Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions
Autor(a) principal: | |
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Data de Publicação: | 2008 |
Outros Autores: | |
Tipo de documento: | Trabalho de conclusão de curso |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFRGS |
Texto Completo: | http://hdl.handle.net/10183/158605 |
Resumo: | Subtype C human immunodeficiency vírus type 1 (HIV-1) is rapidly diversifying among populations, which display extensiva polymorphism of genes encoding class I human leukocyte antigen (HLA) proteins, as detected in different regions of the world. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes considering 128 subtype C externai glycoprotein gp120 sequences selected from GenBank were identified to A*0201, A*0301, A*1101 and 8*07 HLA alleles using Epijen software. NetChop allowed to predict proteasome cleavage followed by prediction of binding to transport associated with antigen processing on TapPred. Glycosylation and positively selected sites within epitope sequences were also observed. Furthermore, three-dimensional structures of subtype C gp120 were predicted from consensus sequences in PHYRE and the PYMOL software was used to verify positions occupied by conserved epitopes. Finally, we predicted discontinuous B cell epitopes in DiscoTope 1.2. There is a recognized evolutionary force of HIV-1 to escape from B cells and CTL responses mutating sites that can negatively select the viral population. ' These types of analyses could be useful to understand HIV-1 epidemiology associated with polymorphisms in HLA alleles frequent in a determined region. 1t is expected that such knowledge may provide additional support for vaccine development. |
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Junqueira, Dennis MaletichMedeiros, Rubia Marília deRohe, Paulo M.Almeida, Sabrina Esteves de MatosSpilki, Fernando Rosado2017-05-26T02:30:14Z2008http://hdl.handle.net/10183/158605000679420Subtype C human immunodeficiency vírus type 1 (HIV-1) is rapidly diversifying among populations, which display extensiva polymorphism of genes encoding class I human leukocyte antigen (HLA) proteins, as detected in different regions of the world. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes considering 128 subtype C externai glycoprotein gp120 sequences selected from GenBank were identified to A*0201, A*0301, A*1101 and 8*07 HLA alleles using Epijen software. NetChop allowed to predict proteasome cleavage followed by prediction of binding to transport associated with antigen processing on TapPred. Glycosylation and positively selected sites within epitope sequences were also observed. Furthermore, three-dimensional structures of subtype C gp120 were predicted from consensus sequences in PHYRE and the PYMOL software was used to verify positions occupied by conserved epitopes. Finally, we predicted discontinuous B cell epitopes in DiscoTope 1.2. There is a recognized evolutionary force of HIV-1 to escape from B cells and CTL responses mutating sites that can negatively select the viral population. ' These types of analyses could be useful to understand HIV-1 epidemiology associated with polymorphisms in HLA alleles frequent in a determined region. 1t is expected that such knowledge may provide additional support for vaccine development.application/pdfengHIV-1GlicoproteinasSubtype CBioinformaticsEpitopegp120HLAHuman Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictionsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/bachelorThesisUniversidade Federal do Rio Grande do SulInstituto de Ciências Básicas da SaúdePorto Alegre, BR-RS2008Ciências Biológicas: Ênfase Molecular, Celular e Funcional: Bachareladograduaçãoinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UFRGSinstname:Universidade Federal do Rio Grande do Sul (UFRGS)instacron:UFRGSORIGINAL000679420.pdf000679420.pdfTexto completo (inglês)application/pdf5293561http://www.lume.ufrgs.br/bitstream/10183/158605/1/000679420.pdf4644d47049fa6cf62d3d27279b2c1097MD51TEXT000679420.pdf.txt000679420.pdf.txtExtracted Texttext/plain62290http://www.lume.ufrgs.br/bitstream/10183/158605/2/000679420.pdf.txtac901cb335b51897a7dd6e808417f861MD5210183/1586052024-08-04 06:24:36.487535oai:www.lume.ufrgs.br:10183/158605Repositório de PublicaçõesPUBhttps://lume.ufrgs.br/oai/requestopendoar:2024-08-04T09:24:36Repositório Institucional da UFRGS - Universidade Federal do Rio Grande do Sul (UFRGS)false |
dc.title.pt_BR.fl_str_mv |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
title |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
spellingShingle |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions Junqueira, Dennis Maletich HIV-1 Glicoproteinas Subtype C Bioinformatics Epitope gp120 HLA |
title_short |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
title_full |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
title_fullStr |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
title_full_unstemmed |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
title_sort |
Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions |
author |
Junqueira, Dennis Maletich |
author_facet |
Junqueira, Dennis Maletich Medeiros, Rubia Marília de |
author_role |
author |
author2 |
Medeiros, Rubia Marília de |
author2_role |
author |
dc.contributor.author.fl_str_mv |
Junqueira, Dennis Maletich Medeiros, Rubia Marília de |
dc.contributor.advisor1.fl_str_mv |
Rohe, Paulo M. |
dc.contributor.advisor-co1.fl_str_mv |
Almeida, Sabrina Esteves de Matos Spilki, Fernando Rosado |
contributor_str_mv |
Rohe, Paulo M. Almeida, Sabrina Esteves de Matos Spilki, Fernando Rosado |
dc.subject.por.fl_str_mv |
HIV-1 Glicoproteinas |
topic |
HIV-1 Glicoproteinas Subtype C Bioinformatics Epitope gp120 HLA |
dc.subject.eng.fl_str_mv |
Subtype C Bioinformatics Epitope gp120 HLA |
description |
Subtype C human immunodeficiency vírus type 1 (HIV-1) is rapidly diversifying among populations, which display extensiva polymorphism of genes encoding class I human leukocyte antigen (HLA) proteins, as detected in different regions of the world. Broadly conserved HIV-1 cytotoxic T cell (CTL) epitopes considering 128 subtype C externai glycoprotein gp120 sequences selected from GenBank were identified to A*0201, A*0301, A*1101 and 8*07 HLA alleles using Epijen software. NetChop allowed to predict proteasome cleavage followed by prediction of binding to transport associated with antigen processing on TapPred. Glycosylation and positively selected sites within epitope sequences were also observed. Furthermore, three-dimensional structures of subtype C gp120 were predicted from consensus sequences in PHYRE and the PYMOL software was used to verify positions occupied by conserved epitopes. Finally, we predicted discontinuous B cell epitopes in DiscoTope 1.2. There is a recognized evolutionary force of HIV-1 to escape from B cells and CTL responses mutating sites that can negatively select the viral population. ' These types of analyses could be useful to understand HIV-1 epidemiology associated with polymorphisms in HLA alleles frequent in a determined region. 1t is expected that such knowledge may provide additional support for vaccine development. |
publishDate |
2008 |
dc.date.issued.fl_str_mv |
2008 |
dc.date.accessioned.fl_str_mv |
2017-05-26T02:30:14Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/bachelorThesis |
format |
bachelorThesis |
status_str |
publishedVersion |
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http://hdl.handle.net/10183/158605 |
dc.identifier.nrb.pt_BR.fl_str_mv |
000679420 |
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http://hdl.handle.net/10183/158605 |
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eng |
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eng |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
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