1
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Al-Okaily A, Abu Khashabeh R, Alsmadi O, Ahmad Y, Sultan I, Tbakhi A, Srivastava PK. ERAMER: A novel in silico tool for prediction of ERAP1 enzyme trimming. J Immunol Methods 2024; 531:113713. [PMID: 38925438 DOI: 10.1016/j.jim.2024.113713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/13/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024]
Abstract
MHC class I pathway consists of four main steps: proteasomal cleavage in the cytosol in which precursor proteins are cleaved into smaller peptides, which are then transported into the endoplasmic reticulum by the transporter associated with antigen processing, TAP, for further processing (trimming) from the N-terminal region by an ER resident aminopeptidases 1 (ERAP1) enzyme, to generate optimal peptides (8-10 amino acids in length) to produce a stable MHCI-peptide complex, that get transited via the Golgi apparatus to the cell surface for presentation to the cellular immune system. Several studies reported specificities related to the ERAP1 trimming process, yet there is no in silico tool for the prediction of the trimming process of the ERAP1 enzyme. In this paper, we provide and implement a prediction model for the trimming process of the ERAP1 enzyme.
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Affiliation(s)
- Anas Al-Okaily
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan.
| | - Razan Abu Khashabeh
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Osama Alsmadi
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Yazan Ahmad
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Iyad Sultan
- Department of Cell Therapy and Applied Genomics, King Hussein Cancer Center, Amman, Jordan
| | - Abdelghani Tbakhi
- Department of Pathology and Molecular Medicine, McMaster University, Ontario, Canada
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
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2
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Brunnberg J, Barends M, Frühschulz S, Winter C, Battin C, de Wet B, Cole DK, Steinberger P, Tampé R. Dual role of the peptide-loading complex as proofreader and limiter of MHC-I presentation. Proc Natl Acad Sci U S A 2024; 121:e2321600121. [PMID: 38771881 PMCID: PMC11145271 DOI: 10.1073/pnas.2321600121] [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: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
Antigen presentation via major histocompatibility complex class I (MHC-I) molecules is essential for surveillance by the adaptive immune system. Central to this process is the peptide-loading complex (PLC), which translocates peptides from the cytosol to the endoplasmic reticulum and catalyzes peptide loading and proofreading of peptide-MHC-I (pMHC-I) complexes. Despite its importance, the impact of individual PLC components on the presented pMHC-I complexes is still insufficiently understood. Here, we used stoichiometrically defined antibody-nanobody complexes and engineered soluble T cell receptors (sTCRs) to quantify different MHC-I allomorphs and defined pMHC-I complexes, respectively. Thereby, we uncovered distinct effects of individual PLC components on the pMHC-I surface pool. Knockouts of components of the PLC editing modules, namely tapasin, ERp57, or calreticulin, changed the MHC-I surface composition to a reduced proportion of HLA-A*02:01 presentation compensated by a higher ratio of HLA-B*40:01 molecules. Intriguingly, these knockouts not only increased the presentation of suboptimally loaded HLA-A*02:01 complexes but also elevated the presentation of high-affinity peptides overexpressed in the cytosol. Our findings suggest that the components of the PLC editing module serve a dual role, acting not only as peptide proofreaders but also as limiters for abundant peptides. This dual function ensures the presentation of a broad spectrum of antigenic peptides.
