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Lee J, Oldham ML, Manon V, Chen J. Principles of peptide selection by the transporter associated with antigen processing. Proc Natl Acad Sci U S A 2024; 121:e2320879121. [PMID: 38805290 PMCID: PMC11161800 DOI: 10.1073/pnas.2320879121] [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: 12/05/2023] [Accepted: 04/05/2024] [Indexed: 05/30/2024] Open
Abstract
Our ability to fight pathogens relies on major histocompatibility complex class I (MHC-I) molecules presenting diverse antigens on the surface of diseased cells. The transporter associated with antigen processing (TAP) transports nearly the entire repertoire of antigenic peptides into the endoplasmic reticulum for MHC-I loading. How TAP transports peptides specific for MHC-I is unclear. In this study, we used cryo-EM to determine a series of structures of human TAP, both in the absence and presence of peptides with various sequences and lengths. The structures revealed that peptides of eight or nine residues in length bind in a similarly extended conformation, despite having little sequence overlap. We also identified two peptide-anchoring pockets on either side of the transmembrane cavity, each engaging one end of a peptide with primarily main chain atoms. Occupation of both pockets results in a global conformational change in TAP, bringing the two halves of the transporter closer together to prime it for isomerization and ATP hydrolysis. Shorter peptides are able to bind to each pocket separately but are not long enough to bridge the cavity to bind to both simultaneously. Mutations that disrupt hydrogen bonds with the N and C termini of peptides almost abolish MHC-I surface expression. Our findings reveal that TAP functions as a molecular caliper that selects peptides according to length rather than sequence, providing antigen diversity for MHC-I presentation.
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Affiliation(s)
- James Lee
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Michael L. Oldham
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
| | - Victor Manon
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
| | - Jue Chen
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY10065
- HHMI, Chevy Chase, MD20815
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2
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Cuadrado-Torroglosa I, Pacheco A, Barrio A, Garrido N, Aparicio P, Pellicer N, García-Velasco JA, Alecsandru D. Increased cytotoxic natural killer cells in the endometrium alone cannot be considered the immunological cause of recurrent miscarriage. Fertil Steril 2023; 120:101-110. [PMID: 36828055 DOI: 10.1016/j.fertnstert.2023.02.024] [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: 07/31/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
OBJECTIVE To study the distribution and gene expression of endometrial immune cell populations, especially natural killer (NK) subsets, between assisted reproductive technology patients and healthy donors and explore a possible relationship of these results with patients' killer cell immunoglobulin-like receptor (KIR) genotypes and KIR-human antigen leukocyte-C (HLA-C) binding. DESIGN Prospective observational cohort study. SETTING Clinic and university laboratories. PATIENT(S) Participants included 39 women with recurrent miscarriages who had undergone in vitro fertilization cycles with donated oocytes and 21 healthy oocyte donors with proven fertility. INTERVENTION(S) Endometrial biopsy samples were collected from both patients and donors, and the KIR genotypes of the assisted reproductive technology patients were analyzed. MAIN OUTCOME MEASURE(S) Endometrial gene expression (cluster of differentiation [CD] antigens and anti-inflammatory and proinflammatory interleukins) and the number and percentage of regulatory T and NK cell populations in patients and donors were determined. Subsequently, the results obtained were categorized in the group of patients by KIR genotype. Killer cell immunoglobulin-like receptor-HLA-C binding was also examined in patients, considering their KIRs. RESULT(S) A higher percentage of CD56dimCD16+ NK cells were observed in patients than those in healthy donors. Nevertheless, when categorizing patients by KIR genotype and comparing the KIR AA (35.9%), AB (43.6%), and BB (20.5%) groups, no statistically significant difference was observed in either endometrial gene expression or any of the immune cell populations analyzed. Finally, no differences in binding between KIR and HLA-C molecules were registered among these 3 sets of patients. CONCLUSION(S) The reported increase in the number of NK cells with a cytotoxic profile in the endometrium of women with a history of recurrent miscarriages cannot alone explain these events because no relationship is observed between such cellular increase and the KIR genotypes, which individually, and in combination with the different HLA-C alleles, have also been associated, by previous studies, with negative reproductive outcomes. CLINICAL TRIAL REGISTRATION NUMBER 1405-MAD-025-JG.
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Affiliation(s)
| | - Alberto Pacheco
- Andrology Laboratory and Sperm Bank, IVIRMA, Madrid, Spain; Department of Health Sciences, Alfonso X "El Sabio" University, Madrid, Spain
| | - Ana Barrio
- Department of Reproductive Endocrinology and Infertility, IVIRMA, Madrid, Spain
| | - Nicolás Garrido
- IVI Foundation, Health Research Institute La Fe, Valencia, Spain
| | - Pilar Aparicio
- Department of Reproductive Endocrinology and Infertility, IVIRMA, Madrid, Spain; Department of Immunology, IVIRMA, Madrid, Spain
| | - Nuria Pellicer
- Women's Health Area, La Fe University Hospital, Valencia, Spain
| | - Juan Antonio García-Velasco
- IVI Foundation, Health Research Institute La Fe, Valencia, Spain; Department of Reproductive Endocrinology and Infertility, IVIRMA, Madrid, Spain; Department of Obstetrics and Gynaecology, Rey Juan Carlos University, Madrid, Spain
| | - Diana Alecsandru
- IVI Foundation, Health Research Institute La Fe, Valencia, Spain; Department of Immunology, IVIRMA, Madrid, Spain.
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3
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Bhatt P, Sharma M, Sharma S. Prediction and identification of T cell epitopes of COVID-19 with balanced cytokine response for the development of peptide based vaccines. In Silico Pharmacol 2021; 9:40. [PMID: 34221846 PMCID: PMC8237047 DOI: 10.1007/s40203-021-00098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Recent outbreak of 2019 novel Corona virus poses serious challenge for the global health system. In lieu of paucity of experimental data, tools and the very basic understanding of host immune responses against SARS-CoV-2, well thought effective measures are needed to control COVID-19 pandemic. We have identified specific overlapping antigenic peptide epitopes (OAPE) within the 4 structural proteins of SARS-CoV-2 predictive of triggering robust CD4 and CD8 T cell responses in host using bio-informatics tools (NetMHC4.0, IEDB, and Vaxijen2.0). We speculate an early release of pro-inflammatory cytokines for protection and later release of anti-inflammatory cytokines for prevention of immunopathology in designing a vaccine for Covid-19. Therefore, the selected immunogenic OAPE were subjected to in silico tools (IL-6-Pred, IFNepitope and PIP-EL) for analyzing their pro-inflammatory response. The OAPEs found to be pro-inflammatory in nature were further subjected to prediction servers (IL-4-Pred, IL-10-Pred, Pre-AIP) to characterize them as inducers of anti-inflammatory response as well. We finally filtered out 12 OAPE which had affinity for both CD4 and CD8 T cells as well as were inducers of pro-inflammatory and anti-inflammatory cytokines. On confirmation of OAPE binding affinity for respective T cell specific MHC allele using docking studies (pepATTRACT, Hex8.0 and Discovery studio) they were found to be have more immunogenic potential than the 3 negative control peptides (NCPs) included in the study. Additionally, we constructed CTxB-adjuvanated multi-epitopic vaccine inclusive of the 12 OAPEs which was non-toxic, non-allergenic and capable of inducing both pro-inflammatory and anti-inflammatory cytokines. A successful in silico cloning and docking of modeled subunit vaccine construct with toll like receptor-2 (TLR-2) confirmed the high efficacy of our multi-epitopic vaccine which can through a balanced interplay of cytokines help in creating a steady-state immune equilibrium. In silico immune simulation studies with the vaccine using C-ImmSim server also showed higher percentage of T cells along with production of pro-inflammatory as well as some anti-inflammatory cytokines. Experimental validation of this prediction based study on Peripheral Blood Mononuclear Cells (PBMCs) of un-infected individuals, patients and recovered individuals will facilitate production of high priority effective SARS -CoV-2 vaccine candidate. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00098-7.
