Back

Investigation of the Effects of N-Linked Glycans on the Stability of the Spike Protein in SARS-CoV-2 by Molecular Dynamics Simulations

Tekin, E. D.

2022-01-12 biophysics
10.1101/2022.01.07.475397 bioRxiv
Show abstract

We perform all-atom molecular dynamics simulations to study the effects of the N-linked glycans on the stability of the spike glycoprotein in SARS-CoV-2. After a 100 ns of simulation on the spike proteins without and with the N-linked glycans, we found that the presence of glycans increases the local stability in their vicinity; even though their effect on the full structure is negligible. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/475397v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@cb1c1dorg.highwire.dtl.DTLVardef@a2ecbeorg.highwire.dtl.DTLVardef@64db68org.highwire.dtl.DTLVardef@180a1aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

Matching journals

The top 9 journals account for 50% of the predicted probability mass.

1
The Journal of Chemical Physics
49 papers in training set
Top 0.1%
14.3%
2
Journal of Chemical Information and Modeling
207 papers in training set
Top 0.7%
8.4%
3
PLOS ONE
4510 papers in training set
Top 29%
6.3%
4
Physical Chemistry Chemical Physics
34 papers in training set
Top 0.1%
4.8%
5
The Journal of Physical Chemistry B
158 papers in training set
Top 0.3%
4.8%
6
Frontiers in Molecular Biosciences
100 papers in training set
Top 0.2%
4.1%
7
The Journal of Physical Chemistry Letters
58 papers in training set
Top 0.3%
3.9%
8
Journal of Chemical Theory and Computation
126 papers in training set
Top 0.4%
2.9%
9
Scientific Reports
3102 papers in training set
Top 46%
2.6%
50% of probability mass above
10
Journal of Biomolecular Structure and Dynamics
43 papers in training set
Top 0.5%
2.1%
11
Biophysics and Physicobiology
10 papers in training set
Top 0.1%
2.1%
12
ACS Omega
90 papers in training set
Top 1%
1.8%
13
Journal of Molecular Graphics and Modelling
16 papers in training set
Top 0.1%
1.7%
14
Viruses
318 papers in training set
Top 3%
1.7%
15
Biophysical Journal
545 papers in training set
Top 3%
1.7%
16
eLife
5422 papers in training set
Top 42%
1.7%
17
PLOS Computational Biology
1633 papers in training set
Top 16%
1.7%
18
Journal of Computational Chemistry
11 papers in training set
Top 0.1%
1.7%
19
International Journal of Molecular Sciences
453 papers in training set
Top 9%
1.5%
20
Physical Biology
43 papers in training set
Top 1%
1.3%
21
Computational and Structural Biotechnology Journal
216 papers in training set
Top 7%
1.1%
22
ACS Chemical Neuroscience
60 papers in training set
Top 2%
0.9%
23
Chemistry – A European Journal
13 papers in training set
Top 0.4%
0.9%
24
Molecules
37 papers in training set
Top 1%
0.9%
25
The European Physical Journal Plus
13 papers in training set
Top 0.7%
0.9%
26
Physica A: Statistical Mechanics and its Applications
10 papers in training set
Top 0.2%
0.9%
27
Biochemistry and Biophysics Reports
28 papers in training set
Top 1%
0.8%
28
Biophysical Chemistry
14 papers in training set
Top 0.1%
0.8%
29
Quantitative Biology
11 papers in training set
Top 0.6%
0.8%
30
Frontiers in Physics
20 papers in training set
Top 1.0%
0.7%