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Affiliation(s)
- Jamina Brunnberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Martina Barends
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Claire Battin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Ben de Wet
- Immunocore Ltd., AbingdonOX14 4RY, United Kingdom
| | | | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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3
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Mpakali A, Barla I, Lu L, Ramesh KM, Thomaidis N, Stern LJ, Giastas P, Stratikos E. Mechanisms of Allosteric Inhibition of Insulin-Regulated Aminopeptidase. J Mol Biol 2024; 436:168449. [PMID: 38244767 DOI: 10.1016/j.jmb.2024.168449] [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: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 01/22/2024]
Abstract
Inhibition of Insulin-Regulated Aminopeptidase is being actively explored for the treatment of several human diseases and several classes of inhibitors have been developed although no clinical applications have been reported yet. Here, we combine enzymological analysis with x-ray crystallography to investigate the mechanism employed by two of the most studied inhibitors of IRAP, an aryl sulfonamide and a 2-amino-4H-benzopyran named HFI-419. Although both compounds have been hypothesized to target the enzyme's active site by competitive mechanisms, we discovered that they instead target previously unidentified proximal allosteric sites and utilize non-competitive inhibition mechanisms. X-ray crystallographic analysis demonstrated that the aryl sulfonamide stabilizes the closed, more active, conformation of the enzyme whereas HFI-419 locks the enzyme in a semi-open, and likely less active, conformation. HFI-419 potency is substrate-dependent and fails to effectively block the degradation of the physiological substrate cyclic peptide oxytocin. Our findings demonstrate alternative mechanisms for inhibiting IRAP through allosteric sites and conformational restricting and suggest that the pharmacology of HFI-419 may be more complicated than initially considered. Such conformation-specific interactions between IRAP and small molecules can be exploited for the design of more effective second-generation allosteric inhibitors.
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Affiliation(s)
- Anastasia Mpakali
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; National Centre for Scientific Research Demokritos, Athens 15341, Greece
| | - Ioanna Barla
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Liying Lu
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Karthik M Ramesh
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA 01650, USA
| | - Petros Giastas
- Department of Biotechnology, School of Applied Biology & Biotechnology, Agricultural University of Athens, Athens 11855, Greece
| | - Efstratios Stratikos
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece; National Centre for Scientific Research Demokritos, Athens 15341, Greece.
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4
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Li L, Peng X, Batliwala M, Bouvier M. Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Nat Commun 2023; 14:5020. [PMID: 37596268 PMCID: PMC10439229 DOI: 10.1038/s41467-023-40736-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between numerous conformational states and these motions support peptide sampling. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. Here, we present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show pronounced distortions at the N-terminus of the groove. Long stretches of N-terminal amino acid residues are missing in the electron density maps creating an open-ended groove. Our structures also reveal highly unusual features in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations indicate that the complexes have varying degrees of conformational flexibility in a manner consistent with the structures. We suggest that our structures have captured the remarkable molecular dynamics of MHC I-peptide interaction. The visualization of peptide-dependent conformational motions in MHC I is a major step forward in our conceptual understanding of dynamics in high-affinity peptide selection.
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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, 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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5
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Advancing our knowledge of antigen processing with computational modelling, structural biology, and immunology. Biochem Soc Trans 2023; 51:275-285. [PMID: 36645000 DOI: 10.1042/bst20220782] [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: 09/19/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Antigen processing is an immunological mechanism by which intracellular peptides are transported to the cell surface while bound to Major Histocompatibility Complex molecules, where they can be surveyed by circulating CD8+ or CD4+ T-cells, potentially triggering an immunological response. The antigen processing pathway is a complex multistage filter that refines a huge pool of potential peptide ligands derived from protein degradation into a smaller ensemble for surface presentation. Each stage presents unique challenges due to the number of ligands, the polymorphic nature of MHC and other protein constituents of the pathway and the nature of the interactions between them. Predicting the ensemble of displayed peptide antigens, as well as their immunogenicity, is critical for improving T cell vaccines against pathogens and cancer. Our predictive abilities have always been hindered by an incomplete empirical understanding of the antigen processing pathway. In this review, we highlight the role of computational and structural approaches in improving our understanding of antigen processing, including structural biology, computer simulation, and machine learning techniques, with a particular focus on the MHC-I pathway.
