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Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study

Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations...

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Autores principales: Coutinho, João Victor Paccini, Macedo-da-Silva, Janaina, Mule, Simon Ngao, Kronenberger, Thales, Rosa-Fernandes, Livia, Wrenger, Carsten, Palmisano, Giuseppe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181370/
https://www.ncbi.nlm.nih.gov/pubmed/35871894
http://dx.doi.org/10.1016/bs.apcsb.2022.05.004
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author Coutinho, João Victor Paccini
Macedo-da-Silva, Janaina
Mule, Simon Ngao
Kronenberger, Thales
Rosa-Fernandes, Livia
Wrenger, Carsten
Palmisano, Giuseppe
author_facet Coutinho, João Victor Paccini
Macedo-da-Silva, Janaina
Mule, Simon Ngao
Kronenberger, Thales
Rosa-Fernandes, Livia
Wrenger, Carsten
Palmisano, Giuseppe
author_sort Coutinho, João Victor Paccini
collection PubMed
description Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion.
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spelling pubmed-91813702022-06-10 Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study Coutinho, João Victor Paccini Macedo-da-Silva, Janaina Mule, Simon Ngao Kronenberger, Thales Rosa-Fernandes, Livia Wrenger, Carsten Palmisano, Giuseppe Adv Protein Chem Struct Biol Article Molecular Dynamics (MD) is a method used to calculate the movement of atoms and molecules broadly applied to several aspects of science. It involves computational simulation, which makes it, at first glance, not easily accessible. The rise of several automated tools to perform molecular simulations has allowed researchers to navigate through the various steps of MD. This enables to elucidate structural properties of proteins that could not be analyzed otherwise, such as the impact of glycosylation. Glycosylation dictates the physicochemical and biological properties of a protein modulating its solubility, stability, resistance to proteolysis, interaction partners, enzymatic activity, binding and recognition. Given the high conformational and compositional diversity of the glycan chains, assessing their influence on the protein structure is challenging using conventional analytical techniques. In this manuscript, we present a step-by-step workflow to build and perform MD analysis of glycoproteins focusing on the SPIKE glycoprotein of SARS-CoV-2 to appraise the impact of glycans in structure stabilization and antibody occlusion. Elsevier Inc. 2022 2022-06-09 /pmc/articles/PMC9181370/ /pubmed/35871894 http://dx.doi.org/10.1016/bs.apcsb.2022.05.004 Text en Copyright © 2022 Elsevier Inc. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Coutinho, João Victor Paccini
Macedo-da-Silva, Janaina
Mule, Simon Ngao
Kronenberger, Thales
Rosa-Fernandes, Livia
Wrenger, Carsten
Palmisano, Giuseppe
Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title_full Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title_fullStr Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title_full_unstemmed Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title_short Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study
title_sort glycoprotein molecular dynamics analysis: sars-cov-2 spike glycoprotein case study
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9181370/
https://www.ncbi.nlm.nih.gov/pubmed/35871894
http://dx.doi.org/10.1016/bs.apcsb.2022.05.004
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