Evidence map›Paper›PMID 35871894›Full record

ArticleAdvances in protein chemistry and structural biology2022

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

João Victor Paccini Coutinho, Janaina Macedo-da-Silva, Simon Ngao Mule, Thales Kronenberger, Livia Rosa-Fernandes, Carsten Wrenger, Giuseppe Palmisano

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Advances in protein chemistry and structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
3.0field-weighted citation impact, top 8% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed, 6 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 1 institution in 1 country.

João Victor Paccini CoutinhoDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Janaina Macedo-da-SilvaDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Simon Ngao MuleDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Thales KronenbergerDepartment of Internal Medicine VIII, University Hospital Tuebingen, Tuebingen, Germany; Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard-Karls-Universität, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany; Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), Tuebingen, Germany.
Livia Rosa-FernandesDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Carsten WrengerDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Giuseppe PalmisanoDepartment of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; Faculty of Science and engineering, Macquarie University, Sydney, NSW, Australia. Electronic address: palmisano.gp@gmail.com.
Universidade de São Paulo · BR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

COVID-19Spike Glycoprotein, CoronavirusGlycoproteinsHumansMolecular Dynamics SimulationPolysaccharidesProtein BindingSARS-CoV-2GlycoproteinsPolysaccharidesSpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2Antibody accessibilityAntigen-antibody interactionGlycansGlycoproteinsMolecular dynamics simulationProtein structureSARS-CoV-2Solvent accessibility

Identifiers

PMID35871894
PMCPMC9181370
OpenAlexW4286426673

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.