TY - CHAP
T1 - Glycoprotein molecular dynamics analysis
T2 - SARS-CoV-2 spike glycoprotein case study
AU - Coutinho, João Victor Paccini
AU - Macedo-da-Silva, Janaina
AU - Mule, Simon Ngao
AU - Kronenberger, Thales
AU - Rosa-Fernandes, Livia
AU - Wrenger, Carsten
AU - Palmisano, Giuseppe
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Antibody accessibility
KW - Antigen-antibody interaction
KW - Glycans
KW - Glycoproteins
KW - Molecular dynamics simulation
KW - Protein structure
KW - SARS-CoV-2
KW - Solvent accessibility
UR - http://www.scopus.com/inward/record.url?scp=85131826439&partnerID=8YFLogxK
U2 - 10.1016/bs.apcsb.2022.05.004
DO - 10.1016/bs.apcsb.2022.05.004
M3 - Chapter
C2 - 35871894
AN - SCOPUS:85131826439
SN - 9780323992312
T3 - Advances in Protein Chemistry and Structural Biology
SP - 277
EP - 309
BT - Protein interaction networks
A2 - Donev, Rossen
PB - Elsevier Academic Press
CY - United States
ER -