Human Immunodeficiency virus type 1 subtype C external glycoproteins epitopes : in silico predictions

Detalhes bibliográficos
Autor(a) principal: Junqueira, Dennis Maletich
Data de Publicação: 2008
Outros Autores: Medeiros, Rubia Marília de
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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spelling 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
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