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Lizbeth RSG, Jazmín GM, José CB, Marlet MA. Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine. J Biomol Struct Dyn 2021; 39:4878-4892. [PMID: 32583729 PMCID: PMC7332869 DOI: 10.1080/07391102.2020.1780944] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/07/2020] [Indexed: 11/01/2022]
Abstract
The Coronavirus disease named COVID-19 is caused by the virus reported in 2019 first identified in China. The cases of this disease have increased and as of June 1st, 2020 there are more than 216 countries affected. Pharmacological treatments have been proposed based on the resemblance of the HIV virus. With regard to prevention there is no vaccine, thus, we proposed to explore the spike protein due to its presence on the viral surface, and it also contains the putative viral entry receptor as well as the fusion peptide (important in the genome release). In this work we have employed In Silico techniques such as immunoinformatics tools which permit the identification of potential immunogenic regions on the viral surface (spike glycoprotein). From these analyses, we identified four epitopes E332-370, E627-651, E440-464 and E694-715 that accomplish essential features such as promiscuity, conservation grade, exposure and universality, and they also form stable complexes with MHCII molecule. We suggest that these epitopes could generate a specific immune response, and thus, they could be used for future applications such as the design of new epitope vaccines against the SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ramírez-Salinas Gema Lizbeth
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - García-Machorro Jazmín
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Correa-Basurto José
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
| | - Martínez-Archundia Marlet
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, México
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2
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Fusco C, Cervelli C, Dal Mas A, Canossi A, Azzarone R, Valdez O, Auriemma L, Madalese D, Maisto G, Toriello M, Penta de Vera d'Aragona R, Scimitarra M, Scarnecchia MA, Battistoni C, Fracassi D, Papola F. Expression profile of HLA-B*38:55Q allele. HLA 2020; 95:449-456. [PMID: 31891446 DOI: 10.1111/tan.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/24/2019] [Accepted: 12/30/2019] [Indexed: 11/29/2022]
Abstract
The identification of null or questionably expressed HLA allelic variants is a major issue in HLA diagnostics, because the mistyping of the aberrant expression of such alleles can have a major impact on the outcome of both hematopoietic stem cell transplantation (HSCT) and solid organ transplants. It is debated how questionable (Q) alleles, because of their unknown expression profile, should be considered in an allogenic HSCT setting. The HLA-B*38:55Q allele was detected as an HLA-B blank specificity; DNA sequencing identified a single polymorphism at position 373 in exon 3 (TGC > CGC), which results in the replacement of cysteine 101 with an arginine in the HLA-B heavy chain, thus, impairing disulfide bridge formation in the alpha-2 domain, essential for the normal expression of the HLA molecules. In order to determine the RNA and protein expression profile of this allelic variant, we analyzed antigenic expression at different levels, transcriptional and transductional, using a combination of cellular methods, such as serological testing and flow cytometric analysis, polymerase chain reaction (PCR) sequence-specific primer (SSP) cDNA group-specific amplification and immunocytochemical assay, demonstrating the prevalent cytoplasmatic distribution of the HLA-B*38:55Q protein. Our findings suggest that in matching process the HLA-B*38:55Q allele needs to be considered as a low expressed allele, able to elicit an allogenic T-cell response in vivo and impair the transplant outcome.