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6
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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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Wang CM, Liu MK, Jan Wu YJ, Lin JC, Zheng JW, Wu J, Chen JY. Functional ERAP1 Variants Distinctively Associate with Ankylosing Spondylitis Susceptibility under the Influence of HLA-B27 in Taiwanese. Cells 2022; 11:cells11152427. [PMID: 35954271 PMCID: PMC9368314 DOI: 10.3390/cells11152427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
Epistasis of ERAP1 single nucleotide variations (SNVs) and HLA-B27 has been linked to ankylosing spondylitis susceptibility (AS). The current study examined how prevalent ERAP1 allelic variants (SNV haplotypes) in Taiwan affect ERAP1 functions and AS susceptibility in the presence or absence of HLA-B27. Sanger sequencing was used to discover all ERAP1 coding SNVs and common allelic variants in Taiwanese full-length cDNAs from 45 human patients. For the genetic association investigation, TaqMan genotyping assays were utilized to establish the genotypes of ERAP1 SNVs in 863 AS patients and 1438 healthy controls. Ex vivo biological analysis of peripheral blood mononuclear cells from homozygous donors of two common-risk ERAP1 allelic variants was performed. Two common-risk ERAP1 allelic variants were also cloned and functionally studied. In Taiwanese, eleven frequent ERAP1 SNVs and six major ERAP1 allelic variants were discovered. We discovered that in Taiwanese, the most prevalent ERAP1-001 variant with 56E, 127R, 276I, 349M, 528K, 575D, 725R, and 730Q interacting with HLA-B27 significantly contributed to the development of AS. In HLA-B27 negative group, however, the second most prevalent ERAP1-002 variant with 56E, 127P, 276M, 349M, 528R, 575D, 725R, and 730E was substantially related with an increased risk of AS. Ex vivo and in vitro research demonstrated that ERAP1 allelic variants have a significant impact on ERAP1 functions, suggesting that ERAP1 plays a role in the development of AS. In an HLA-B27-dependent manner, common ERAP1 allelic variants are related with AS susceptibility.
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Affiliation(s)
- Chin-Man Wang
- Department of Rehabilitation, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
| | - Ming-Kun Liu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
| | - Yeong-Jian Jan Wu
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
| | - Jing-Chi Lin
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
| | - Jian-Wen Zheng
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
| | - Jianming Wu
- Department of Veterinary and Biomedical Sciences, Department of Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Ji-Yih Chen
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan City 333, Taiwan
- Correspondence: ; Tel.: +886-3-3281200 (ext. 2410); Fax: +886-3-3288287
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8
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Papakyriakou A, Mpakali A, Stratikos E. Can ERAP1 and ERAP2 Form Functional Heterodimers? A Structural Dynamics Investigation. Front Immunol 2022; 13:863529. [PMID: 35514997 PMCID: PMC9065437 DOI: 10.3389/fimmu.2022.863529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2) play important roles in the generation of antigenic peptides presented by Major Histocompatibility Class I (MHCI) molecules and indirectly regulate adaptive immune responses. Although the discrete function of these enzymes has been extensively characterized, recent reports have suggested that they can also form heterodimers with functional consequences. However, lack of structural characterization of a putative ERAP1/ERAP2 dimer has limited our understanding of its biological role and significance. To address this, we employed computational molecular dynamics calculations to explore the topology of interactions between these two, based on experimentally determined homo-dimerization interfaces observed in crystal structures of ERAP2 or homologous enzymes. Our analysis of 8 possible dimerization models, suggested that the most likely ERAP1/ERAP2 heterodimerization topology involves the exon 10 loop, a non-conserved loop previously implicated in interactions between ERAP1 and the disulfide-bond shuffling chaperone ERp44. This dimerization topology allows access to the active site of both enzymes and is consistent with a previously reported construct in which ERAP1 and ERAP2 were linked by Fos/Jun zipper tags. The proposed model constitutes a tentative structural template to help understand the physiological role and significance of ERAP1/ERAP2 molecular interactions.
