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1.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(11): 1133-1135, 2019 Nov 10.
Artigo em Chinês | MEDLINE | ID: mdl-31703144

RESUMO

OBJECTIVE: To identify a novel human leukocyte antigen (HLA) B allele in a Chinese Han individual and construct its three-dimensional structure. METHODS: The initial HLA genotyping was performed by PCR-sequence-based typing (PCR-SBT). The ambiguous allele was confirmed with single-strand DNA sequencing. The DNA sequence was analyzed to identify the difference between the novel allele and its closest matching allele. Finally, the three-dimensional molecular structure of the novel allele was constructed using a Swiss-Model. RESULTS: One allele of the subject at the HLA-B locus was B*44:03:01, whilst the other was a novel allele which differed from the closest matching allele B*51:01:01:01 by nucleotide (nt) 329 A to C in exon 2, resulting in an amino acid change at codon 86 (p.Asn86Thr). CONCLUSION: A novel HLA-B allele has been identified and officially named as HLA-B*51:159 by the WHO Nomenclature Committee for Factors of the HLA System. The three-dimensional structure of B*51:159 was simulated.


Assuntos
Grupo com Ancestrais do Continente Asiático , Antígenos HLA-B/química , Antígenos HLA-B/genética , Alelos , Sequência de Bases , Humanos , Conformação Molecular , Análise de Sequência de DNA
2.
PLoS Pathog ; 15(9): e1008040, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31527904

RESUMO

To escape CD8+ T-cell immunity, human cytomegalovirus (HCMV) US11 redirects MHC-I for rapid ER-associated proteolytic degradation (ERAD). In humans, classical MHC-I molecules are encoded by the highly polymorphic HLA-A, -B and -C gene loci. While HLA-C resists US11 degradation, the specificity for HLA-A and HLA-B products has not been systematically studied. In this study we analyzed the MHC-I peptide ligands in HCMV-infected cells. A US11-dependent loss of HLA-A ligands was observed, but not of HLA-B. We revealed a general ability of HLA-B to assemble with ß2m and exit from the ER in the presence of US11. Surprisingly, a low-complexity region between the signal peptide sequence and the Ig-like domain of US11, was necessary to form a stable interaction with assembled MHC-I and, moreover, this region was also responsible for changing the pool of HLA-B ligands. Our data suggest a two-pronged strategy by US11 to escape CD8+ T-cell immunity, firstly, by degrading HLA-A molecules, and secondly, by manipulating the HLA-B ligandome.


Assuntos
Citomegalovirus/imunologia , Citomegalovirus/metabolismo , Antígenos HLA-B/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteínas Virais/metabolismo , Apresentação do Antígeno , Linhagem Celular , Citomegalovirus/genética , Degradação Associada com o Retículo Endoplasmático/imunologia , Antígenos HLA-A/metabolismo , Antígenos HLA-B/química , Células HeLa , Humanos , Evasão da Resposta Imune , Ligantes , Modelos Imunológicos , Modelos Moleculares , Domínios e Motivos de Interação entre Proteínas , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/genética , Proteínas Virais/química , Proteínas Virais/genética
3.
Contact Dermatitis ; 81(3): 174-183, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30957232

RESUMO

BACKGROUND: Over 4000 small chemicals have been identified as allergens capable of inducing skin sensitization. Many sensitizers are hypothesized to act as haptens producing novel antigens, which can be presented to T cells by human leukocyte antigens (HLAs). Recent studies suggest that some chemical allergens use hapten-independent mechanisms. OBJECTIVE: To determine whether molecular docking can identify HLA molecules that bind skin-sensitizing chemical allergens. METHODS: Structural models of HLA molecules were used as the basis for molecular docking of 22 chemical allergens. Allergens predicted to bind HLA-B*57:01 were tested for their ability to stimulate T cells by the use of proliferation and interferon-gamma enzyme-linked immunospot assays. RESULTS: Chemical allergens that did not satisfy the criteria for hapten activity in vitro were predicted to bind more strongly to common HLA isoforms than those with known hapten activity. HLA-B*57:01, which is an HLA allele required for drug hypersensitivity reactions, was predicted to bind several allergens, including benzyl benzoate, benzyl cinnamate, and benzyl salicylate. In in vitro T cell stimulation assays, benzyl salicylate and benzyl cinnamate were found to stimulate T cell responses from HLA-B*57:01 carriers. CONCLUSIONS: These data suggest that small-molecule skin sensitizers have the potential to interact with HLA, and show that T cell-based in vitro assays may be used to evaluate the immunogenicity of skin-sensitizing chemicals.


