1
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Kormos J, Veres AJ, Imre L, Mátyus L, Benkő S, Szöllősi J, Jenei A. HLA DQ protein changes the cell surface distribution pattern of HLA proteins as monitored by Förster resonance energy transfer and high-resolution electron microscopy. Cytometry A 2023; 103:978-991. [PMID: 37605541 DOI: 10.1002/cyto.a.24787] [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: 02/24/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Peptide presentation by MHC class I and MHC class II molecules plays important roles in the regulation of the immune response. One factor in these displays is the density of antigen, which must exceed a critical threshold for the effective activation of T cells. Nonrandom distribution of MHC class I and class II has already been detected at the nanometer level and at higher hierarchical levels. It is not clear how the absence and reappearance of some protein molecules can influence the nonrandom distribution. Therefore, we performed experiments on HLA II-deficient bare lymphocyte syndrome (BLS1) cells: we created a stable transfected cell line, tDQ6-BLS-1, and were able to detect the effect of the appearance of HLA-DQ6 molecules on the homo and heteroassociation of different cell surface molecules by comparing Förster resonance energy transfer (FRET) efficiency on transfected cells to that on nontransfected BLS-1 and JY human B-cell lines. Our FRET results show a decrease in homoassociation FRET between HLA I chains in HLA-DQ6-transfected tDQ6-BLS-1 cells compared with the parent BLS-1 cell line and an increase in heteroassociation FRET between HLA I and HLA II (compared with JY cells), suggesting a similar pattern of antigen presentation by the HLA-DQ6 allele. Transmission electron microscopy (TEM) revealed that both HLA class I and class II molecules formed clusters at higher hierarchical levels on the tDQ6-BLS-1 cells, and the de novo synthesized HLA DQ molecules did not intersperse with HLA class I islands. These observations could be important in understanding the fine tuning of the immune response.
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Affiliation(s)
- József Kormos
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Adrienn J Veres
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - László Imre
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - László Mátyus
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Szilvia Benkő
- Department of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- ELKH-DE Cell Biology and Signaling Research Group (Eötvös Loránd Research Network-University of Debrecen), Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Jenei
- Department of Biophysics and Cell Biology, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
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2
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Ser Z, Gu Y, Yap J, Lim YT, Wang SM, Hamidinia M, Murali TM, Kumar R, Gascoigne NR, MacAry PA, Sobota RM. Hybrid structural modeling of alloantibody binding to human leukocyte antigen with rapid and reproducible cross-linking mass spectrometry. CELL REPORTS METHODS 2023; 3:100569. [PMID: 37751693 PMCID: PMC10545907 DOI: 10.1016/j.crmeth.2023.100569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 08/07/2023] [Indexed: 09/28/2023]
Abstract
Alloantibody recognition of donor human leukocyte antigen (HLA) is associated with poor clinical transplantation outcomes. However, the molecular and structural basis for the alloantibody-HLA interaction is not well understood. Here, we used a hybrid structural modeling approach on a previously studied alloantibody-HLA interacting pair with inputs from ab initio, in silico, and in vitro data. Highly reproducible cross-linking mass spectrometry data were obtained with both discovery- and targeted mass spectrometry-based approaches approaches. The cross-link information was then used together with predicted antibody Fv structure, predicted antibody paratope, and in silico-predicted interacting surface to model the antibody-HLA interaction. This hybrid structural modeling approach closely recapitulates the key interacting residues from a previously solved crystal structure of an alloantibody-HLA-A∗11:01 pair. These results suggest that a predictive-based hybrid structural modeling approach supplemented with cross-linking mass spectrometry data can provide functionally relevant structural models to understand the structural basis of antibody-HLA mismatch in transplantation.
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Affiliation(s)
- Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Yue Gu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Jiawei Yap
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Shi Mei Wang
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Maryam Hamidinia
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Tanusya Murali Murali
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Ragini Kumar
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Nicholas Rj Gascoigne
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Paul A MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore.