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Affiliation(s)
- Parul Bhatt
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Monika Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Sadhna Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
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4
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Souza AS, Sonon P, Paz MA, Tokplonou L, Lima THA, Porto IOP, Andrade HS, Silva NDSB, Veiga-Castelli LC, Oliveira MLG, Sadissou IA, Massaro JD, Moutairou KA, Donadi EA, Massougbodji A, Garcia A, Ibikounlé M, Meyer D, Sabbagh A, Mendes-Junior CT, Courtin D, Castelli EC. Hla-C genetic diversity and evolutionary insights in two samples from Brazil and Benin. HLA 2020; 96:468-486. [PMID: 32662221 DOI: 10.1111/tan.13996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/18/2020] [Accepted: 07/09/2020] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen-C (HLA-C) is a classical HLA class I molecule that binds and presents peptides to cytotoxic T lymphocytes in the cell surface. HLA-C has a dual function because it also interacts with Killer-cell immunoglobulin-like receptors (KIR) receptors expressed in natural killer and T cells, modulating their activity. The structure and diversity of the HLA-C regulatory regions, as well as the relationship among variants along the HLA-C locus, are poorly addressed, and few population-based studies explored the HLA-C variability in the entire gene in different population samples. Here we present a molecular and bioinformatics method to evaluate the entire HLA-C diversity, including regulatory sequences. Then, we applied this method to survey the HLA-C diversity in two population samples with different demographic histories, one highly admixed from Brazil with major European contribution, and one from Benin with major African contribution. The HLA-C promoter and 3'UTR were very polymorphic with the presence of few, but highly divergent haplotypes. These segments also present conserved sequences that are shared among different primate species. Nucleotide diversity was higher in other segments rather than exons 2 and 3, particularly around exon 5 and the second half of the 3'UTR region. We detected evidence of balancing selection on the entire HLA-C locus and positive selection in the HLA-C leader peptide, for both populations. HLA-C motifs previously associated with KIR interaction and expression regulation are similar between both populations. Each allele group is associated with specific regulatory sequences, reflecting the high linkage disequilibrium along the entire HLA-C locus in both populations.
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Affiliation(s)
- Andreia S Souza
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Paulin Sonon
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Michelle A Paz
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Léonidas Tokplonou
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France.,Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin.,Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Thálitta H A Lima
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Iane O P Porto
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Heloisa S Andrade
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Nayane Dos S B Silva
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Luciana C Veiga-Castelli
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Maria Luiza G Oliveira
- Department of Genetics, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Ibrahim Abiodoun Sadissou
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin
| | - Eduardo A Donadi
- Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance, Cotonou, Benin
| | - André Garcia
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Moudachirou Ibikounlé
- Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo (USP), São Paulo, Brazil
| | - Audrey Sabbagh
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, São Paulo, Brazil
| | - David Courtin
- Institut de Recherche pour le Développement (IRD), UMR 261 MERIT, Université de Paris, Paris, France
| | - Erick C Castelli
- Molecular Genetics and Bioinformatics Laboratory-Experimental Research Unity, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Genetics Program, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.,Pathology Program, School of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
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5
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Alecsandru D, Pacheco A, Guerrero-Mayo A, Fabris A, Aparicio P, Barrio A, Pellicer A, Garcia-Velasco JA. Ovarian stimulation does not influence the uterine immune environment in healthy infertile women. Reprod Biomed Online 2019; 40:113-123. [PMID: 31761720 DOI: 10.1016/j.rbmo.2019.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/15/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
RESEARCH QUESTION There is some controversy regarding the impact of ovarian stimulation on immune cells in women undergoing IVF. The study's aim was to determine whether ovarian stimulation affected immune uterine cells in healthy women undergoing IVF. DESIGN This prospective cohort study included 28 patients undergoing IVF and 47 healthy oocyte donors. Endometrial biopsies were taken in a natural cycle and after ovarian stimulation. All participants had a normal karyotype, pelvic ultrasound and cervical cytology results and thyroid-stimulating hormone concentration, as well as normal glucose and insulin concentrations and inherited and acquired thrombophilia test results. Screening tests including human papillomavirus were normal. Immune cells were analysed using three techniques: fluorescence-activated cell sorting, immunohistochemistry and gene expression. A human leukocyte antigen (HLA)-C tetramer was used as an 'artificial embryo'. The expression of genes including those for tumour necrosis factor (TNF)-α and interleukin-10 (IL-10) was analysed. RESULTS A comparison was made of the percentage and gene expression of CD56brightCD16- uterine natural killer (uNK), CD56dimCD16+ natural killer cells, CD56-CD16+ natural killer cells and TregCD25+CD4+FoxP3+ cells, uNK binding to the HLA-C tetramer, and TNF-α and IL-10 expression. No between- or within-group differences were observed in natural versus ovarian stimulation cycles. CONCLUSIONS Ovarian stimulation does not affect the uterine immune cell population or HLA-C binding in healthy women undergoing ovarian stimulation. Further studies are underway to find out if different responses might be seen in women with previous autoimmune disorders.
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Affiliation(s)
- D Alecsandru
- Department of Immunology, IVI RMA, Madrid, Spain; Rey Juan Carlos University, Madrid, Spain; Health Research Institute La Fe, Valencia, Spain.
| | - A Pacheco
- Health Research Institute La Fe, Valencia, Spain; Department of Andrology, IVI RMA, Madrid, Spain; Alfonso X 'El Sabio' University, Madrid, Spain
| | | | - A Fabris
- Department of Reproductive Endocrinology and Infertility, IVI RMA, Madrid, Spain
| | - P Aparicio
- Department of Immunology, IVI RMA, Madrid, Spain
| | - A Barrio
- Department of Reproductive Endocrinology and Infertility, IVI RMA, Madrid, Spain
| | - A Pellicer
- Health Research Institute La Fe, Valencia, Spain; Universidad de Valencia, IVI Learning Center; Department of Reproductive Endocrinology and Infertility, IVI RMA, Roma, Italy
| | - Juan A Garcia-Velasco
- Rey Juan Carlos University, Madrid, Spain; Health Research Institute La Fe, Valencia, Spain; Universidad de Valencia, IVI Learning Center; Department of Reproductive Endocrinology and Infertility, IVI RMA, Madrid, Spain
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6
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Prasasty VD, Grazzolie K, Rosmalena R, Yazid F, Ivan FX, Sinaga E. Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches. Microorganisms 2019; 7:E226. [PMID: 31370224 PMCID: PMC6722788 DOI: 10.3390/microorganisms7080226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain-Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine.
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Affiliation(s)
- Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia.
| | - Karel Grazzolie
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Rosmalena Rosmalena
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fatmawaty Yazid
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fransiskus Xaverius Ivan
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Ernawati Sinaga
- Faculty of Biology, Universitas Nasional, Jakarta 12520, Indonesia
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7
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Singh M, Bhatt P, Sharma M, Varma-Basil M, Chaudhry A, Sharma S. Immunogenicity of late stage specific peptide antigens of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 74:103930. [PMID: 31228643 DOI: 10.1016/j.meegid.2019.103930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/06/2019] [Accepted: 06/18/2019] [Indexed: 01/05/2023]
Abstract
Global burden of latent TB infection comprises one-third of the world population. Identifying potential Mycobacterium tuberculosis (Mtb) latency associated antigens that can generate protective immunity against the pathogen is crucial for designing an effective TB vaccine. Usually the immune system responds to a small number of amino acids as MHC Class I or Class II peptides. The precision to trigger epitope specific protective T-cell immune response could therefore be achieved with synthetic peptide-based subunit vaccine. In the present study we have considered an immunoinformatic approach using available softwares (ProPred, IEDB, NETMHC, BIMAS, Vaxijen2.0) and docking and visualizing softwares (CABSDOCK, HEX, Pymol, Discovery Studio) to select 10 peptides as latency antigens from 4 proteins (Rv2626, Rv2627, Rv2628, and Rv2032) of DosR regulon of Mtb. As Intracellular IFN-γ secreted by T cells is the most essential cytokine in Th1 mediated protective immunity, these peptides were verified as potential immunogenic epitopes in Peripheral Blood Mononuclear Cells (PBMCs) of 10 healthy contacts of TB patients (HTB) and 10 Category I Pulmonary TB patients (PTB).The antigen-specific CD4 and CD8 T cells expressing intracellular IFN-γ were analyzed using monoclonal antibodies in all subjects by multi-parameter flow cytometry. Both, PTB and HTB individuals responded to DosR peptides by showing increased frequency of IFN-γ+CD4 and IFN-γ+CD8 T cells. The T-cell responses were significantly higher in PTB patients in comparision to the HTB individuals. Additionally, our synthetic peptides and pools showed higher frequencies of IFN-γ+CD4 and IFN-γ+CD8 T cells than the peptides of Ag85B. This pilot study can be taken up further in larger sample size which may support the untapped opportunity of designing Mtb DosR inclusive peptide based post-exposure subunit vaccine.
