Reversal of the unique Q493R mutation increases the affinity of Omicron S1-RBD for ACE2
Computational and Structural Biotechnology Journal,
Год журнала:
2023,
Номер
21, С. 1966 - 1977
Опубликована: Янв. 1, 2023
The
SARS-CoV-2
Omicron
variant
containing
15
mutations,
including
the
unique
Q493R,
in
spike
protein
receptor
binding
domain
(S1-RBD)
is
highly
infectious.
While
comparison
with
previously
reported
mutations
provide
some
insights,
mechanism
underlying
increased
infections
and
impact
of
reversal
Q493R
mutation
seen
BA.4,
BA.5,
BA.2.75,
BQ.1
XBB
lineages
not
yet
completely
understood.
Here,
using
structural
modelling
molecular
dynamics
(MD)
simulations,
we
show
that
increases
affinity
S1-RBD
for
ACE2,
a
further
ACE2-S1-RBD
affinity.
Specifically,
performed
all
atom,
explicit
solvent
MD
simulations
modelled
structure
S1-RBD-ACE2
compared
trajectories
WT
complex
revealing
substantial
reduction
Cα-atom
fluctuation
hydrogen
bond
other
interactions.
Residue
level
analysis
revealed
an
alteration
interaction
between
several
residues
switch
ACE2
D38
from
Y449
to
mutated
R
residue
(Q493R)
complex.
Importantly,
Revertant
(Omicron
without
mutation)
enhancement
ACE2.
Thus,
results
presented
here
only
insights
into
infectious
potential
but
also
mechanistic
basis
will
aid
understanding
evolution.
Язык: Английский
Investigating the Therapeutic Ability of Novel Antimicrobial Peptide Dendropsophin 1 and Its Analogues through Membrane Disruption and Monomeric Pore Formation
Fahmida Rahman,
Subrata Halder,
Sadaqur Rahman
и другие.
The Journal of Physical Chemistry B,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 12, 2025
Antimicrobial
peptides
(AMPs)
are
an
alternative
source
of
antibiotics
that
fight
worldwide
antibiotic-resistant
catastrophes.
Dendropsophin
1
(Dc1)
is
a
recently
invented
novel
AMP
with
17
amino
acid
residues
obtained
from
the
screen
secretion
frog
named
Dendropsophus
columbianus.
Dc1
has
two
slightly
mutated
analogues,
namely,
Dc1.1
and
Dc1.2,
improved
cationicity
mean
amphipathic
moment
to
enhance
selective
toxicity
against
microorganisms.
Experimental
results
indicate
have
similar
antimicrobial
activity
Gram-negative
bacteria
Escherichia
coli
Gram-positive
Staphylococcus
aureus,
whereas
synthesized
peptide
Dc1.2
shown
wide
range
However,
molecular
level
details
peptide–membrane
interaction
corresponding
changes
in
structure
remain
elusive.
In
this
study,
we
investigate
bacterial
membrane
disruption
capability
these
AMPs
by
running
total
14.2
μs
long
dynamics
(MD)
simulations.
Our
findings
suggest
all
three
affect
upper
layer
different
degrees
disruption.
After
penetration,
retain
stable
α-helices
core
region,
indicating
potential
disrupt
second
layer.
secondary
analysis
shows
attains
extended
helical
regions
on
C-terminus,
suggesting
it
as
superior
candidate
among
analogues
pore
formation,
leading
cell
death.
To
speed
up
our
adopt
one-transmembrane
configuration
Dc1,
Dc1.1,
find
toroidal
pores
subsequent
water
leakage
for
Dc1.2.
Язык: Английский
The Omicron variant BA.2.86.1 of SARS- CoV-2 demonstrates an altered interaction network and dynamic features to enhance the interaction with the hACE2
Scientific Reports,
Год журнала:
2025,
Номер
15(1)
Опубликована: Фев. 22, 2025
Язык: Английский
Structural Evaluation of Interleukin-19 Cytokine and Interleukin-19-Bound Receptor Complex Using Computational Immuno-Engineering Approach
Targets,
Год журнала:
2024,
Номер
2(4), С. 385 - 395
Опубликована: Ноя. 19, 2024
Interleukin
19
(IL-19)
is
an
anti-inflammatory
cytokine
that
belongs
to
the
IL-10
family,
where
IL-20
and
IL-24
also
exist.
