Guidelines To Predict Binding Poses of Antibody−Integrin Complexes
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2020 |
| Outros Autores: | , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Institucional da FIOCRUZ (ARCA) |
| Texto Completo: | https://www.arca.fiocruz.br/handle/icict/45545 |
Resumo: | Fundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil. |
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Chaves, BeatrizSartori, Geraldo R.Vasconcelos, Disraeli C. A.Savino, WilsonCaffarena, Ernesto R.Almeida, Vinicius Cotta deSilva, João H. M. da2021-01-09T18:35:18Z2021-01-09T18:35:18Z2020CHAVES, Beatriz et al. Guidelines To Predict Binding Poses of Antibody−Integrin Complexes. ACS Omega, v. 5, p. 16379-16385, June 2020.2470-1343https://www.arca.fiocruz.br/handle/icict/4554510.1021/acsomega.0c00226engAmerican Chemical SocietyDiretrizesAnticorpos-integrin ComplexosPrever poses de vinculaçãoGuidelinesPredict Binding PosesAntibody−Integrin ComplexesGuidelines To Predict Binding Poses of Antibody−Integrin Complexesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil.Fundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil.Fundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa sobre o Timo. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Grupo de Modelagem Molecular e Biofísica Computacional. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa sobre o Timo. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil.Integrins are cell adhesion receptors that transmit bidirectional signals across the plasma membrane. They are noncovalently linked heterodimeric molecules consisting of two subunits and act as biomarkers in several pathologies. Thus, according to the increase of therapeutic antibody production, some efforts have been applied to produce anti-integrin antibodies. Here, we purposed to evaluate methods of generation and identification of the binding pose of integrin−antibody complexes, through protein− protein docking and molecular dynamics simulations, and propose a strategy to assure the confidence of the final model and avoid falsepositive poses. The results show that ClusPro and GRAMM-X were the best programs to generate the native pose of integrin−antibody complexes. Furthermore, we were able to recover and to ensure that the selected pose is the native one by using a simple rule. All complexes from ClusPro in which the first model had the lowest energy, at least 5% more negative than the second one, were correctly predicted. Therefore, our methodology seems to be efficient to avoid misranking of wrong poses for integrin−antibody complexes. In cases where the rule is inconclusive, we proposed the use of heated molecular dynamics to identify the native pose characterized by RMSDi <0.5 nm. We believe that the set of methods presented here helps in the rational design of anti-integrin antibodies, giving some insights on the development of new biopharmaceuticals.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/45545/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALWilsonSavino_ViniciusCAlmeida_etal_IOC_2020.pdfWilsonSavino_ViniciusCAlmeida_etal_IOC_2020.pdfapplication/pdf1606442https://www.arca.fiocruz.br/bitstream/icict/45545/2/WilsonSavino_ViniciusCAlmeida_etal_IOC_2020.pdfae13afdcc59a46cb3c0d04d287757fc1MD52TEXTWilsonSavino_ViniciusCAlmeida_etal_IOC_2020.pdf.txtWilsonSavino_ViniciusCAlmeida_etal_IOC_2020.pdf.txtExtracted 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| dc.title.pt_BR.fl_str_mv |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| title |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| spellingShingle |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes Chaves, Beatriz Diretrizes Anticorpos-integrin Complexos Prever poses de vinculação Guidelines Predict Binding Poses Antibody−Integrin Complexes |
| title_short |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| title_full |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| title_fullStr |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| title_full_unstemmed |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| title_sort |
Guidelines To Predict Binding Poses of Antibody−Integrin Complexes |
| author |
Chaves, Beatriz |
| author_facet |
Chaves, Beatriz Sartori, Geraldo R. Vasconcelos, Disraeli C. A. Savino, Wilson Caffarena, Ernesto R. Almeida, Vinicius Cotta de Silva, João H. M. da |
| author_role |
author |
| author2 |
Sartori, Geraldo R. Vasconcelos, Disraeli C. A. Savino, Wilson Caffarena, Ernesto R. Almeida, Vinicius Cotta de Silva, João H. M. da |
| author2_role |
author author author author author author |
| dc.contributor.author.fl_str_mv |
Chaves, Beatriz Sartori, Geraldo R. Vasconcelos, Disraeli C. A. Savino, Wilson Caffarena, Ernesto R. Almeida, Vinicius Cotta de Silva, João H. M. da |
| dc.subject.other.pt_BR.fl_str_mv |
Diretrizes Anticorpos-integrin Complexos Prever poses de vinculação |
| topic |
Diretrizes Anticorpos-integrin Complexos Prever poses de vinculação Guidelines Predict Binding Poses Antibody−Integrin Complexes |
| dc.subject.en.pt_BR.fl_str_mv |
Guidelines Predict Binding Poses Antibody−Integrin Complexes |
| description |
Fundação Oswaldo Cruz. Fiocruz Ceará. Grupo de Modelagem Computacional. Eusébio, CE, Brasil. |
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2020 |
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2020 |
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2021-01-09T18:35:18Z |
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2021-01-09T18:35:18Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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CHAVES, Beatriz et al. Guidelines To Predict Binding Poses of Antibody−Integrin Complexes. ACS Omega, v. 5, p. 16379-16385, June 2020. |
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https://www.arca.fiocruz.br/handle/icict/45545 |
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2470-1343 |
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10.1021/acsomega.0c00226 |
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CHAVES, Beatriz et al. Guidelines To Predict Binding Poses of Antibody−Integrin Complexes. ACS Omega, v. 5, p. 16379-16385, June 2020. 2470-1343 10.1021/acsomega.0c00226 |
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American Chemical Society |
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