Assuntos
Alérgenos/química , Dermatite Alérgica de Contato/imunologia , Antígenos HLA-B/química , Haptenos/química , Perfumes/química , Alérgenos/imunologia , Alérgenos/farmacologia , Benzoatos/química , Benzoatos/farmacologia , Compostos de Benzil/química , Compostos de Benzil/farmacologia , Proliferação de Células , Células Cultivadas , Cinamatos/química , Cinamatos/farmacologia , Antígenos HLA-B/imunologia , Haptenos/imunologia , Humanos , Ativação Linfocitária/efeitos dos fármacos , Simulação de Acoplamento Molecular , Estrutura Molecular , Perfumes/farmacologia , Salicilatos/química , Salicilatos/farmacologia , Linfócitos T/fisiologia
4.
Front Immunol ; 10: 61, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30761133

RESUMO

The particular HLA class I variants an individual carries influences their resistance and susceptibility to a multitude of diseases. Expression level and variation in the peptide binding region correlates with, for example, a person's progression to AIDS after HIV infection. One factor which has not yet been addressed is whether or not different HLA class I proteins organize differently in the cell membrane on a nanoscale. Here, we examined the organization of three HLA-B allotypes (B*2705, B*5301, and B*5701) and two HLA-C allotypes (C*0602 and C*0702) in the membrane of 721.221 cells which otherwise lack expression of HLA-B or HLA-C. All these allotypes are ligands for the T cell receptor and leukocyte immunoglobulin-like receptors, but additionally, the HLA-B allotypes are ligands for the killer-cell immunoglobulin-like receptor family member KIR3DL1, HLA-C*0602 is a ligand for KIR2DL1, and HLA-C*0702 is a ligand for KIR2DL2/3. Using super-resolution microscopy, we found that both HLA-B and HLA-C formed more clusters and a greater proportion of HLA contributed to clusters, when expressed at lower levels. Thus, HLA class I organization is a covariate in genetic association studies of HLA class I expression level with disease progression. Surprisingly, we also found that HLA-C was more clustered than HLA-B when expression level was controlled. HLA-C consistently formed larger and more numerous clusters than HLA-B and a greater proportion of HLA-C contributed to clusters than for HLA-B. We also found that the organization of HLA class I proteins varied with cell type. T cells exhibited a particularly clustered organization of HLA class I while B cells expressed a more uniform distribution. In summary, HLA class I variants are organized differently in the cell surface membrane which may impact their functions.


Assuntos
Membrana Celular/metabolismo , Antígenos HLA-B/imunologia , Antígenos HLA-C/metabolismo , Sequência de Aminoácidos , Linfócitos B/imunologia , Linfócitos B/metabolismo , Cisteína/química , Imunofluorescência , Expressão Gênica , Antígenos HLA-B/química , Antígenos HLA-B/genética , Antígenos HLA-B/metabolismo , Antígenos HLA-C/química , Antígenos HLA-C/genética , Antígenos HLA-C/imunologia , Humanos , Sinapses Imunológicas/imunologia , Sinapses Imunológicas/metabolismo , Células Matadoras Naturais/imunologia , Células Matadoras Naturais/metabolismo , Ligação Proteica
5.
Nat Commun ; 9(1): 4693, 2018 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-30410026

RESUMO

Immunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes.


Assuntos
Antígenos HLA-B/genética , Peptídeos/metabolismo , Polimorfismo Genético , Proteoma/metabolismo , Motivos de Aminoácidos , Sequência de Aminoácidos , Sequência de Bases , Linhagem Celular , Antígenos HLA-B/química , Ligantes , Modelos Moleculares , Peptídeos/química , Ligação Proteica , Conformação Proteica , Estabilidade Proteica , Proteoma/química , Linfócitos T/metabolismo
6.
Int J Immunogenet ; 45(3): 143-145, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29676515

RESUMO

A novel allelic variant in HLA-B*40 lineage, HLA-B*40:298:02, has been identified in an individual of Han ethnicity afflicted with nasopharyngeal carcinoma in Hunan province, southern China. Following polymerase chain reaction-Sanger sequence-based typing (PCR-SBT), this new variant was further confirmed by two distinct strategies of cloning and sequencing. HLA-B*40:298:02 differs from HLA-B*40:298:01 by a single synonymous cytosine substitution at nucleotide position 26 (T→C) in exon 3, which corresponds to codon 99 of the mature HLA-B mRNA molecule. This new allele has an estimated frequency of 0.0002, in about 2,500 sequence-based typed subjects from the same population.


