Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study.
Adv Protein Chem Struct Biol
; 131: 277-309, 2022.
Article
in English
| MEDLINE | ID: covidwho-1881585
ABSTRACT
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.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Spike Glycoprotein, Coronavirus
/
COVID-19
Type of study:
Case report
Limits:
Humans
Language:
English
Journal:
Adv Protein Chem Struct Biol
Journal subject:
Biology
/
Biochemistry
Year:
2022
Document Type:
Article
Affiliation country:
Bs.apcsb.2022.05.004
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