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Affiliation(s)
- Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Anastasia Mpakali
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
| | - Efstratios Stratikos
- Institute of Biosciences and Applications, National Centre for Scientific Research “Demokritos”, Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
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9
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Sethumadhavan S, Barth M, Spaapen RM, Schmidt C, Trowitzsch S, Tampé R. Viral immune evasins impact antigen presentation by allele-specific trapping of MHC I at the peptide-loading complex. Sci Rep 2022; 12:1516. [PMID: 35087068 PMCID: PMC8795405 DOI: 10.1038/s41598-022-05000-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/30/2021] [Indexed: 11/30/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) molecules present antigenic peptides to cytotoxic T cells to eliminate infected or cancerous cells. The transporter associated with antigen processing (TAP) shuttles proteasomally generated peptides into the ER for MHC I loading. As central part of the peptide-loading complex (PLC), TAP is targeted by viral factors, which inhibit peptide supply and thereby impact MHC I-mediated immune responses. However, it is still poorly understood how antigen presentation via different MHC I allotypes is affected by TAP inhibition. Here, we show that conditional expression of herpes simplex viral ICP47 suppresses surface presentation of HLA-A and HLA-C, but not of HLA-B, while the human cytomegaloviral US6 reduces surface levels of all MHC I allotypes. This marked difference in HLA-B antigen presentation is echoed by an enrichment of HLA-B allomorphs at US6-arrested PLC in comparison to ICP47-PLC. Although both viral factors prevent TAP-mediated peptide supply, our data imply that MHC I allomorphs favor different conformationally arrested states of the PLC, leading to differential downregulation of MHC I surface presentation. These findings will help understand MHC I biology in general and will even advance the targeted treatment of infections depending on patients' allotypes.
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Affiliation(s)
- Sunesh Sethumadhavan
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Robbert M Spaapen
- Department of Immunopathology, Sanquin Research, Plesmanlaan 125, 1066 CX, Amsterdam, The Netherlands
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany.
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10
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Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ. Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat Commun 2021; 12:5302. [PMID: 34489420 PMCID: PMC8421391 DOI: 10.1038/s41467-021-25564-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/10/2021] [Indexed: 11/27/2022] Open
Abstract
The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.
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Affiliation(s)
- Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Richa Arya
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dimitris Georgiadis
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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11
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Ma C, Zheng Y, Liu X, Zhang W. Association study of polymorphisms of endoplasmic reticulum aminopeptidase 1 gene with preeclampsia in Chinese populations. Clin Exp Hypertens 2021; 43:550-554. [PMID: 33794716 DOI: 10.1080/10641963.2021.1907400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To explore the correlation of polymorphisms of endoplasmic reticulum aminopeptidase-1 (ERAP-1) gene in Chinese women with preeclampsia. METHOD In this case-control study, 51 severely preeclamptic and 48 healthy pregnant women were retrospectively involved in Beijing Obstetrics and Gynecology Hospital from October 2017 to October 2019. The venous blood and umbilical cord blood were collected to analyze different single nucleotide polymorphisms (SNPs) in ERAP-1 gene in both groups. RESULT We firstly screened nine SNPs that were significantly different between two groups (P< .1) via univariate analysis. Pearson Chi-Square Test and Fisher's Exact Test were performed to verify the correlation of SNPs with preeclampsia. Finally, genotype TC located in 96121524 position was associated with an increased risk of preeclampsia (P= .020, OR = 2.002, 95% CI: 0.687-5.831). CONCLUSION There might be a correlation between polymorphism of 96121524 in ERAP-1 gene and preeclampsia susceptibility in pregnant women of Han nationality in Beijing.
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Affiliation(s)
- Cui Ma
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yuanyuan Zheng
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xiaowei Liu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Weiyuan Zhang
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
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12
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Mavridis G, Mpakali A, Zoidakis J, Makridakis M, Vlahou A, Kaloumenou E, Ziotopoulou A, Georgiadis D, Papakyriakou A, Stratikos E. The ERAP1 active site cannot productively access the N-terminus of antigenic peptide precursors stably bound onto MHC class I. Sci Rep 2021; 11:16475. [PMID: 34389743 PMCID: PMC8363620 DOI: 10.1038/s41598-021-95786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022] Open
Abstract
Processing of N-terminally elongated antigenic peptide precursors by Endoplasmic Reticulum Aminopeptidase 1 (ERAP1) is a key step in antigen presentation and the adaptive immune response. Although ERAP1 can efficiently process long peptides in solution, it has been proposed that it can also process peptides bound onto Major Histocompatibility Complex I molecules (MHCI). In a previous study, we suggested that the occasionally observed “ontο MHCI” trimming by ERAP1 is likely due to fast peptide dissociation followed by solution trimming, rather than direct action of ERAP1 onto the MHCI complex. However, other groups have proposed that ERAP1 can trim peptides covalently bound onto MHCI, which would preclude peptide dissociation. To explore this interaction, we constructed disulfide-linked MHCI-peptide complexes using HLA-B*08 and a 12mer kinetically labile peptide, or a 16mer carrying a phosphinic transition-state analogue N-terminus with high-affinity for ERAP1. Kinetic and biochemical analyses suggested that while both peptides could access the ERAP1 active site when free in solution, they were unable to do so when tethered in the MHCI binding groove. Our results suggest that MHCI binding protects, rather than promotes, antigenic peptide precursor trimming by ERAP1 and thus solution trimming is the more likely model of antigenic peptide processing.