Assuntos
Alelos , Variação Genética , Antígenos HLA-B/genética , Sequência de Aminoácidos , Clonagem Molecular , Códon , Éxons , Antígenos HLA-B/química , Humanos , Masculino , Pessoa de Meia-Idade , Análise de Sequência de DNA
7.
Int J Immunogenet ; 45(3): 140-142, 2018 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29516629

RESUMO

Three new HLA class I alleles were described in the Spanish population. HLA-A*68:169 and -B*39:129 show one amino acid replacement at the α1-domain, compared to A*68:02 (P47 > L47) and -B*39:06 (S11 > A11), respectively. HLA-B*07:298 presents one nucleotide mutation within exon 1, resulting in a new amino acid position -14, L>Q, which has not been previously described in any HLA protein. Prediction of the B*07:298 signal peptide cleavage did not show significant differences in comparison with that obtained for the rest of HLA-B genes.


Assuntos
Alelos , Sequência de Bases , Antígenos HLA-A/genética , Antígenos HLA-B/genética , Antígeno HLA-B7/genética , Análise de Sequência de DNA , Sequência de Aminoácidos , Antígenos HLA-A/química , Antígenos HLA-B/química , Antígeno HLA-B7/química , Haplótipos , Humanos , Peptídeos/química
8.
Proteomics ; 18(12): e1700253, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29437277

RESUMO

The recognition of pathogen-derived peptides by T lymphocytes is the cornerstone of adaptive immunity, whereby intracellular antigens are degraded in the cytosol and short peptides assemble with class I human leukocyte antigen (HLA) molecules in the ER. These peptide-HLA complexes egress to the cell surface and are scrutinized by cytotoxic CD8+ T-cells leading to the eradication of the infected cell. Here, naturally presented HLA-B*57:01 bound peptides derived from the envelope protein of the human immunodeficiency virus (HIVenv) are identified. HIVenv peptides are present at a very small percentage of the overall HLA-B*57:01 peptidome (<0.1%) and both native and posttranslationally modified forms of two distinct HIV peptides are identified. Notably, a peptide bearing a natively encoded C-terminal tryptophan residue is also present in a modified form containing a kynurenine residue. Kynurenine is a major product of tryptophan catabolism and is abundant during inflammation and infection. Binding of these peptides at a molecular level and their immunogenicity in preliminary functional studies are examined. Modest immune responses are observed to the modified HIVenv peptide, highlighting a potential role for kynurenine-modified peptides in the immune response to HIV and other viral infections.


Assuntos
Linfócitos B/imunologia , Epitopos/imunologia , Produtos do Gene env/imunologia , Antígenos HIV/imunologia , HIV-1/imunologia , Antígenos HLA-B/imunologia , Processamento de Proteína Pós-Traducional , Linfócitos B/virologia , Células Cultivadas , Epitopos/metabolismo , Produtos do Gene env/metabolismo , Antígenos HIV/metabolismo , Infecções por HIV/imunologia , Infecções por HIV/virologia , Antígenos HLA-B/química , Antígenos HLA-B/metabolismo , Humanos
9.
J Virol ; 92(7)2018 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-29321314