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Affiliation(s)
- Medha Singh
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Parul Bhatt
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | | | - Anil Chaudhry
- Rajan Babu Institute of Pulmonary Medicine and Tuberculosis Hospital, GTB Nagar, Delhi 110009, India
| | - Sadhna Sharma
- DS Kothari Centre for Research and Innovation in Science Education, Miranda House and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
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8
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Gwozdowicz S, Nestorowicz K, Graczyk-Pol E, Szlendak U, Rogatko-Koros M, Mika-Witkowska R, Pawliczak D, Zubala M, Malinowska A, Witkowska A, Nowak J. KIR specificity and avidity of standard and unusual C1, C2, Bw4, Bw6 and A3/11 amino acid motifs at entire HLA:KIR interface between NK and target cells, the functional and evolutionary classification of HLA class I molecules. Int J Immunogenet 2019; 46:217-231. [PMID: 31210416 DOI: 10.1111/iji.12433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/04/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022]
Abstract
Natural killer (NK) cells make vital contributions to the immune system and the reproductive system. Notably, NK cells of donor origin can recognize and kill residual leukaemic cells and cure malignant patients in hematopoietic stem cell (HSC) transplant setting. NK cell function is regulated by KIRs that recognize cognate HLA class I molecules on target cells, depending on their amino acid residues. In review, we addressed the question of binding capacity and avidity of HLA class I molecules to different killer cell immunoglobulin-like receptors (KIRs) depending on all interacting amino acid residues both on HLA and KIR side. We searched PubMed database and analysed available HLA:KIR crystallographic data for amino acid residues in HLA molecules, those physically involved in binding KIRs (termed here the "entire KIR interface"). Within entire KIR interface, we selected five functional sequence motifs (14-19, 66-76, 77-84, 88-92 and 142-151) and classified them according to the conservation of their amino acid sequences among 8,942 HLA class I molecules. Although some conserved amino acid motifs were shared by different groups of KIR ligands, the HLA motif combinations were exclusive for the ligand groups. In 135 common HLA class I molecules with known HLA:KIR recognition, we found 54 combinations of five motifs in each of the KIR-binding interfaces (C1, C2, Bw4, A3/11) and conserved non-KIR-binding interfaces. Based on the entire KIR interface, this analysis allowed to classify 8,942 HLA class I molecules into KIR specificity groups. This functional and evolutionary classification of entire KIR interfaces provides a tool for unambiguously predicting HLA:KIR interactions for common and those HLA molecules that have not yet been functionally tested. Considering the entire KIR interface in HLA class I molecules, functional interactions of HLA and KIR can be predicted in immune responses, reproduction and allotransplantation. Further functional studies are needed on the HLA:KIR interaction variations caused by the repertoires of peptides presented by HLA molecules and KIR polymorphisms at allelic level.
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Affiliation(s)
- Slawomir Gwozdowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Klaudia Nestorowicz
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Elzbieta Graczyk-Pol
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Urszula Szlendak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Rogatko-Koros
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Renata Mika-Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Daria Pawliczak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Marta Zubala
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Malinowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Agnieszka Witkowska
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Jacek Nowak
- Department of Immunogenetics, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
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9
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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10
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Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles. Sci Rep 2017; 7:8653. [PMID: 28819312 PMCID: PMC5561238 DOI: 10.1038/s41598-017-08876-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/05/2017] [Indexed: 11/08/2022] Open
Abstract
Genes of the human leukocyte antigen (HLA) system encode cell-surface proteins involved in regulation of immune responses, and the way drugs interact with the HLA peptide binding groove is important in the immunopathogenesis of T-cell mediated drug hypersensitivity syndromes. Nevirapine (NVP), is an HIV-1 antiretroviral with treatment-limiting hypersensitivity reactions (HSRs) associated with multiple class I and II HLA alleles. Here we utilize a novel analytical approach to explore these multi-allelic associations by systematically examining HLA molecules for similarities in peptide binding specificities and binding pocket structure. We demonstrate that primary predisposition to cutaneous NVP HSR, seen across ancestral groups, can be attributed to a cluster of HLA-C alleles sharing a common binding groove F pocket with HLA-C*04:01. An independent association with a group of class II alleles which share the HLA-DRB1-P4 pocket is also observed. In contrast, NVP HSR protection is afforded by a cluster of HLA-B alleles defined by a characteristic peptide binding groove B pocket. The results suggest drug-specific interactions within the antigen binding cleft can be shared across HLA molecules with similar binding pockets. We thereby provide an explanation for multiple HLA associations with cutaneous NVP HSR and advance insight into its pathogenic mechanisms.
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11
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Nakamura S, Ohmura R, Nakanishi I. An Interaction-based Approach for Affinity Prediction between Antigen Peptide and Human Leukocyte Antigen Using COMBINE Analysis. CHEM-BIO INFORMATICS JOURNAL 2017. [DOI: 10.1273/cbij.17.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Rie Ohmura
- Department of Pharmaceutical Sciences, Kindai University
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kindai University
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12
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Pandey K, Sharma M, Saarav I, Singh S, Dutta P, Bhardwaj A, Sharma S. Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach. Int J Mycobacteriol 2016; 5:34-43. [DOI: 10.1016/j.ijmyco.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 10/22/2022] Open
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13
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Rasmussen M, Harndahl M, Stryhn A, Boucherma R, Nielsen LL, Lemonnier FA, Nielsen M, Buus S. Uncovering the peptide-binding specificities of HLA-C: a general strategy to determine the specificity of any MHC class I molecule. THE JOURNAL OF IMMUNOLOGY 2014; 193:4790-802. [PMID: 25311805 DOI: 10.4049/jimmunol.1401689] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
MHC class I molecules (HLA-I in humans) present peptides derived from endogenous proteins to CTLs. Whereas the peptide-binding specificities of HLA-A and -B molecules have been studied extensively, little is known about HLA-C specificities. Combining a positional scanning combinatorial peptide library approach with a peptide-HLA-I dissociation assay, in this study we present a general strategy to determine the peptide-binding specificity of any MHC class I molecule. We applied this novel strategy to 17 of the most common HLA-C molecules, and for 16 of these we successfully generated matrices representing their peptide-binding motifs. The motifs prominently shared a conserved C-terminal primary anchor with hydrophobic amino acid residues, as well as one or more diverse primary and auxiliary anchors at P1, P2, P3, and/or P7. Matrices were used to generate a large panel of HLA-C-specific peptide-binding data and update our pan-specific NetMHCpan predictor, whose predictive performance was considerably improved with respect to peptide binding to HLA-C. The updated predictor was used to assess the specificities of HLA-C molecules, which were found to cover a more limited sequence space than HLA-A and -B molecules. Assessing the functional significance of these new tools, HLA-C*07:01 transgenic mice were immunized with stable HLA-C*07:01 binders; six of six tested stable peptide binders were immunogenic. Finally, we generated HLA-C tetramers and labeled human CD8(+) T cells and NK cells. These new resources should support future research on the biology of HLA-C molecules. The data are deposited at the Immune Epitope Database, and the updated NetMHCpan predictor is available at the Center for Biological Sequence Analysis and the Immune Epitope Database.
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Affiliation(s)
- Michael Rasmussen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Mikkel Harndahl
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Anette Stryhn
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rachid Boucherma
- INSERM, Unité 1016, Institut Cochin, Equipe Immunologie du Diabète, Groupe Hospitalier Cochin-Port-Royal, 75014 Paris, France
| | - Lise Lotte Nielsen
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - François A Lemonnier
- INSERM, Unité 1016, Institut Cochin, Equipe Immunologie du Diabète, Groupe Hospitalier Cochin-Port-Royal, 75014 Paris, France
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby 2800, Denmark; and Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires, Argentina
| | - Søren Buus
- Laboratory of Experimental Immunology, Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark;
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14
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Abstract
UNLABELLED The extent to which HIV-1 clade B strains exhibit population-specific adaptations to host HLA alleles remains incompletely known, in part due to incomplete characterization of HLA-associated HIV-1 polymorphisms (HLA-APs) in different global populations. Moreover, it remains unknown to what extent the same HLA alleles may drive significantly different escape pathways across populations. As the Japanese population exhibits distinctive HLA class I allele distributions, comparative analysis of HLA-APs between HIV-1 clade B-infected Japanese and non-Asian cohorts could shed light on these questions. However, HLA-APs remain incompletely mapped in Japan. In a cohort of 430 treatment-naive Japanese with chronic HIV-1 clade B infection, we identified 284 HLA-APs in Gag, Pol, and Nef using phylogenetically corrected methods. The number of HLA-associated substitutions in Pol, notably those restricted by HLA-B*52:01, was weakly inversely correlated with the plasma viral load (pVL), suggesting that the transmission and persistence of B*52:01-driven Pol mutations could modulate the pVL. Differential selection of HLA-APs between HLA subtype members, including those differing only with respect to substitutions outside the peptide-binding groove, was observed, meriting further investigation as to their mechanisms of selection. Notably, two-thirds of HLA-APs identified in Japan had not been reported in previous studies of predominantly Caucasian cohorts and were attributable to HLA alleles unique to, or enriched in, Japan. We also identified 71 cases where the same HLA allele drove significantly different escape pathways in Japan versus predominantly Caucasian cohorts. Our results underscore the distinct global evolution of HIV-1 clade B as a result of host population-specific cellular immune pressures. IMPORTANCE Cytotoxic T lymphocyte (CTL) escape mutations in HIV-1 are broadly predictable based on the HLA class I alleles expressed by the host. Because HLA allele distributions differ among worldwide populations, the pattern and diversity of HLA-associated escape mutations are likely to be somewhat distinct to each race and region. HLA-associated polymorphisms (HLA-APs) in HIV-1 have previously been identified at the population level in European, North American, Australian, and African cohorts; however, large-scale analyses of HIV-1 clade B-specific HLA-APs in Asians are lacking. Differential intraclade HIV-1 adaptation to global populations can be investigated via comparative analyses of HLA-associated polymorphisms across ethnic groups, but such studies are rare. Here, we identify HLA-APs in a large Japanese HIV-1 clade B cohort using phylogenetically informed methods and observe that the majority of them had not been previously characterized in predominantly Caucasian populations. The results highlight HIV's unique adaptation to cellular immune pressures imposed by different global populations.