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Affiliation(s)
- George Mavridis
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Anastasia Mpakali
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Jerome Zoidakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - Eleni Kaloumenou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Angeliki Ziotopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece
| | - Athanasios Papakyriakou
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, National Centre for Scientific Research Demokritos, 15341, Agia Paraskevi, Greece. .,Biochemistry Laboratory, National and Kapodistrian University of Athens, 15784, Panepistimiopolis Zografou, Greece.
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13
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Sui L, Guo HC. ERAP1 binds peptide C-termini of different sequences and/or lengths by a common recognition mechanism. Immunobiology 2021; 226:152112. [PMID: 34247019 DOI: 10.1016/j.imbio.2021.152112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 01/25/2023]
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) plays a key role in controlling the immunopeptidomes available for presentation by MHC (major histocompatibility complex) molecules, thus influences immunodominance and cell-mediated immunity. It carries out this critical function by a unique molecular ruler mechanism that trims antigenic precursors in a peptide-length and sequence dependent manner. Acting as a molecular ruler, ERAP1 is capable of concurrently binding antigen peptide N- and C-termini by its N-terminal catalytic and C-terminal regulatory domains, respectively. As such ERAP1 can not only monitor substrate's lengths, but also exhibit a degree of sequence specificity at substrates' N- and C-termini. On the other hand, it also allows certain sequence and length flexibility in the middle part of peptide substrates that is critical for shaping MHC restricted immunopeptidomes. Here we report structural and biochemical studies to understand the molecular details on how ERAP1 can accommodate side chains of different anchoring residues at the substrate's C-terminus. We also examine how ERAP1 can accommodate antigen peptide precursors with length flexibility. Based on two newly determined complex structures, we find that ERAP1 binds the C-termini of peptides similarly even with different substrate sequences and/or lengths, by utilizing the same hydrophobic specificity pocket to accommodate peptides with either a Phe or Leu as the C-terminal anchor residue. In addition, SPR (surface plasmon resonance) binding analyses in solution further confirm the biological significance of these peptide-ERAP1 interactions. Similar to the binding mode of MHC-I molecules, ERAP1 accommodates for antigenic peptide length difference by allowing the peptide middle part to kink or bulge at the middle of its substrate binding cleft. This explains how SNP coded variants located at the middle of ERAP1 substrate binding cleft would influence the antigen pool and an individual's susceptibility to diseases.
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Affiliation(s)
- Lufei Sui
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | - Hwai-Chen Guo
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA.
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14
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Venema WJ, Hiddingh S, de Boer JH, Claas FHJ, Mulder A, den Hollander AI, Stratikos E, Sarkizova S, van der Veken LT, Janssen GMC, van Veelen PA, Kuiper JJW. ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29. Front Immunol 2021; 12:634441. [PMID: 33717175 PMCID: PMC7950316 DOI: 10.3389/fimmu.2021.634441] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/12/2021] [Indexed: 11/13/2022] Open
Abstract
Birdshot Uveitis (BU) is a blinding inflammatory eye condition that only affects HLA-A29-positive individuals. Genetic association studies linked ERAP2 with BU, an aminopeptidase which trims peptides before their presentation by HLA class I at the cell surface, which suggests that ERAP2-dependent peptide presentation by HLA-A29 drives the pathogenesis of BU. However, it remains poorly understood whether the effects of ERAP2 on the HLA-A29 peptidome are distinct from its effect on other HLA allotypes. To address this, we focused on the effects of ERAP2 on the immunopeptidome in patient-derived antigen presenting cells. Using complementary HLA-A29-based and pan-class I immunopurifications, isotope-labeled naturally processed and presented HLA-bound peptides were sequenced by mass spectrometry. We show that the effects of ERAP2 on the N-terminus of ligands of HLA-A29 are shared across endogenous HLA allotypes, but discover and replicate that one peptide motif generated in the presence of ERAP2 is specifically bound by HLA-A29. This motif can be found in the amino acid sequence of putative autoantigens. We further show evidence for internal sequence specificity for ERAP2 imprinted in the immunopeptidome. These results reveal that ERAP2 can generate an HLA-A29-specific antigen repertoire, which supports that antigen presentation is a key disease pathway in BU.