RESUMO

HIV-1 downregulates human leukocyte antigen A (HLA-A) and HLA-B from the surface of infected cells primarily to evade CD8 T cell recognition. HLA-C was thought to remain on the cell surface and bind inhibitory killer immunoglobulin-like receptors, preventing natural killer (NK) cell-mediated suppression. However, a recent study found HIV-1 primary viruses have the capacity to downregulate HLA-C. The goal of this study was to assess the heterogeneity of HLA-A, HLA-B, and HLA-C downregulation among full-length primary viruses from six chronically infected and six newly infected individuals from transmission pairs and to determine whether transmitted/founder variants exhibit common HLA class I downregulation characteristics. We measured HLA-A, HLA-B, HLA-C, and total HLA class I downregulation by flow cytometry of primary CD4 T cells infected with 40 infectious molecular clones. Primary viruses mediated a range of HLA class I downregulation capacities (1.3- to 6.1-fold) which could differ significantly between transmission pairs. Downregulation of HLA-C surface expression on infected cells correlated with susceptibility to in vitro NK cell suppression of virus release. Despite this, transmitted/founder variants did not share a downregulation signature and instead were more similar to the quasispecies of matched donor partners. These data indicate that a range of viral abilities to downregulate HLA-A, HLA-B, and HLA-C exist within and between individuals that can have functional consequences on immune recognition.IMPORTANCE Subtype C HIV-1 is the predominant subtype involved in heterosexual transmission in sub-Saharan Africa. Authentic subtype C viruses that contain natural sequence variations throughout the genome often are not used in experimental systems due to technical constraints and sample availability. In this study, authentic full-length subtype C viruses, including transmitted/founder viruses, were examined for the ability to disrupt surface expression of HLA class I molecules, which are central to both adaptive and innate immune responses to viral infections. We found that the HLA class I downregulation capacity of primary viruses varied, and HLA-C downregulation capacity impacted viral suppression by natural killer cells. Transmitted viruses were not distinct in the capacity for HLA class I downregulation or natural killer cell evasion. These results enrich our understanding of the phenotypic variation existing among natural HIV-1 viruses and how that might impact the ability of the immune system to recognize infected cells in acute and chronic infection.


Assuntos
Infecções por HIV/imunologia , HIV-1/genética , Antígenos HLA-A/química , Antígenos HLA-B/química , Antígenos HLA-C/química , Interações Hospedeiro-Patógeno/imunologia , Evasão da Resposta Imune/imunologia , Infecções por HIV/transmissão , Infecções por HIV/virologia , Soropositividade para HIV , HIV-1/classificação , HIV-1/imunologia , Antígenos HLA-A/imunologia , Antígenos HLA-B/imunologia , Antígenos HLA-C/imunologia , Interações Hospedeiro-Patógeno/genética , Proteínas do Vírus da Imunodeficiência Humana/metabolismo , Humanos , Células Matadoras Naturais/imunologia , Células Matadoras Naturais/metabolismo , Linfócitos T/imunologia , Linfócitos T/metabolismo , Proteínas Virais Reguladoras e Acessórias/metabolismo , Produtos do Gene nef do Vírus da Imunodeficiência Humana/metabolismo
10.
HLA ; 91(2): 132-133, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29278462

RESUMO

Two novel HLA-B alleles, B*07:299 and B*35:350, were characterized by genomic full-length sequencing.


Assuntos
Alelos , Antígenos HLA-B/genética , Sequência de Aminoácidos , Antígenos HLA-B/química , Humanos , Domínios Proteicos
11.
J Mol Diagn ; 19(5): 742-754, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28732216

RESUMO

HLA-B*57:01 genotyping before abacavir (ABC) administration is a standard of care to avoid ABC-driven hypersensitivity reactions. Several HLA-B*57:01 tests have been developed, each with advantages and disadvantages. Some have limited accuracy, require special instrumentation, and/or are labor intensive and expensive. We developed a novel hydrolysis probe-based real-time PCR method of HLA-B*57:01 genotyping. Primer and probes were designed based on published sequence variations in exon 3 of HLA-B that distinguish HLA-B*57:01 from ABC-insensitive alleles such as HLA-B*57:03 and HLA-B*58:01. We designed PCR primers to amplify HLA-B*57:01 along with closely related alleles, such as HLA-B*57:03, directly from genomic DNA. Most ABC-insensitive alleles, including HLA-B*58:01, would not produce any products in the PCR reaction. Our hydrolysis probes enable differentiation of HLA-B*57:01 from the other amplified, but ABC-insensitive, alleles. In addition to using real-time PCR, we used restriction enzymes to generate differential digestion patterns that led to the development of an HLA-B*57:01 PCR-restriction fragment length polymorphism marker. When used to genotype a set of 75 selected clinical samples, our real-time PCR assay demonstrated 100% accuracy in distinguishing between the HLA-B*57:01-positive and -negative alleles when results were compared to those of sequence-specific oligonucleotide probe typing and reference laboratory testing. Our newly developed test will allow clinical laboratories with real-time PCR capabilities to perform HLA-B*57:01 genotyping in a timely and economical manner.