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15
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Schittenhelm RB, Dudek NL, Croft NP, Ramarathinam SH, Purcell AW. A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides. ACTA ACUST UNITED AC 2014; 83:174-9. [PMID: 24397554 DOI: 10.1111/tan.12282] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/06/2013] [Accepted: 12/03/2013] [Indexed: 02/01/2023]
Abstract
The human B lymphoblastoid cell line C1R is widely regarded as human leukocyte antigen-A (HLA-A)/HLA-B negative and is therefore frequently exploited as a recipient cell line to study HLA class I functions. However, the normal levels of HLA-C*04:01 often hamper the investigation of introduced HLA class I allomorphs, which is particularly evident in sensitive applications such as mass spectrometry. Here we describe the comprehensive analysis of endogenous HLA-C*04:01 ligands expressed on the surface of C1R cells to (i) define a large sequence dataset of HLA-C*04:01 ligands, to (ii) refine the HLA-C*04:01 peptide-binding motif and (iii) to provide a resource that allows discrimination between peptides bound to introduced HLA class I subtypes and to the endogenous HLA-C*04:01 molecules.
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Affiliation(s)
- R B Schittenhelm
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia
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16
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Dynamics of free versus complexed β2-microglobulin and the evolution of interfaces in MHC class I molecules. Immunogenetics 2012; 65:157-72. [PMID: 23229474 DOI: 10.1007/s00251-012-0667-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
In major histocompatibility complex (MHC) class I molecules, monomorphic β(2)-microglobulin (β(2)m) is non-covalently bound to a heavy chain (HC) exhibiting a variable degree of polymorphism. β(2)M can stabilize a wide variety of complexes ranging from classical peptide binding to nonclassical lipid presenting MHC class I molecules as well as to MHC class I-like molecules that do not bind small ligands. Here we aim to assess the dynamics of individual regions in free as well as complexed β(2)m and to understand the evolution of the interfaces between β(2)m and different HC. Using human β(2)m and the HLA-B*27:09 complex as a model system, a comparison of free and HC-bound β(2)m by nuclear magnetic resonance spectroscopy was initially carried out. Although some regions retain their flexibility also after complex formation, these studies reveal that most parts of β(2)m gain rigidity upon binding to the HC. Sequence analyses demonstrate that some of the residues exhibiting flexibility participate in evolutionarily conserved β(2)m-HC contacts which are detectable in diverse vertebrate species or characterize a particular group of MHC class I complexes such as peptide- or lipid-binding molecules. Therefore, the spectroscopic experiments and the interface analyses demonstrate that β(2)m fulfills its role of interacting with diverse MHC class I HC as well as effector cell receptors not only by engaging in conserved intermolecular contacts but also by falling back upon key interface residues that exhibit a high degree of flexibility.
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17
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Zipeto D, Beretta A. HLA-C and HIV-1: friends or foes? Retrovirology 2012; 9:39. [PMID: 22571741 PMCID: PMC3386009 DOI: 10.1186/1742-4690-9-39] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 05/09/2012] [Indexed: 12/20/2022] Open
Abstract
The major histocompatibility complex class I protein HLA-C plays a crucial role as a molecule capable of sending inhibitory signals to both natural killer (NK) cells and cytotoxic T lymphocytes (CTL) via binding to killer cell Ig-like receptors (KIR). Recently HLA-C has been recognized as a key molecule in the immune control of HIV-1. Expression of HLA-C is modulated by a microRNA binding site. HLA-C alleles that bear substitutions in the microRNA binding site are more expressed at the cell surface and associated with the control of HIV-1 viral load, suggesting a role of HLA-C in the presentation of antigenic peptides to CTLs. This review highlights the role of HLA-C in association with HIV-1 viral load, but also addresses the contradiction of the association between high cell surface expression of an inhibitory molecule and strong cell-mediated immunity. To explore additional mechanisms of control of HIV-1 replication by HLA-C, we address specific features of the molecule, like its tendency to be expressed as open conformer upon cell activation, which endows it with a unique capacity to associate with other cell surface molecules as well as with HIV-1 proteins.
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Affiliation(s)
- Donato Zipeto
- Department of Life and Reproduction Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
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18
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Moraru M, Balas A, de Pablo R, Vicario JL, Vilches C. Allele-specific amplification of the complete HLA-C gene from genomic DNA - a novel Cw4 allele (C*04:71) with a Cw1 motif in the peptide-binding site. ACTA ACUST UNITED AC 2012; 79:291-4. [DOI: 10.1111/j.1399-0039.2011.01833.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Qutob N, Balloux F, Raj T, Liu H, Marion de Procé S, Trowsdale J, Manica A. Signatures of historical demography and pathogen richness on MHC class I genes. Immunogenetics 2011; 64:165-75. [PMID: 21947542 DOI: 10.1007/s00251-011-0576-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/09/2011] [Indexed: 12/20/2022]
Abstract
The extreme polymorphism of MHC class I has been argued to be driven by balancing selection from pathogens, with the prediction that populations exposed to a wider variety of diseases should have higher diversity. We assembled a global database of allotype frequencies for MHC class I genes and investigated possible drivers of genetic diversity, measured in different ways. We first looked for a decline in diversity with distance from Africa (a consequence of drift during human expansions) and then investigated the link with pathogen richness once the effect of drift had been corrected for. Using heterozygosity, we recovered a clear decline in diversity from Africa and confirmed the positive relationship between genetic diversity and pathogen richness for all three classical MHC class I genes. However, when we considered a sequence-based measure of genetic diversity, the correlation with geographic distance from Africa vanished for HLA-C, and the correlations with pathogen richness for the three MHC class I genes were much weaker. HLA-C is known to consist of two functional classes of allotypes (classified with respect to the 80th residue), which interact with different KIR receptors. While this separation provided some improvement in the fit between genetic diversity and distance from Africa for one class, much clearer and consistent patterns were recovered when we used the 90th residue to separate HLA-C allotypes into two new classes. This suggests that this residue, which is also involved in the binding of KIR, might have had an important evolutionary role that has been overlooked.
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Affiliation(s)
- Nouar Qutob
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
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20
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Abstract
NK cell effector function is regulated by a range of activating and inhibitory receptors, and many of their known ligands are MHC class I molecules. Human NK receptors encoded by the Killer immunoglobulin-like receptor (KIR) gene family recognize polymorphic HLA-C as well as some HLA-A and HLA-B molecules. KIRs are expressed by uterine NK (uNK) cells, which are distinctive NK cells directly in contact with the invading fetal placental cells that transform the uterine arteries during the first trimester. Trophoblast cells express both maternal and paternal HLA-C allotypes and can therefore potentially interact with KIRs expressed by uNK. Therefore, allorecognition of paternal HLA-C by maternal KIR might influence trophoblast invasion and vascular remodeling, with subsequent effects on placental development and the outcome of pregnancy. We discuss here the studies relating to KIR/HLA-C interactions with an emphasis on how these function during pregnancy to regulate placentation.
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Affiliation(s)
- Olympe Chazara
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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21
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Merino A, Malhotra R, Morton M, Mulenga J, Allen S, Hunter E, Tang J, Kaslow RA. Impact of a functional KIR2DS4 allele on heterosexual HIV-1 transmission among discordant Zambian couples. J Infect Dis 2011; 203:487-95. [PMID: 21216870 DOI: 10.1093/infdis/jiq075] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs) and their HLA ligands interact to regulate natural killer (NK) cell function. KIR gene content and allelic variations are reported to influence human immunodeficiency virus (HIV)-1 infection and pathogenesis. We investigated the impact of KIR genes on heterosexual HIV-1 transmission among 566 discordant couples from Lusaka, Zambia. KIR2DS4*001, the only allele of KIR2DS4 known to encode a functional activating receptor, was associated with relatively high viral load for HIV-1 in index (HIV-1 seroprevalent) partners (β [standard error (SE)], .17 [.8] log₁₀; P = .04) and with accelerated transmission of HIV-1 to cohabiting seronegative partners (relative hazard [RH], 2.00; P = .004). The latter association was independent of the direction of transmission (male-to-female or female-to-male), genital ulcers, and carriage of the putative ligand (HLA-Cw*04). No KIR-gene variant in the initially seronegative partners was associated with HIV-1 acquisition or early viral load following seroconversion. Further analysis of NK cell function should clarify the role of KIR2DS4*001 in HIV-1 transmission.
