past several decades. Until recently, however, dynamic aspects of the interactions of peptide with MHC, MHC with molecular chaperones, or of pMHC with TCR have been difficult to address experimentally, although computational approaches such as molecular dynamics (MD) simulations have been illuminating. Studies exploiting X-ray crystallography, cryo-electron microscopy, and multidimensional nuclear magnetic resonance (NMR) spectroscopy are beginning to reveal the importance of molecular flexibility as it pertains to peptide loading onto MHC molecules, the interactions between pMHC and TCR, and subsequent TCR-mediated signals. In addition, recent structural and dynamic insights into how molecular chaperones define peptide selection and fine-tune the MHC displayed antigen repertoire are discussed. Here, we offer a review of current knowledge that highlights experimental data obtained by X-ray crystallography and multidimensional NMR methodologies. Collectively, these findings strongly support a multifaceted role for protein plasticity and conformational dynamics throughout the antigen processing and presentation pathway in dictating antigen selection and recognition.
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Nathan A May
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael G Mage
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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34
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McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstübner M, Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG. Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle. Nat Chem Biol 2018; 14:811-820. [PMID: 29988068 PMCID: PMC6202177 DOI: 10.1038/s41589-018-0096-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 05/02/2018] [Accepted: 05/21/2018] [Indexed: 01/09/2023]
Abstract
Chaperones TAPBPR and tapasin associate with class-I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR, and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product, and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, where the lifetime and structural features of transiently bound peptides controls the regulation of a conformational switch, located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex.
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Affiliation(s)
- Andrew C McShan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Vlad K Kumirov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David Flores-Solis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Mareike Badstübner
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Clive R Bagshaw
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MA, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
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35
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Mpakali A, Maben Z, Stern LJ, Stratikos E. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 113:50-57. [PMID: 29678301 DOI: 10.1016/j.molimm.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that can generate or destroy potential peptide ligands for MHC class I molecules. ERAP1 activity influences the cell-surface immunopeptidome and epitope immunodominance patterns but in complex and poorly understood manners. Two main distinct pathways have been proposed to account for ERAP1's effects on the nature and quantity of MHCI-bound peptides: i) ERAP1 trims peptides in solution, generating the correct length for binding to MHCI or overtrimming peptides so that they are too short to bind, and ii) ERAP1 trims peptides while they are partially bound onto MHCI in manner that leaves the peptide amino terminus accessible. For both pathways, once an appropriate length peptide is generated it could bind conventionally to MHCI, competing with further trimming by ERAP1. The two pathways, although not necessarily mutually exclusive, provide distinct vantage points for understanding of the rules behind the generation of the immunopeptidome. Resolution of the mechanistic details of ERAP1-mediated antigenic peptide generation can have important consequences for pharmacological efforts to regulate the immunopeptidome for therapeutic applications, and for understanding association of ERAP1 alleles with susceptibility to autoimmune disease and cancer. We review current evidence in support of these two pathways and discuss their relative importance and potential complementarity.
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Affiliation(s)
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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36
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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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