Assuntos
Alelos , Sondas de DNA , Técnicas de Genotipagem , Antígenos HLA-B/genética , Teste de Histocompatibilidade/métodos , Reação em Cadeia da Polimerase em Tempo Real/métodos , Sequência de Bases , Frequência do Gene , Genótipo , Antígenos HLA-B/química , Teste de Histocompatibilidade/normas , Humanos , Hidrólise , Reação em Cadeia da Polimerase em Tempo Real/normas , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Análise de Sequência de DNA
12.
Int J Mol Sci ; 18(7)2017 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-28686208

RESUMO

Adverse drug reactions are one of the leading causes of morbidity and mortality in health care worldwide. Human leukocyte antigen (HLA) alleles have been strongly associated with drug hypersensitivities, and the causative drugs have been shown to stimulate specific T cells at the sites of autoimmune destruction. The structural elements recognized by drug-specific T cell receptors (TCRs) in vivo are poorly defined. Drug-stimulated T cells express TCRs specific for peptide/HLA complexes, but the characteristics of peptides (sequence, or endogenous or exogenous origin) presented in the context of small molecule drugs are not well studied. Using HLA-B*57:01 mediated hypersensitivity to abacavir as a model system, this study examines structural similarities of HLA presented peptides recognized by drug-specific TCRs. Using the crystal structure of HLA-B*57:01 complexed with abacavir and an immunogenic self peptide, VTTDIQVKV SPT5a 976-984, peptide side chains exhibiting flexibility and solvent exposure were identified as potential drug-specific T cell recognition motifs. Viral sequences with structural motifs similar to the immunogenic self peptide were identified. Abacavir-specific T cell clones were used to determine if virus peptides presented in the context of abacavir stimulate T cell responsiveness. An abacavir-specific T cell clone was stimulated by VTQQAQVRL, corresponding to HSV1/2 230-238, in the context of HLA-B*57:01. These data suggest the T cell polyclonal response to abacavir consists of multiple subsets, including T cells that recognize self peptide/HLA-B*57:01 complexes and crossreact with viral peptide/HLA-B*57:01 complexes due to similarity in TCR contact residues.


Assuntos
Didesoxinucleosídeos/farmacologia , Linfócitos T/imunologia , Sequência de Aminoácidos , Cristalografia por Raios X , Epitopos/imunologia , Antígenos HLA-B/química , Antígenos HLA-B/imunologia , Herpes Simples/imunologia , Humanos , Peptídeos/química , Peptídeos/imunologia , Receptores de Antígenos de Linfócitos T/química , Receptores de Antígenos de Linfócitos T/imunologia , Linfócitos T/efeitos dos fármacos , Transfecção
14.
Cell Rep ; 19(7): 1394-1405, 2017 05 16.
Artigo em Inglês | MEDLINE | ID: mdl-28514659

RESUMO

HLA-B∗46:01 was formed by an intergenic mini-conversion, between HLA-B∗15:01 and HLA-C∗01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B∗46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B∗46:01 has a low-diversity peptidome that is distinct from those of its parents. A minority (21%) of HLA-B∗46:01 peptides, with common C-terminal characteristics, form ligands for KIR2DL3. The HLA-B∗46:01 peptidome is predicted to be enriched for peptide antigens derived from Mycobacterium leprae. Overall, the results indicate that the distinctive peptidome and functions of HLA-B∗46:01 provide carriers with resistance to leprosy, which drove its rapid rise in frequency in Southeast Asia.


Assuntos
Antígenos HLA-B/metabolismo , Peptídeos/metabolismo , Proteoma/metabolismo , Receptores KIR2DL3/metabolismo , Motivos de Aminoácidos , Citotoxicidade Imunológica , Antígenos HLA-B/química , Antígenos HLA-C , Humanos , Células Matadoras Naturais/imunologia , Ligantes , Modelos Biológicos , Ligação Proteica , Recombinação Genética/genética
15.
BMC Bioinformatics ; 18(1): 258, 2017 May 12.
Artigo em Inglês | MEDLINE | ID: mdl-28499414

RESUMO

BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, -B, and -DRB1 typing by HLAscan using data generated by NextGen were identical to those obtained using a Sanger sequencing-based method. We also applied HLAscan to a family dataset with various coverage depths generated on the Illumina HiSeq X-TEN platform. HLAscan identified allele types of HLA-A, -B, -C, -DQB1, and -DRB1 with 100% accuracy for sequences at ≥ 90× depth, and the overall accuracy was 96.9%. CONCLUSIONS: HLAscan, an alignment-based program that takes read distribution into account to determine true allele types, outperformed previously developed HLA typing tools. Therefore, HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences.