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Affiliation(s)
- Aimee Merino
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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22
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Yanover C, Petersdorf EW, Malkki M, Gooley T, Spellman S, Velardi A, Bardy P, Madrigal A, Bignon JD, Bradley P. HLA mismatches and hematopoietic cell transplantation: structural simulations assess the impact of changes in peptide binding specificity on transplant outcome. Immunome Res 2011; 7:4. [PMID: 24482668 PMCID: PMC3904355 DOI: 10.4172/1745-7580.1000048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The success of hematopoietic cell transplantation from an unrelated donor depends in part on the degree of Human Histocompatibility Leukocyte Antigen (HLA) matching between donor and patient. We present a structure-based analysis of HLA mismatching, focusing on individual amino acid mismatches and their effect on peptide binding specificity. Using molecular modeling simulations of HLA-peptide interactions, we find evidence that amino acid mismatches predicted to perturb peptide binding specificity are associated with higher risk of mortality in a large and diverse dataset of patient-donor pairs assembled by the International Histocompatibility Working Group in Hematopoietic Cell Transplantation consortium. This analysis may represent a first step toward sequence-based prediction of relative risk for HLA allele mismatches.
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Affiliation(s)
- Chen Yanover
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Effie W Petersdorf
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mari Malkki
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ted Gooley
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, USA
| | - Andrea Velardi
- European Group for Blood and Marrow Transplantation, Italy
| | - Peter Bardy
- Australian Bone Marrow Donor Registry, Australia
| | | | | | - Philip Bradley
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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23
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Unusual viral ligand with alternative interactions is presented by HLA-Cw4 in human respiratory syncytial virus-infected cells. Immunol Cell Biol 2010; 89:558-65. [PMID: 20975736 DOI: 10.1038/icb.2010.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Short viral antigens bound to human major histocompatibility complex (HLA) class I molecules are presented on infected cells. Vaccine development frequently relies on synthetic peptides to identify optimal HLA class I ligands. However, when natural peptides are analyzed, more complex mixtures are found. By immunoproteomics analysis, we identify in this study a physiologically processed HLA ligand derived from the human respiratory syncytial virus matrix protein that is very different from what was expected from studies with synthetic peptides. This natural HLA-Cw4 class I ligand uses alternative interactions to the anchor motifs previously described for its presenting HLA-Cw4 class I molecule. Finally, this octameric peptide shares its C-terminal core with the H-2D(b) nonamer ligand previously identified in the mouse model. These data have implications for the identification of antiviral cytotoxic T lymphocyte responses and for vaccine development.
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24
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Kumar P, Vahedi-Faridi A, Saenger W, Ziegler A, Uchanska-Ziegler B. Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity. Protein Sci 2009; 18:37-49. [PMID: 19177349 DOI: 10.1002/pro.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although there is X-ray crystallographic evidence that the interaction between major histocompatibility complex (MHC, in humans HLA) class I molecules and T cell receptors (TCR) or killer cell Ig-like receptors (KIR) may be accompanied by considerable changes in the conformation of selected residues or even entire loops within TCR or KIR, conformational changes between receptor-bound and -unbound MHC class I molecules of comparable magnitude have not been observed so far. We have previously determined the structure of the MHC class I molecule HLA-A1 bound to a melanoma antigen-encoding gene (MAGE)-A1-derived peptide in complex with a recombinant antibody fragment with TCR-like specificity, Fab-Hyb3. Here, we compare the X-ray structure of HLA-A1:MAGE-A1 with that complexed with Fab-Hyb3 to gain insight into structural changes of the MHC molecule that might be induced by the interaction with the antibody fragment. Apart from the expulsion of several water molecules from the interface, Fab-Hyb3 binding results in major rearrangements (up to 5.5 A) of heavy chain residues Arg65, Gln72, Arg145, and Lys146. Residue 65 is frequently and residues 72 and 146 are occasionally involved in TCR binding-induced conformational changes, as revealed by a comparison with MHC class I structures in TCR-liganded and -unliganded forms. On the other hand, residue 145 is subject to a reorientation following engagement of HLA-Cw4 and KIR2DL1. Therefore, conformational changes within the HLA-A1:MAGE-A1:Fab-Hyb3 complex include MHC residues that are also involved in reorientations in complexes with natural ligands, pointing to their central importance for the peptide-dependent recognition of MHC molecules.
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Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, Berlin 14195, Germany
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25
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Tong JC, Zhang ZH, August JT, Brusic V, Tan TW, Ranganathan S. In silico characterization of immunogenic epitopes presented by HLA-Cw*0401. Immunome Res 2007; 3:7. [PMID: 17705876 PMCID: PMC2040137 DOI: 10.1186/1745-7580-3-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 08/20/2007] [Indexed: 11/13/2022] Open
Abstract
Background HLA-C locus products are poorly understood in part due to their low expression at the cell surface. Recent data indicate that these molecules serve as major restriction elements for human immunodeficiency virus type 1 (HIV-1) cytotoxic T lymphocyte (CTL) epitopes. We report here a structure-based technique for the prediction of peptides binding to Cw*0401. The models were rigorously trained, tested and validated using experimentally verified Cw*0401 binding and non-binding peptides obtained from biochemical studies. A new scoring scheme facilitates the identification of immunological hot spots within antigens, based on the sum of predicted binding energies of the top four binders within a window of 30 amino acids. Results High predictivity is achieved when tested on the training (r2 = 0.88, s = 3.56 kJ/mol, q2 = 0.84, spress = 5.18 kJ/mol) and test (AROC = 0.93) datasets. Characterization of the predicted Cw*0401 binding sequences indicate that amino acids at key anchor positions share common physico-chemical properties which correlate well with existing experimental studies. Conclusion The analysis of predicted Cw*0401-binding peptides showed that anchor residues may not be restrictive and the Cw*0401 binding pockets may possibly accommodate a wide variety of peptides with common physico-chemical properties. The potential Cw*0401-specific T-cell epitope repertoires for HIV-1 p24gag and gp160gag glycoproteins are well distributed throughout both glycoproteins, with thirteen and nine immunological hot spots for HIV-1 p24gag and gp160gag glycoproteins respectively. These findings provide new insights into HLA-C peptide selectivity, indicating that pre-selection of candidate HLA-C peptides may occur at the TAP level, prior to peptide loading in the endoplasmic reticulum.
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Affiliation(s)
- Joo Chuan Tong
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
| | - Zong Hong Zhang
- Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore
| | - J Thomas August
- Department of Pharmacology and Molecular Sciences, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vladimir Brusic
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- Department of Chemistry and Biomolecular Sciences & Biotechnology Research Institute, Macquarie University, NSW 2109, Australia
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26
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Yun G, Tolar J, Yerich AK, Marsh SG, Robinson J, Noreen H, Blazar BR, Miller JS. A novel method for KIR-ligand typing by pyrosequencing to predict NK cell alloreactivity. Clin Immunol 2007; 123:272-80. [PMID: 17446137 PMCID: PMC1991282 DOI: 10.1016/j.clim.2007.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 12/09/2006] [Accepted: 01/23/2007] [Indexed: 10/23/2022]
Abstract
Studies have shown that KIR-ligand mismatching to predict NK cell alloreactivity may result in less relapse and better survival in patients with AML. KIR-ligands are distinguished by single nucleotide polymorphisms (SNPs) from HLA-B and HLA-C sequences. We hypothesized that pyrosequencing to determine KIR-ligand status by direct sequencing of the ligand epitope can be done as an alternative to high-resolution HLA-typing. Pyrosequencing is rapid and would be particularly useful in analysis of retrospective cohorts where high-resolution HLA-typing is unavailable or too expensive. To validate this assay, RNA and DNA from 70 clinical samples were tested for KIR-ligand by pyrosequencing. Primer binding to invariant regions without known SNPs was critical for KIR-ligand assignment by pyrosequencing to be in full concordance with high-resolution HLA-typing. Pyrosequencing is sensitive, specific, high-throughput, inexpensive, and can rapidly screen KIR-ligand status to evaluate potential alloreactive NK cell or transplant donors.