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Affiliation(s)
- Caterina Fusco
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Carla Cervelli
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Antonella Dal Mas
- UOC Pathological Anatomy, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Angelica Canossi
- CNR Institute of Translational Pharmacology, L'Aquila, L'Aquila, Italy
| | - Raffaella Azzarone
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Olaida Valdez
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Laura Auriemma
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Donato Madalese
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Giovanna Maisto
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | - Mario Toriello
- SSD Cryopreservation and Ba.S.C.O, Oncohaematology Department, A.O.R.N. Santobono-Pausilipon of Napoli, Naples, Italy
| | | | - Maria Scimitarra
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Maria A Scarnecchia
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Carla Battistoni
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Daniela Fracassi
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
| | - Franco Papola
- Regional Centre of Immunohaematology and Tissue Typing, S.Salvatore Hospital of L'Aquila, L'Aquila, Italy
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3
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Zhu S, Liu K, Chai Y, Wu Y, Lu D, Xiao W, Cheng H, Zhao Y, Ding C, Lyu J, Lou Y, Gao GF, Liu WJ. Divergent Peptide Presentations of HLA-A *30 Alleles Revealed by Structures With Pathogen Peptides. Front Immunol 2019; 10:1709. [PMID: 31396224 PMCID: PMC6664060 DOI: 10.3389/fimmu.2019.01709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/08/2019] [Indexed: 12/30/2022] Open
Abstract
Human leukocyte antigen (HLA) alleles have a high degree of polymorphism, which determines their peptide-binding motifs and subsequent T-cell receptor recognition. The simplest way to understand the cross-presentation of peptides by different alleles is to classify these alleles into supertypes. A1 and A3 HLA supertypes are widely distributed in humans. However, direct structural and functional evidence for peptide presentation features of key alleles (e.g., HLA-A*30:01 and -A*30:03) are lacking. Herein, the molecular basis of peptide presentation of HLA-A*30:01 and -A*30:03 was demonstrated by crystal structure determination and thermostability measurements of complexes with T-cell epitopes from influenza virus (NP44), human immunodeficiency virus (RT313), and Mycobacterium tuberculosis (MTB). When binding to the HIV peptide, RT313, the PΩ-Lys anchoring modes of HLA-A*30:01, and -A*30:03 were similar to those of HLA-A*11:01 in the A3 supertype. However, HLA-A*30:03, but not -A*30:01, also showed binding with the HLA*01:01-favored peptide, NP44, but with a specific structural conformation. Thus, different from our previous understanding, HLA-A*30:01 and -A*30:03 have specific peptide-binding characteristics that may lead to their distinct supertype-featured binding peptide motifs. Moreover, we also found that residue 77 in the F pocket was one of the key residues for the divergent peptide presentation characteristics of HLA-A*30:01 and -A*30:03. Interchanging residue 77 between HLA-A*30:01 and HLA-A*30:03 switched their presented peptide profiles. Our results provide important recommendations for screening virus and tumor-specific peptides among the population with prevalent HLA supertypes for vaccine development and immune interventions.
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Affiliation(s)
- Shiyan Zhu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Kefang Liu
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China.,Faculty of Health Sciences, University of Macau, Macau, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanan Wu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dan Lu
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wenling Xiao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Hao Cheng
- Beijing Institutes of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yingze Zhao
- NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jianxin Lyu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Yongliang Lou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - George F Gao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - William J Liu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
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4
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Bieling M, Tischer S, Kalinke U, Blasczyk R, Buus S, Maecker-Kolhoff B, Eiz-Vesper B. Personalized adoptive immunotherapy for patients with EBV-associated tumors and complications: Evaluation of novel naturally processed and presented EBV-derived T-cell epitopes. Oncotarget 2017; 9:4737-4757. [PMID: 29435138 PMCID: PMC5797009 DOI: 10.18632/oncotarget.23531] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/04/2017] [Indexed: 01/03/2023] Open
Abstract
Morbidity and mortality of immunocompromised patients are increased by primary infection with or reactivation of Epstein-Barr virus (EBV), possibly triggering EBV+ post-transplant lymphoproliferative disease (PTLD). Adoptive transfer of EBV-specific cytotoxic T cells (EBV-CTLs) promises a non-toxic immunotherapy to effectively prevent or treat these complications. To improve immunotherapy and immunomonitoring this study aimed at identifying and evaluating naturally processed and presented HLA-A*03:01-restricted EBV-CTL epitopes as immunodominant targets. More than 15000 peptides were sequenced from EBV-immortalized B cells transduced with soluble HLA-A*03:01, sorted using different epitope prediction tools and eleven candidates were preselected. T2 and Flex-T peptide-binding and dissociation assays confirmed the stability of peptide-MHC complexes. Their immunogenicity and clinical relevance were evaluated by assessing the frequencies and functionality of EBV-CTLs in healthy donors (n > 10) and EBV+ PTLD-patients (n = 5) by multimer staining, Eli- and FluoroSpot assays. All eleven peptides elicited EBV-CTL responses in the donors. Their clinical applicability was determined by small-scale T-cell enrichment using Cytokine Secretion Assay and immunophenotyping. Mixtures of these peptides when added to the EBV Consensus pool revealed enhanced stimulation and enrichment efficacy. These EBV-specific epitopes broadening the repertoire of known targets will improve manufacturing of clinically applicable EBV-CTLs and monitoring of EBV-specific T-cell responses in patients.