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3
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Shcherbakova L, Pardo M, Roumeliotis T, Choudhary J. Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry. Wellcome Open Res 2023; 6:260. [PMID: 35865489 PMCID: PMC9270653 DOI: 10.12688/wellcomeopenres.17160.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2022] [Indexed: 01/09/2023] Open
Abstract
Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising XL-MS to characterise individual protein complexes' topology have been carried out on over-expressed or recombinant proteins, which might not accurately represent native cellular conditions. Methods: We performed XL-MS using MS-cleavable crosslinker disuccinimidyl sulfoxide (DSSO) after immunoprecipitation of endogenous BRG/Brahma-associated factors (BAF) complex and co-purifying proteins. Data are available via ProteomeXchange with identifier PXD027611. Results: Although we did not detect the expected enrichment of crosslinks within the BAF complex, we identified numerous crosslinks between three co-purifying proteins, namely Thrap3, Bclaf1 and Erh. Thrap3 and Bclaf1 are mostly disordered proteins for which no 3D structure is available. The XL data allowed us to map interaction surfaces on these proteins, which overlap with the non-disordered portions of both proteins. The identified XLs are in agreement with homology-modelled structures suggesting that the interaction surfaces are globular. Conclusions: Our data shows that MS-cleavable crosslinker DSSO can be used to characterise in detail the topology and interaction surfaces of endogenous protein complexes without the need for overexpression. We demonstrate that Bclaf1, Erh and Thrap3 interact closely with each other, suggesting they might form a novel complex, hereby referred to as TEB complex. This data can be exploited for modelling protein-protein docking to characterise the three-dimensional structure of the complex. Endogenous XL-MS might be challenging due to crosslinker accessibility, protein complex abundance or isolation efficiency, and require further optimisation for some complexes like the BAF complex to detect a substantial number of crosslinks.
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Affiliation(s)
| | - Mercedes Pardo
- Cancer Biology, Institute of Cancer Research, UK, London, UK
| | | | - Jyoti Choudhary
- Cancer Biology, Institute of Cancer Research, UK, London, UK,
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4
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Bauzá-Martinez J, Armony G, Pronker MF, Wu W. Characterization of protein complexes in extracellular vesicles by intact extracellular vesicle crosslinking mass spectrometry (iEVXL). J Extracell Vesicles 2022; 11:e12245. [PMID: 35918900 PMCID: PMC9346492 DOI: 10.1002/jev2.12245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/05/2022] [Accepted: 06/25/2022] [Indexed: 11/15/2022] Open
Abstract
Extracellular vesicles (EVs) are blood‐borne messengers that coordinate signalling between different tissues and organs in the body. The specificity of such crosstalk is determined by preferential EV docking to target sites, as mediated through protein‐protein interactions. As such, the need to structurally characterize the EV surface precedes further understanding of docking selectivity and recipient‐cell uptake mechanisms. Here, we describe an intact extracellular vesicle crosslinking mass spectrometry (iEVXL) method that can be applied for structural characterization of protein complexes in EVs. By using a partially membrane‐permeable disuccinimidyl suberate crosslinker, proteins on the EV outer‐surface and inside EVs can be immobilized together with their interacting partners. This not only provides covalent stabilization of protein complexes before extraction from the membrane‐enclosed environment, but also generates a set of crosslinking distance restraints that can be used for structural modelling and comparative screening of changes in EV protein assemblies. Here we demonstrate iEVXL as a powerful approach to reveal high‐resolution information, about protein determinants that govern EV docking and signalling, and as a crucial aid in modelling docking interactions.
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Affiliation(s)
- Julia Bauzá-Martinez
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Gad Armony
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.,Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore, Singapore
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5
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Dirscherl C, Löchte S, Hein Z, Kopicki JD, Harders AR, Linden N, Karner A, Preiner J, Weghuber J, Garcia-Alai M, Uetrecht C, Zacharias M, Piehler J, Lanzerstorfer P, Springer S. Dissociation of β2m from MHC class I Triggers formation of Noncovalent, transient heavy chain dimers. J Cell Sci 2022; 135:274997. [PMID: 35393611 DOI: 10.1242/jcs.259498] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/30/2022] [Indexed: 11/20/2022] Open
Abstract
At the plasma membrane of mammalian cells, major histocompatibility complex class I molecules (MHC-I) present antigenic peptides to cytotoxic T cells. Following the loss of the peptide and the light chain beta-2 microglobulin (β2m), the resulting free heavy chains (FHCs) can associate into homotypic complexes in the plasma membrane. Here, we investigate the stoichiometry and dynamics of MHC-I FHCs assemblies by combining a micropattern assay with fluorescence recovery after photobleaching (FRAP) and with single molecule co-tracking. We identify non-covalent MHC-I FHC dimers mediated by the α3 domain as the prevalent species at the plasma membrane, leading a moderate decrease in the diffusion coefficient. MHC-I FHC dimers show increased tendency to cluster into higher order oligomers as concluded from an increased immobile fraction with higher single molecule co-localization. In vitro studies with isolated proteins in conjunction with molecular docking and dynamics simulations suggest that in the complexes, the α3 domain of one FHC binds to another FHC in a manner similar to the β2m light chain.