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Affiliation(s)
- Gong Yun
- Division of Medical, University of Minnesota Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Jakub Tolar
- Division of Pediatric Hematology-Oncology and Transplantation, University of Minnesota Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Anton K. Yerich
- Division of Pediatric Hematology-Oncology and Transplantation, University of Minnesota Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Steven G.E. Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, United Kingdom
- Royal Free & University College London Medical School, Royal Free Hospital, London NW3 2QG United Kingdom
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, London NW3 2QG, United Kingdom
| | - Harriet Noreen
- University of Minnesota Medical Cancer, Minneapolis, Minnesota
| | - Bruce R. Blazar
- Division of Pediatric Hematology-Oncology and Transplantation, University of Minnesota Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Jeffrey S. Miller
- Division of Medical, University of Minnesota Cancer Center, University of Minnesota, Minneapolis, Minnesota
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27
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Doytchinova IA, Guan P, Flower DR. EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics 2006; 7:131. [PMID: 16533401 PMCID: PMC1421443 DOI: 10.1186/1471-2105-7-131] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/13/2006] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The main processing pathway for MHC class I ligands involves degradation of proteins by the proteasome, followed by transport of products by the transporter associated with antigen processing (TAP) to the endoplasmic reticulum (ER), where peptides are bound by MHC class I molecules, and then presented on the cell surface by MHCs. The whole process is modeled here using an integrated approach, which we call EpiJen. EpiJen is based on quantitative matrices, derived by the additive method, and applied successively to select epitopes. EpiJen is available free online. RESULTS To identify epitopes, a source protein is passed through four steps: proteasome cleavage, TAP transport, MHC binding and epitope selection. At each stage, different proportions of non-epitopes are eliminated. The final set of peptides represents no more than 5% of the whole protein sequence and will contain 85% of the true epitopes, as indicated by external validation. Compared to other integrated methods (NetCTL, WAPP and SMM), EpiJen performs best, predicting 61 of the 99 HIV epitopes used in this study. CONCLUSION EpiJen is a reliable multi-step algorithm for T cell epitope prediction, which belongs to the next generation of in silico T cell epitope identification methods. These methods aim to reduce subsequent experimental work by improving the success rate of epitope prediction.
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Affiliation(s)
| | - Pingping Guan
- Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, UK
| | - Darren R Flower
- Edward Jenner Institute for Vaccine Research, Compton, RG20 7NN, UK
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28
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Thilo C, Berglund P, Applequist SE, Yewdell JW, Ljunggren HG, Achour A. Dissection of the interaction of the human cytomegalovirus-derived US2 protein with major histocompatibility complex class I molecules: prominent role of a single arginine residue in human leukocyte antigen-A2. J Biol Chem 2006; 281:8950-7. [PMID: 16452487 DOI: 10.1074/jbc.m507121200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus encodes several proteins that interfere with expression of major histocompatibility complex (MHC) class I molecules on the surface of infected cells. The unique short protein 2 (US2) binds to many MHC class I allomorphs in the endoplasmic reticulum, preventing cell surface expression of the class I molecule in question. The molecular interactions underlying US2 binding to MHC class I molecules and its allele specificity have not been fully clarified. In the present study, we first compared the sequences and the structures of US2 retained versus non-retained human leukocyte antigen (HLA) class I allomorphs to identify MHC residues of potential importance for US2 binding. On the basis of this analysis, 18 individual HLA-A2 mutants were generated and the ability of full-length US2 to bind wild-type and mutated HLA-A2 complexes was assessed. We demonstrate that Arg181 plays a critical role in US2-mediated inhibition of HLA-A2 cell surface expression. The structural comparison of all known crystal structures of HLA-A2 either alone, or in complex with T cell receptor or the CD8 co-receptor, indicates that binding of US2 to HLA-A2 results in a unique, large conformational change of the side chain of Arg181. However, although the presence of Arg181 seems to be a prerequisite for US2 binding to HLA-A2, it is not sufficient for binding to all MHC class I alleles.
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Affiliation(s)
- Claudia Thilo
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
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29
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Hwang SH, Cha CH, Kwon OJ, Heo YS, Hur SS, Lee MN, Oh HB. Novel HLA-Cw*06 allele, Cw*0612, identified by sequence-based typing. ACTA ACUST UNITED AC 2005; 66:330-1. [PMID: 16185332 DOI: 10.1111/j.1399-0039.2005.00460.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this report, we describe the identification of an human leucocyte antigen-Cw*06 (HLA-Cw*06) nucleotide sequence variant, a new HLA-Cw*0612. The new allele was detected during routine HLA typing by high-resolution sequence-based typing. Allele Cw*0612 showed one nucleotide difference with Cw*0602 at codon 153 (GCG-->ACG) resulting in an amino acid change from alanine to threonine.
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Affiliation(s)
- S-H Hwang
- Department of Laboratory Medicine, Asan Medical Center and University of Ulsan College of Medicine, Seoul, Korea
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30
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Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2005; 356:521-46. [PMID: 16368108 DOI: 10.1016/j.jmb.2005.11.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 11/16/2005] [Accepted: 11/17/2005] [Indexed: 11/29/2022]
Abstract
An ab initio structure prediction approach adapted to the peptide-major histocompatibility complex (MHC) class I system is presented. Based on structure comparisons of a large set of peptide-MHC class I complexes, a molecular dynamics protocol is proposed using simulated annealing (SA) cycles to sample the conformational space of the peptide in its fixed MHC environment. A set of 14 peptide-human leukocyte antigen (HLA) A0201 and 27 peptide-non-HLA A0201 complexes for which X-ray structures are available is used to test the accuracy of the prediction method. For each complex, 1000 peptide conformers are obtained from the SA sampling. A graph theory clustering algorithm based on heavy atom root-mean-square deviation (RMSD) values is applied to the sampled conformers. The clusters are ranked using cluster size, mean effective or conformational free energies, with solvation free energies computed using Generalized Born MV 2 (GB-MV2) and Poisson-Boltzmann (PB) continuum models. The final conformation is chosen as the center of the best-ranked cluster. With conformational free energies, the overall prediction success is 83% using a 1.00 Angstroms crystal RMSD criterion for main-chain atoms, and 76% using a 1.50 Angstroms RMSD criterion for heavy atoms. The prediction success is even higher for the set of 14 peptide-HLA A0201 complexes: 100% of the peptides have main-chain RMSD values < or =1.00 Angstroms and 93% of the peptides have heavy atom RMSD values < or =1.50 Angstroms. This structure prediction method can be applied to complexes of natural or modified antigenic peptides in their MHC environment with the aim to perform rational structure-based optimizations of tumor vaccines.
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Affiliation(s)
- Theres Fagerberg
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
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31
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Sibilio L, Martayan A, Setini A, Fraioli R, Fruci D, Shabanowitz J, Hunt DF, Giacomini P. Impaired Assembly Results in the Accumulation of Multiple HLA-C Heavy Chain Folding Intermediates. THE JOURNAL OF IMMUNOLOGY 2005; 175:6651-8. [PMID: 16272320 DOI: 10.4049/jimmunol.175.10.6651] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Class I MHC H chains assemble with beta2-microglobulin (beta2m) and are loaded with peptide Ags through multiple folding steps. When free of beta2m, human H chains react with Abs to linear epitopes, such as L31. Immunodepletion and coimmunoprecipitation experiments, performed in this study, detected a preferential association of L31-reactive, beta2m-free H chains with calnexin in beta2m-defective cells, and with calreticulin and TAP in beta2m-expressing cells. In beta2m-defective cells, the accumulation of calnexin-bound H chains stoichiometrically exceeded their overall accumulation, a finding that supports both chaperoning preferences and distinct sorting abilities for different class I folds. No peptide species, in a mass range compatible with that of the classical class I ligands, could be detected by mass spectrometry of acidic eluates from L31-reactive HLA-Cw1 H chains. In vitro assembly experiments in TAP-defective T2 cells, and in cells expressing an intact Ag-processing machinery, demonstrated that L31 H chains are not only free of, but also unreceptive to, peptides. L31 and HC10, which bind nearly adjacent linear epitopes of the alpha1 domain alpha helix, reciprocally immunodepleted free HLA-C H chains, indicating the existence of a local un-/mis-folding involving the N-terminal end of the alpha1 domain alpha helix and peptide-anchoring residues of the class I H chain. Thus, unlike certain murine free H chains, L31-reactive H chains are not the immediate precursors of conformed class I molecules. A model inferring their precursor-product relationships with other known class I intermediates is presented.
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Affiliation(s)
- Leonardo Sibilio
- Laboratory of Immunology, Regina Elena Cancer Institute Centro della Ricerca Sperimentale, Rome, Italy
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32
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Doytchinova IA, Guan P, Flower DR. Identifiying human MHC supertypes using bioinformatic methods. THE JOURNAL OF IMMUNOLOGY 2004; 172:4314-23. [PMID: 15034046 DOI: 10.4049/jimmunol.172.7.4314] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Classification of MHC molecules into supertypes in terms of peptide-binding specificities is an important issue, with direct implications for the development of epitope-based vaccines with wide population coverage. In view of extremely high MHC polymorphism (948 class I and 633 class II HLA alleles) the experimental solution of this task is presently impossible. In this study, we describe a bioinformatics strategy for classifying MHC molecules into supertypes using information drawn solely from three-dimensional protein structure. Two chemometric techniques-hierarchical clustering and principal component analysis-were used independently on a set of 783 HLA class I molecules to identify supertypes based on structural similarities and molecular interaction fields calculated for the peptide binding site. Eight supertypes were defined: A2, A3, A24, B7, B27, B44, C1, and C4. The two techniques gave 77% consensus, i.e., 605 HLA class I alleles were classified in the same supertype by both methods. The proposed strategy allowed "supertype fingerprints" to be identified. Thus, the A2 supertype fingerprint is Tyr(9)/Phe(9), Arg(97), and His(114) or Tyr(116); the A3-Tyr(9)/Phe(9)/Ser(9), Ile(97)/Met(97) and Glu(114) or Asp(116); the A24-Ser(9) and Met(97); the B7-Asn(63) and Leu(81); the B27-Glu(63) and Leu(81); for B44-Ala(81); the C1-Ser(77); and the C4-Asn(77).