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Affiliation(s)
- Maren Bieling
- Institute for Transfusion Medicine, Hannover Medical School (MHH), Hanover, Germany.,Integrated Research and Treatment Center (IFB-Tx), MHH, Hanover, Germany
| | - Sabine Tischer
- Institute for Transfusion Medicine, Hannover Medical School (MHH), Hanover, Germany.,Integrated Research and Treatment Center (IFB-Tx), MHH, Hanover, Germany
| | - Ulrich Kalinke
- Division of Experimental Infection Research, TWINCORE, Centre of Experimental and Clinical Infection Research, MHH, Hanover, Germany
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School (MHH), Hanover, Germany.,Integrated Research and Treatment Center (IFB-Tx), MHH, Hanover, Germany
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Britta Maecker-Kolhoff
- Integrated Research and Treatment Center (IFB-Tx), MHH, Hanover, Germany.,Department of Pediatric Hematology and Oncology, MHH, Hanover, Germany
| | - Britta Eiz-Vesper
- Institute for Transfusion Medicine, Hannover Medical School (MHH), Hanover, Germany.,Integrated Research and Treatment Center (IFB-Tx), MHH, Hanover, Germany
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5
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Fusco C, Azzarone R, Penta R, Canossi A, Di Iulio B, Toriello M, Auriemma L, Pagano M, Poggi V, Papola F. HLA-B*38:55Q: a new alternatively expressed allele identified in a three-generation Italian family. Int J Immunogenet 2015; 42:294-6. [DOI: 10.1111/iji.12208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 04/02/2015] [Accepted: 04/23/2015] [Indexed: 11/28/2022]
Affiliation(s)
- C. Fusco
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - R. Azzarone
- Regional Centre of Immunohaematology and Tissue Typing (ASL 1) of L'Aquila; L'Aquila Italy
| | - R. Penta
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - A. Canossi
- CNR Institute of Translational Pharmacology; L'Aquila Italy
| | - B. Di Iulio
- Regional Centre of Immunohaematology and Tissue Typing (ASL 1) of L'Aquila; L'Aquila Italy
| | - M. Toriello
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - L. Auriemma
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - M. Pagano
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - V. Poggi
- Ba.S.C.O; Oncohaematology Department; A.O.R.N. Santobono-Pausilipon of Napoli; Napoli Italy
| | - F. Papola
- Regional Centre of Immunohaematology and Tissue Typing (ASL 1) of L'Aquila; L'Aquila Italy
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6
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Foster L, Tate D, Poulton K. A group-specific sequencing approach to investigate the presence of atypical human leucocyte antigen alleles. Int J Immunogenet 2013; 40:453-9. [PMID: 23724946 DOI: 10.1111/iji.12070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/26/2013] [Accepted: 05/15/2013] [Indexed: 11/29/2022]
Abstract
Accurate human leucocyte antigen (HLA) typing results are essential in determining the degree of compatibility between donor and recipient in both solid organ (SO) and hematopoietic stem cell (HSC) transplantation. Current HLA typing methodologies can generate ambiguous results which may need resolving. This group-specific sequencing approach allowed investigation into the presence of the low expressor HLA-A*24:02:01:02L allele and the rare HLA-A*02:64 allele in a SO transplant recipient and a HSC transplant recipient, respectively. Locus-specific amplification of HLA-A was performed. Exons 2 and 3 were sequenced in both directions followed by group-specific sequencing to resolve ambiguities. Hemizygous sequence data of intron 2 generated from the HLA-A*24 allele indicated the presence of the HLA-A*24:02:01:01 allele. HLA-A*02:64 was identified by sequencing the allele in isolation over exons 2 and 3 and allowed confirmation of this allele sequence with the IMGT/HLA database (Accession number AY297166). This approach is cost efficient and can be modified to sequence alleles at other HLA loci. It has also been adapted to characterize the novel HLA-DQB1*06:48 allele (Accession number HE647646) as well as the non-HLA gene, UGT2B17, making it a useful tool to augment existing typing methodologies.