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Affiliation(s)
- Cindy Dirscherl
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Sara Löchte
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Noemi Linden
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
| | - Andreas Karner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Johannes Preiner
- University of Applied Sciences Upper Austria, 4020 Linz, Austria
| | - Julian Weghuber
- University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany.,Centre for Structural Systems Biology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,European XFEL, Schenefeld, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, Garching, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics, Osnabrück University, 49076 Osnabrück, Germany
| | | | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Germany
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6
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Klykov O, Kopylov M, Carragher B, Heck AJ, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding author for cryo-EM/ET/FIB-SEM: Alex J. Noble, tel: (+1) 212-939-0660;
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands,Corresponding author for MS: Richard A. Scheltema, tel: (+31) 30 253 6804;
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7
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Ruggiero FM, Springer S. Homotypic and heterotypic in cis associations of MHC class I molecules at the cell surface. CURRENT RESEARCH IN IMMUNOLOGY 2022; 3:85-99. [PMID: 35647522 PMCID: PMC9133507 DOI: 10.1016/j.crimmu.2022.05.001] [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: 01/27/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Through the presentation of peptide antigens to cytotoxic T lymphocytes, major histocompatibility complex (MHC) class I molecules mediate the adaptive immune response against tumors and viruses. Additional non-immunological functions include the heterotypic association of class I molecules with cell surface receptors, regulating their activities by unknown mechanisms. Also, homotypic associations resulting in class I dimers and oligomers - of unknown function - have been related to pathological outcomes. In this review, we provide an overview of the current knowledge about the occurrence, biochemical nature, and dynamics of homotypic and heterotypic associations of class I molecules at the cell surface with special focus on the molecular species that take part in the complexes and on the evidence that supports novel biological roles for class I molecules. We show that both heterotypic and homotypic class I associations reported in the literature describe not one but several kinds of oligomers with distinctive stoichiometry and biochemical properties. Major histocompatibility complex class I molecules form homotypic and heterotypic associations at the cell surface. Associations show distinctive stoichiometry and biochemical properties. Associations might regulate immunological and non-immunological processes. Heterotypic association with cell surface receptors might regulate receptor's activity. Homotypic associations have been related to pathological outcomes.
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8
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Advances in the Field of Micro- and Nanotechnologies Applied to Extracellular Vesicle Research: Take-Home Message from ISEV2021. MICROMACHINES 2021; 12:mi12121563. [PMID: 34945413 PMCID: PMC8707249 DOI: 10.3390/mi12121563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
Abstract
Extracellular Vesicles (EVs) are naturally secreted nanoparticles with a plethora of functions in the human body and remarkable potential as diagnostic and therapeutic tools. Starting from their discovery, EV nanoscale dimensions have hampered and slowed new discoveries in the field, sometimes generating confusion and controversies among experts. Microtechnological and especially nanotechnological advances have sped up biomedical research dealing with EVs, but efforts are needed to further clarify doubts and knowledge gaps. In the present review, we summarize some of the most interesting data presented in the Annual Meeting of the International Society for Extracellular Vesicles (ISEV), ISEV2021, to stimulate discussion and to share knowledge with experts from all fields of research. Indeed, EV research requires a multidisciplinary knowledge exchange and effort. EVs have demonstrated their importance and significant biological role; still, further technological achievements are crucial to avoid artifacts and misleading conclusions in order to enable outstanding discoveries.
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9
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Hoek M, Demmers LC, Wu W, Heck AJR. Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. J Proteome Res 2021; 20:4518-4528. [PMID: 34415762 PMCID: PMC8419865 DOI: 10.1021/acs.jproteome.1c00466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Presentation of antigens
by human leukocyte antigen (HLA) complexes
at the cell surface is a key process in the immune response. The α-chain,
containing the peptide-binding groove, is one of the most polymorphic
proteins in the proteome. All HLA class I α-chains carry a conserved
N-glycosylation site, but little is known about its nature and function.
Here, we report an in-depth characterization of N-glycosylation features
of HLA class I molecules. We observe that different HLA-A α-chains
carry similar glycosylation, distinctly different from the HLA-B,
HLA-C, and HLA-F α-chains. Although HLA-A displays the broadest
variety of glycan characteristics, HLA-B α-chains carry mostly
mature glycans, and HLA-C and HLA-F α-chains carry predominantly
high-mannose glycans. We expected these glycosylation features to
be directly linked to cellular localization of the HLA complexes.
Indeed, analyzing HLA class I complexes from crude plasma and inner
membrane-enriched fractions confirmed that most HLA-B complexes can
be found at the plasma membrane, while most HLA-C and HLA-F molecules
reside in the endoplasmic reticulum and Golgi membrane, and HLA-A
molecules are more equally distributed over these cellular compartments.
This allotype-specific cellular distribution of HLA molecules should
be taken into account when analyzing peptide antigen presentation
by immunopeptidomics.
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Affiliation(s)
- Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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