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Affiliation(s)
- Wouter J Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Joke H de Boer
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Efstratios Stratikos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Greece
| | - Siranush Sarkizova
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lars T van der Veken
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands
| | - Jonas J W Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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15
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Colbert JD, Rock KL. How a tailor achieves the perfect fit. J Biol Chem 2020; 295:7211-7212. [PMID: 32444419 DOI: 10.1074/jbc.h120.013868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most antigenic peptides that bind stably to a major histocompatibility complex (MHC) I molecule for display to the immune system are approximately the same length, thanks in part to the expert trimming done by endoplasmic reticulum aminopeptidases (ERAPs), the final peptidases in the antigen-presentation pathway. An open question is whether ERAPs edit peptides to this optimal length while they are bound to MHC I molecules (using the latter as a pattern of sorts) or by free hand. Mavridis et al. present multiple lines of evidence that this trimming cannot readily occur on MHC I molecules, but rather only in solution, suggesting that ERAPs work alone to tailor the perfect fit for the immunopeptidome.
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Affiliation(s)
- Jeff D Colbert
- Department of Pathology, University of Massachusetts, Worcester, Massachusetts 01655
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts, Worcester, Massachusetts 01655.
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16
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Kuiper JJW, Venema WJ. HLA-A29 and Birdshot Uveitis: Further Down the Rabbit Hole. Front Immunol 2020; 11:599558. [PMID: 33262772 PMCID: PMC7687429 DOI: 10.3389/fimmu.2020.599558] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
HLA class I alleles constitute established risk factors for non-infectious uveitis and preemptive genotyping of HLA class I alleles is standard practice in the diagnostic work-up. The HLA-A29 serotype is indispensable to Birdshot Uveitis (BU) and renders this enigmatic eye condition a unique model to better understand how the antigen processing and presentation machinery contributes to non-infectious uveitis or chronic inflammatory conditions in general. This review will discuss salient points regarding the protein structure of HLA-A29 and how key amino acid positions impact the peptide binding preference and interaction with T cells. We discuss to what extent the risk genes ERAP1 and ERAP2 uniquely affect HLA-A29 and how the discovery of a HLA-A29-specific submotif may impact autoantigen discovery. We further provide a compelling argument to solve the long-standing question why BU only affects HLA-A29-positive individuals from Western-European ancestry by exploiting data from the 1000 Genomes Project. We combine novel insights from structural and immunopeptidomic studies and discuss the functional implications of genetic associations across the HLA class I antigen presentation pathway to refine the etiological basis of Birdshot Uveitis.
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Affiliation(s)
- Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Wouter J. Venema
- Department of Ophthalmology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
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17
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Stamatakis G, Samiotaki M, Mpakali A, Panayotou G, Stratikos E. Generation of SARS-CoV-2 S1 Spike Glycoprotein Putative Antigenic Epitopes in Vitro by Intracellular Aminopeptidases. J Proteome Res 2020; 19:4398-4406. [PMID: 32931291 PMCID: PMC7640968 DOI: 10.1021/acs.jproteome.0c00457] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/20/2022]
Abstract
Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2, and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes.
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Affiliation(s)
- George Stamatakis
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Martina Samiotaki
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Anastasia Mpakali
- National
Centre for Scientific Research “Demokritos”, 15310 Agia Paraskevi,
Attica, Greece
| | - George Panayotou
- Biomedical
Sciences Research Center “Alexander Fleming”, 16672 Vari, Attica, Greece
| | - Efstratios Stratikos
- National
Centre for Scientific Research “Demokritos”, 15310 Agia Paraskevi,
Attica, Greece
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