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Affiliation(s)
- L Foster
- Transplantation Laboratory, Manchester Royal Infirmary, Manchester, UK
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Föll D, Hinrichs J, Tischer S, Battermann A, Schambach A, Figueiredo C, Immenschuh S, Blasczyk R, Eiz-Vesper B. Closing the gap: discrimination of the expression profile of HLA questionable alleles by a cytokine-induced secretion approach using HLA-A*32:11Q. ACTA ACUST UNITED AC 2012; 79:340-50. [PMID: 22489943 DOI: 10.1111/j.1399-0039.2012.01864.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Matching of human leukocyte antigen (HLA) alleles between donors and recipients plays a major role in hematopoietic stem cell transplantation (HSCT). Null or questionably expressed HLA allelic variants are a major issue in HLA matching, because the aberrant expression of such alleles can have a major impact on the outcome of HSCT and/or its complications such as graft-versus-host disease. The goal of this study was to investigate the potential of a recently developed cytokine-induced secretion assay to differentiate the expression levels of HLA-A*32:11Q (questionable) into a null (N) or low (L) expression variant. An amino acid mutation at position 164 of HLA-A*32:11Q disrupts the disulfide bridge in the α2 domain. HLA-A*32:11Q is not detectable by standard microlymphocytotoxicity assay. To this end, we cloned soluble HLA-A*32:11Q and a reference allele (HLA-A*32:01) into expression vectors and transfected/transduced HEK293 and K562 cells. Allele-expressing K562 cells were simultaneously transfected/transduced with a β2-microglobulin (B2M)-encoding vector to ensure the intact HLA structure with B2M. After treatment with proinflammatory cytokines, secreted soluble HLA molecules were determined by enzyme-linked immunosorbent assay in the supernatant and intracellular accumulation of the recombinant proteins by flow cytometry. HLA-A*32:11Q was nearly undetectable in untreated transfectants. Cytokine treatment increased the secretion of HLA-A*32:11Q to detectable levels and resulted in intracellular accumulation of the allele. There was no difference in mRNA transcription between the A*32 alleles. On the basis of these results, we recommend reclassification of HLA-A*32:11Q as a low expression (L) variant.
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Affiliation(s)
- D Föll
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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Badrinath S, Huyton T, Schumacher H, Blasczyk R, Bade-Doeding C. Position 45 influences the peptide binding motif of HLA-B*44:08. Immunogenetics 2011; 64:245-9. [PMID: 22009320 DOI: 10.1007/s00251-011-0583-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 10/10/2011] [Indexed: 01/30/2023]
Abstract
Position 45 represents a highly polymorphic residue within HLA class I alleles, which contacts the p2 position of bound peptides in 85% of the peptide-HLA structures analyzed, while the neighboring residues 41 and 46 are not involved in peptide binding. To investigate the influence of residue 45 at the functional level, we sequenced peptides eluted from recombinant HLA-B*44:08(41Ala/45Met/46Ala) molecules and compared their features with known peptides from B*44:02(41Thr/45Lys/46Glu). While HLA-B*44:02 has an anchor motif of E at the p2 anchor position, HLA-B*44:08 exhibits Q and L as anchor motif. The 45(Met/Lys) polymorphism contributes to the alteration in the peptide-binding motif and provides further evidence that mismatches at position 45 should be considered as nonpermissive in a transplantation setting.
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Affiliation(s)
- Soumya Badrinath
- Institute for Transfusion Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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