While
IL-19
share
some
comparable
structural
folds,
there
are
certain
divergences
in
their
N-terminal
ends.
To
date,
no
reported
receptors;
although,
it
has
been
suggested
literature
would
bind
lL-20
receptor
(IL-20R)
trigger
JAK-STAT
signaling
pathways.
The
present
report
examines
structure
of
its
complex
using
a
computational
approach.
Specifically,
postulated
modes
interactions
for
IL-20R
as
examined
on
basis
set
findings.
author
used
molecular
docking
dynamics
simulation
generate
3D
model
with
IL-20R.
When
protein’s
crystal
not
available
literature,
predictive
modeling
often
employed
determine
structure.
assessment
can
be
based
various
factors,
which
include
stability
analysis
RMSD
calculations,
tracking
changes
time-based
secondary
structures
associated
Gibbs
energies,
ΔG.
Since
one
(referred
A
throughout
this
paper)
working
hypothesis
future
experiments,
explored
here
detail
check
stability,
subunit
interfaces,
binding
residues.
information
gathered
approach
potentially
help
design
specific
experiments
test
validity
protein
Additionally,
results
research
should
relevant
understanding
mechanisms
and,
eventually,
could
contribute
efforts
therapeutic
developments
targeted
therapy.
Язык: Английский
Molecular evolutionary analysis of the SARS-CoV-2 through the mutation analysis of Spike, Envelope and RdRp proteins
Genetics & Applications,
Год журнала:
2024,
Номер
8(1)
Опубликована: Июнь 18, 2024
COVID-19
pandemic,
caused
by
the
Severe
Acute
Respiratory
Syndrome
Coronavirus
2
(SARS-CoV-2),
was
declared
in
2020
World
Health
Organization.
New
mutations
have
been
identified,
leading
to
various
variants
of
this
virus,
including
Alpha,
Beta,
Gamma,
Delta,
and
Omicron,
which
are
classified
as
concern
(VOCs)
raised
considerable
concerns
for
global
public
health.
Such
constant
spread
changes
genome
virus
require
continuous
monitoring.
This
research
focuses
on
evolution
SARS-CoV-2
through
a
detailed
presentation
viral
genome,
protein
structure
interpretation,
with
phylogenetic
characteristics
patterns.
We
obtained
sequence
data
from
European
region
focusing
S,
E,
RdRp
proteins
publicly
available
NCBI
database.
next
used
MEGA11
package
generate
multiple
alignments
create
trees.
The
SWISS-MODEL
server
connected
Protein
Data
Bank
tertiary
images
all
presented
paper.
Stability
studies
were
performed
via
MUpro
online
tool.
results
indicate
substantial
impact
Omicron
variant
relative
others,
particularly
concerning
alterations
observed
spike
(S)
protein,
is
crucial
infection
process.
Язык: Английский
Fast Viral Diagnostics: FTIR-Based Identification, Strain-Typing, and Structural Characterization of SARS-CoV-2
Analytical Chemistry,
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 31, 2024
Severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
has
triggered
an
ongoing
global
pandemic,
necessitating
rapid
and
accurate
diagnostic
tools
to
monitor
emerging
variants
preparedness
for
the
next
outbreak.
This
study
introduces
a
multidisciplinary
approach
combining
Fourier
Transform
Infrared
(FTIR)
microspectroscopy
Machine
learning
comprehensively
characterize
strain-type
SARS-CoV-2
variants.
FTIR
analysis
of
pharyngeal
swabs
from
different
pandemic
waves
revealed
distinct
vibrational
profiles,
particularly
in
nucleic
acid
protein
vibrations.
The
spectral
wavenumber
range
between
1150
1240
cm
Язык: Английский