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Affiliation(s)
- Irini A Doytchinova
- Edward Jenner Institute for Vaccine Research, Compton, Berkshire, United Kingdom
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33
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Natarajan K, Dimasi N, Wang J, Mariuzza RA, Margulies DH. Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination. Annu Rev Immunol 2002; 20:853-85. [PMID: 11861620 DOI: 10.1146/annurev.immunol.20.100301.064812] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In contrast to T cell receptors, signal transducing cell surface membrane molecules involved in the regulation of responses by cells of the innate immune system employ structures that are encoded in the genome rather than generated by somatic recombination and that recognize either classical MHC-I molecules or their structural relatives (such as MICA, RAE-1, or H-60). Considerable progress has recently been made in our understanding of molecular recognition by such molecules based on the determination of their three-dimensional structure, either in isolation or in complex with their MHC-I ligands. Those best studied are the receptors that are expressed on natural killer (NK) cells, but others are found on populations of T cells and other hematopoietic cells. These molecules fall into two major structural classes, those of the immunoglobulin superfamily (KIRs and LIRs) and of the C-type lectin-like family (Ly49, NKG2D, and CD94/NKG2). Here we summarize, in a functional context, the structures of the murine and human molecules that have recently been determined, with emphasis on how they bind different regions of their MHC-I ligands, and how this allows the discrimination of tumor or virus-infected cells from normal cells of the host.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Animals
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Ly
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/metabolism
- Humans
- Killer Cells, Natural/immunology
- Lectins, C-Type
- Leukocyte Immunoglobulin-like Receptor B1
- Macromolecular Substances
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Models, Molecular
- Molecular Sequence Data
- Molecular Structure
- NK Cell Lectin-Like Receptor Subfamily D
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, KIR
- Receptors, KIR2DL1
- Receptors, NK Cell Lectin-Like
- Self Tolerance
- Sequence Homology, Amino Acid
- Signal Transduction
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Affiliation(s)
- Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, NIAID, NIH, Bethesda, Maryland 20892-1892, USA.
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34
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Fan QR, Long EO, Wiley DC. Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex. Nat Immunol 2001; 2:452-60. [PMID: 11323700 DOI: 10.1038/87766] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Inhibitory natural killer (NK) cell receptors down-regulate the cytotoxicity of NK cells upon recognition of specific class I major histocompatibility complex (MHC) molecules on target cells. We report here the crystal structure of the inhibitory human killer cell immunoglobulin-like receptor 2DL1 (KIR2DL1) bound to its class I MHC ligand, HLA-Cw4. The KIR2DL1-HLA-Cw4 interface exhibits charge and shape complementarity. Specificity is mediated by a pocket in KIR2DL1 that hosts the Lys80 residue of HLA-Cw4. Many residues conserved in HLA-C and in KIR2DL receptors make different interactions in KIR2DL1-HLA-Cw4 and in a previously reported KIR2DL2-HLA-Cw3 complex. A dimeric aggregate of KIR-HLA-C complexes was observed in one KIR2DL1-HLA-Cw4 crystal. Most of the amino acids that differ between human and chimpanzee KIRs with HLA-C specificities form solvent-accessible clusters outside the KIR-HLA interface, which suggests undiscovered interactions by KIRs.
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Affiliation(s)
- Q R Fan
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA
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35
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Baba E, Erskine R, Boyson JE, Cohen GB, Davis DM, Malik P, Mandelboim O, Reyburn HT, Strominger JL. N-linked carbohydrate on human leukocyte antigen-C and recognition by natural killer cell inhibitory receptors. Hum Immunol 2000; 61:1202-18. [PMID: 11163076 DOI: 10.1016/s0198-8859(00)00184-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The possible role of carbohydrate in the interaction of HLA-C with a human inhibitory natural Killer cell Immunoglobulin-like Receptor with two Ig domains, KIR2DL1, was investigated. Transfectants of 721.221 (a class I MHC-negative human B cell line) expressing only HLA-Cw4 or -Cw6 or their respective non-glycosylated mutants (N86Q, S88A) were made. The binding of a KIR2DL1-Ig fusion protein to the non-glycosylated mutant HLA-Cw4- or -Cw6-expressing cells was markedly decreased compared to the wild type-expressing cells. The ability to induce an inhibitory signal in the NK tumor line YTS transfected with KIR2DL1 was also impaired in the nonglycosylated mutant expressing cells. Furthermore, in a second functional assay, mutant HLA-Cw4 and -Cw6 molecules had impaired ability to induce signal transduction in BW cells expressing a KIR2DL1-CD3 zeta chain chimeric protein. Thus, the deletion of the N-linked glycosylation signal in HLA-Cw4 and -Cw6 greatly reduced recognition by KIR2DL1. Alternative interpretations of the data are discussed.
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MESH Headings
- Amino Acid Substitution/genetics
- Amino Acid Substitution/immunology
- Animals
- Antigens, CD/metabolism
- Asparagine/genetics
- COS Cells
- Carbohydrate Conformation/drug effects
- Carbohydrate Metabolism
- Carbohydrates/antagonists & inhibitors
- Cell Line, Transformed
- Cytotoxicity Tests, Immunologic
- Cytotoxicity, Immunologic/drug effects
- Cytotoxicity, Immunologic/genetics
- Glutamine/genetics
- Glycosylation/drug effects
- HLA-C Antigens/biosynthesis
- HLA-C Antigens/genetics
- HLA-C Antigens/metabolism
- Humans
- Immunoglobulins/genetics
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lectins, C-Type
- Membrane Glycoproteins/metabolism
- Mice
- NK Cell Lectin-Like Receptor Subfamily D
- Protein Binding/drug effects
- Protein Binding/genetics
- Protein Binding/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, KIR
- Receptors, KIR2DL1
- Receptors, Natural Killer Cell
- Recombinant Fusion Proteins/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- Swainsonine/pharmacology
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- E Baba
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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36
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Kozłowska A, Gorczyca W, Maćkiewicz Z, Wojciechowska I, Kuśnierczyk P. Octapeptide but not nonapeptide from HIV-1 p24gag protein upregulates cell surface HLA-C expression. HIV Med 2000; 1:200-4. [PMID: 11737349 DOI: 10.1046/j.1468-1293.2000.00029.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVES The HLA-Cw3 molecule has been reported to present peptides derived from HIV-1 p24gag protein to a cytotoxic T lymphocyte clone. We have shown previously that the synthetic octapeptide 145-152 derived from the p24gag sequence upregulated cell surface HLA-C expression on HLA-Cw*0303+ cells. Here, we examined the question of whether the nonapeptide 144-152 also exerts a similar effect. METHODS The HLA-Cw*0303+ B-LCL PAJ and control HLA-Cw3-negative cells B-LCL HAJ and T-LCL 500/C9 were used. HLA expression on peptide-pulsed and non-pulsed cells was evaluated using specific antibodies and flow cytofluorimetry. Binding of dansylated peptides onto different cell lines was measured spectrofluorimetrically. RESULTS The HIV-1 p24gag octapeptide upregulated cell surface HLA-C on PAJ (Cw*0303+) cells, whereas the nonapeptide did not. HLA-A2 expression was not affected by these peptides. Specificity of the effect of octapeptide was confirmed by the lack of HLA-C upregulation on HLA-Cw3- cells and by lower binding of dansylated peptide to the HLA-Cw3- cells HAJ and 500/C9. CONCLUSIONS The above results indicate that HLA-Cw*0303 preferentially binds the octapeptide rather than the nonapeptide derived from HIV-1 p24gag protein.
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Affiliation(s)
- A Kozłowska
- Laboratory of Immunogenetics and Laboratory of Signalling Proteins, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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37
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Maenaka K, Maenaka T, Tomiyama H, Takiguchi M, Stuart DI, Jones EY. Nonstandard peptide binding revealed by crystal structures of HLA-B*5101 complexed with HIV immunodominant epitopes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 165:3260-7. [PMID: 10975842 DOI: 10.4049/jimmunol.165.6.3260] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The crystal structures of the human MHC class I allele HLA-B*5101 in complex with 8-mer, TAFTIPSI, and 9-mer, LPPVVAKEI, immunodominant peptide epitopes from HIV-1 have been determined by x-ray crystallography. In both complexes, the hydrogen-bonding network in the N-terminal anchor (P1) pocket is rearranged as a result of the replacement of the standard tyrosine with histidine at position 171. This results in a nonstandard positioning of the peptide N terminus, which is recognized by B*5101-restricted T cell clones. Unexpectedly, the P5 peptide residues appear to act as anchors, drawing the peptides unusually deeply into the peptide-binding groove of B51. The unique characteristics of P1 and P5 are likely to be responsible for the zig-zag conformation of the 9-mer peptide and the slow assembly of B*5101. A comparison of the surface characteristics in the alpha1-helix C-terminal region for B51 and other MHC class I alleles highlights mainly electrostatic differences that may be important in determining the specificity of human killer cell Ig-like receptor binding.