Assuntos
Antígenos HLA/genética , Teste de Histocompatibilidade/métodos , Alelos , Área Sob a Curva , Éxons , Genótipo , Antígenos HLA/química , Antígenos HLA/metabolismo , Antígenos HLA-A/química , Antígenos HLA-A/genética , Antígenos HLA-A/metabolismo , Antígenos HLA-B/química , Antígenos HLA-B/metabolismo , Cadeias HLA-DRB1/química , Cadeias HLA-DRB1/genética , Cadeias HLA-DRB1/metabolismo , Projeto HapMap , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Curva ROC , Análise de Sequência de DNA
16.
Mol Cell Proteomics ; 16(2): 181-193, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27920218

RESUMO

As aberrant protein phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify 256 unique phosphorylated ligands associated with HLA-B*40, -B*27, -B*39, or -B*07. Remarkably, these phosphopeptides showed similar molecular features. Besides the specific anchor motifs imposed by the binding groove of each allotype, the predominance of phosphorylation at peptide position 4 (P4) became strikingly evident, as was the enrichment of basic residues at P1. To determine the structural basis of this observation, we carried out a series of peptide binding assays and solved the crystal structures of HLA-B*40 in complex with a phosphorylated ligand or its nonphosphorylated counterpart. Overall, our data provide a clear explanation to the common motif found in the phosphopeptidomes associated to different HLA-B molecules. The high prevalence of phosphorylation at P4 is dictated by the presence of the conserved residue Arg62 in the heavy chain, a structural feature shared by most HLA-B alleles. In contrast, the preference for basic residues at P1 is allotype-dependent and might be linked to the structure of the A pocket. This molecular understanding of the presentation of phosphopeptides by HLA-B molecules provides a base for the improved prediction and identification of phosphorylated neo-antigens, as potentially used for cancer immunotherapy.


Assuntos
Antígenos HLA-B/química , Antígenos HLA-B/metabolismo , Peptídeos/química , Proteômica/métodos , Motivos de Aminoácidos , Linhagem Celular , Cristalografia por Raios X , Antígeno HLA-B40/química , Antígeno HLA-B40/metabolismo , Humanos , Modelos Moleculares , Peptídeos/análise , Fosforilação , Ligação Proteica
19.
HLA ; 87(5): 392-4, 2016 May.
Artigo em Inglês | MEDLINE | ID: mdl-26990239

RESUMO

HLA-B*40:167 has one nucleotide change from HLA-B*40:06:01:01 at nucleotide 388 where 106D is changed to H.


Assuntos
Alelos , Grupo com Ancestrais do Continente Asiático/genética , Antígenos HLA-B/genética , Sequência de Aminoácidos , Sequência de Bases , Éxons/genética , Antígenos HLA-B/química , Teste de Histocompatibilidade , Humanos
20.
J Chem Inf Model ; 56(1): 46-53, 2016 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-26633740

RESUMO

The recognition of peptide/MHC by T-cell receptors is one of the most important interactions in the adaptive immune system. A large number of computational studies have investigated the structural dynamics of this interaction. However, to date only limited attention has been paid to differences between the dynamics of peptide/MHC with the T-cell receptor bound and unbound. Here we present the first large-scale molecular dynamics simulation study of this type investigating HLA-B*08:01 in complex with the Epstein-Barr virus peptide FLRGRAYGL and all possible single-point mutations (n = 172). All of the simulations were performed with and without the LC 13 T-cell receptor for a simulation time of 100 ns, yielding 344 simulations and a total simulation time of 34 400 ns. Our study is 2 orders of magnitude larger than the average T-cell receptor/peptide/MHC molecular dynamics simulation study. This data set provides reliable insights into alterations of the peptide/MHC-I dynamics caused by the presence of the T-cell receptor. We found that simulations in the presence of T-cell receptors have more hydrogen bonds between the peptide and MHC, altered flexibility patterns in the MHC helices and the peptide, a lower MHC groove width range, and altered solvent-accessible surface areas. This indicates that without a T-cell receptor the MHC binding groove can open and close, while the presence of the T-cell receptor inhibits these breathing-like motions.


Assuntos
Antígenos HLA-B/metabolismo , Simulação de Dinâmica Molecular , Oligopeptídeos/metabolismo , Receptores de Antígenos de Linfócitos T/metabolismo , Sequência de Aminoácidos , Antígenos HLA-B/química , Herpesvirus Humano 4 , Dados de Sequência Molecular , Oligopeptídeos/química , Ligação Proteica , Conformação Proteica , Receptores de Antígenos de Linfócitos T/química , Solventes/química
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