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MESH Headings
- Amino Acid Motifs/immunology
- Animals
- Binding Sites/immunology
- Cell Line
- Computer Simulation
- Cross Reactions
- Crystallography, X-Ray
- Cytotoxicity Tests, Immunologic
- HIV-1/chemistry
- HIV-1/immunology
- HIV-1/metabolism
- HLA-B Antigens/chemistry
- HLA-B Antigens/metabolism
- HLA-B51 Antigen
- Humans
- Immunodominant Epitopes/chemistry
- Immunodominant Epitopes/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Macromolecular Substances
- Mice
- Models, Molecular
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding/immunology
- Protein Conformation
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/metabolism
- Receptors, KIR
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- K Maenaka
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, Oxford, United Kingdom.
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38
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Boyington JC, Motyka SA, Schuck P, Brooks AG, Sun PD. Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand. Nature 2000; 405:537-43. [PMID: 10850706 DOI: 10.1038/35014520] [Citation(s) in RCA: 307] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Target cell lysis is regulated by natural killer (NK) cell receptors that recognize class I MHC molecules. Here we report the crystal structure of the human immunoglobulin-like NK cell receptor KIR2DL2 in complex with its class I ligand HLA-Cw3 and peptide. KIR binds in a nearly orthogonal orientation across the alpha1 and alpha2 helices of Cw3 and directly contacts positions 7 and 8 of the peptide. No significant conformational changes in KIR occur on complex formation. The receptor footprint on HLA overlaps with but is distinct from that of the T-cell receptor. Charge complementarity dominates the KIR/HLA interface and mutations that disrupt interface salt bridges substantially diminish binding. Most contacts in the complex are between KIR and conserved HLA-C residues, but a hydrogen bond between Lys 44 of KIR2DL2 and Asn 80 of Cw3 confers the allotype specificity. KIR contact requires position 8 of the peptide to be a residue smaller than valine. A second KIR/HLA interface produced an ordered receptor-ligand aggregation in the crystal which may resemble receptor clustering during immune synapse formation.
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MESH Headings
- Amino Acid Sequence
- Crystallography, X-Ray
- Electrochemistry
- Escherichia coli
- HLA-C Antigens/chemistry
- HLA-C Antigens/immunology
- Humans
- Killer Cells, Natural/chemistry
- Killer Cells, Natural/immunology
- Ligands
- Major Histocompatibility Complex
- Models, Molecular
- Molecular Sequence Data
- Protein Binding
- Protein Conformation
- Receptor Aggregation
- Receptors, Antigen, T-Cell/immunology
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/immunology
- Receptors, KIR
- Receptors, KIR2DL2
- Recombinant Proteins/chemistry
- Recombinant Proteins/immunology
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Affiliation(s)
- J C Boyington
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
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39
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Abstract
NK cells recognize several HLA class Ib molecules employing both immunoglobulin-like (Ig-like) and C-type lectin receptors. The CD94/NKG2 and NKG2D lectin-like molecules, respectively, interact with HLA-E and MICA; CD94/NKG2A functions as an inhibitory receptor, while CD94/NKG2C and NKG2D trigger NK cell activity. HLA-E predominantly presents nonamers from the leader sequences of other class I molecules; a peptide derived from HLA-G1 constitutes the highest affinity ligand for both CD94/NKG2 receptors. Members of the Ig-like transcript (ILT) or leucocyte Ig-like receptor (LIR) family (ILT2 or LIR-1 and ILT4 or LIR-2), expressed by other leucocyte lineages, interact with a broad spectrum of HLA class Ia molecules and HLA-G1. Among Ig-like KIRs, the KIR2DL4 (p49) receptor has been shown to specifically recognize HLA-G1; this molecule displays an unusual hybrid structure, sharing features with inhibitory and triggering KIRs.
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Affiliation(s)
- M López-Botet
- Servicio de Inmunología, Hospital Universitario de la Princesa, Diego de Léon 62, Madrid, 28006, Spain
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40
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Affiliation(s)
- E O Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
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41
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Hansen T, Balendiran G, Solheim J, Ostrov D, Nathenson S. Structural features of MHC class I molecules that might facilitate alternative pathways of presentation. IMMUNOLOGY TODAY 2000; 21:83-8. [PMID: 10652466 DOI: 10.1016/s0167-5699(98)01426-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Comparisons of the structures of different mouse MHC class I molecules define how polymorphic residues determine the unique structural motif and atomic anchoring of their bound peptides. Here, Ted Hansen and colleagues speculate that quantitative differences in how class I molecules interact with peptide, beta2-microglobulin and molecular chaperones that facilitate peptide loading might determine their relative participation in different pathways of antigen presentation.
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Affiliation(s)
- T Hansen
- Washington University School of Medicine, St Louis, MO 63110, USA.
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42
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López-Botet M, Bellón T, Llano M, Navarro F, García P, de Miguel M. Paired inhibitory and triggering NK cell receptors for HLA class I molecules. Hum Immunol 2000; 61:7-17. [PMID: 10658973 DOI: 10.1016/s0198-8859(99)00161-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human natural killer (NK) cells specifically interact with major histocompatibility complex (MHC) class I molecules employing different receptor systems, shared with subsets of alphabeta and gammadelta T lymphocytes. Killer cell immunoglobulin-like receptors (KIRs) recognize groups of human leukocyte antigen (HLA) class Ia proteins displaying common structural features at the alpha-1 domain; among them, KIR2DL4 has been proposed to specifically interact with the class Ib molecule HLA-G1. Members of a related family of immunoglobulin (Ig)-like receptors (ILT2 or LIR-1 and ILT4 or LIR-2), expressed by other leukocyte lineages, interact with a broad spectrum of class Ia molecules and HLA-G1. On the other hand, CD94/NKG2-A(-C) and NKG2D lectin-like receptors, respectively, recognize the class Ib molecules HLA-E and MICA. A recurrent finding within the different receptor families is the existence of pairs of homologous molecules that often share the same ligands but display divergent functions. Inhibitory receptors tend to exhibit an affinity for HLA molecules higher than their activating counterparts. Recruitment of SH2 domain-bearing tyrosine phosphatases (SHP) by cytoplasmic phosphorylated immunoreceptor tyrosine-based inhibition motifs (ITIMs) is a crucial event for the inhibitory signalling pathway. By contrast, triggering receptors assemble with homodimers of immune tyrosine-based activation motif (ITAM)-bearing adaptor molecules (i.e., DAP12, CD3 xi) that engage tyrosine kinases (ZAP70 and syk).
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Affiliation(s)
- M López-Botet
- Servicio de Immunología, Hospital Universitario de la Princesa, Madrid, Spain.
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43
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Davis DM, Chiu I, Fassett M, Cohen GB, Mandelboim O, Strominger JL. The human natural killer cell immune synapse. Proc Natl Acad Sci U S A 1999; 96:15062-7. [PMID: 10611338 PMCID: PMC24773 DOI: 10.1073/pnas.96.26.15062] [Citation(s) in RCA: 320] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/1999] [Accepted: 10/22/1999] [Indexed: 01/31/2023] Open
Abstract
Inhibitory killer Ig-like receptors (KIR) at the surface of natural killer (NK) cells induced clustering of HLA-C at the contacting surface of target cells. In this manner, inhibitory immune synapses were formed as human NK cells surveyed target cells. At target/NK cell synapses, HLA-C/KIR distributed into rings around central patches of intercellular adhesion molecule-1/lymphocyte function-associated antigen-1, the opposite orientation to mature murine T cell-activating synapses. This organization of protein was stable for at least 20 min. Cells could support multiple synapses simultaneously, and clusters of HLA-C moved as NK cells crawled over target cells. Clustering required a divalent metal cation, explaining how metal chelators inhibit KIR function. Surprisingly, however, formation of inhibitory synapses was unaffected by ATP depletion and the cytoskeletal inhibitors, colchicine and cytochalsins B and D. Clearly, supramolecular organization within plasma membranes is critical for NK cell immunosurveillance.
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Affiliation(s)
- D M Davis
- Department of Molecular Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA 02143, USA
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44
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Abstract
During the past year, a plethora of structural information has provided detailed insights into the interactions between classical MHC class I molecules and their cognate receptors on T cells. Likewise, there have been major advances in our knowledge of the structures and functions of five nonclassical MHC-like molecules: HLA-DM (murine H2-M), HLA-E, HFE, ZAG and MIC-A.
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Affiliation(s)
- K Maenaka
- Structural Biology, Wellcome Trust Centre for Human Genetics, Headington, OX3 7BN, UK.
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