bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: June 15, 2023
Hydrogen/deuterium
exchange
mass
spectrometry
(HDX-MS)
can
provide
precise
analysis
of
a
protein’s
conformational
dynamics
across
varied
states,
such
as
heat-denatured
vs.
native
protein
structures,
localizing
regions
that
are
specifically
affected
by
conditional
changes.
Maximizing
sequence
coverage
provides
high
confidence
interest
were
located
HDX-MS,
but
one
challenge
for
complete
is
N-glycosylation
sites.
The
deuteration
glycopeptides
has
not
always
been
identified
in
previous
reports
HDX-MS
analyses,
causing
significant
gaps
heavily
glycosylated
proteins
and
uncertainty
structural
many
throughout
glycoprotein.
We
report
the
SARS-CoV-2
spike
ectodomain
its
trimeric
pre-fusion
form,
which
22
predicted
sites
per
monomer,
with
without
heat
treatment.
calculated
their
isotopic
shifts
from
deuteration.
Inclusion
deu-terated
increased
76%
to
84%,
demonstrated
had
deuterated,
improved
results
re-arrangements.
deuterated
improves
glycoproteins
viral
surface
antigens
cellular
receptors.
Abstract
Figure
Research Square (Research Square),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Sept. 9, 2024
Abstract
A
pandemic
of
acute
respiratory
disease
referred
to
as
COVID-19
has
been
caused
by
the
highly
infectious
and
transmissible
Severe
Acute
Respiratory
Syndrome
Coronavirus
2
(SARS-CoV-2),
which
threatened
human
health.
Although
SARS-CoV-2
RNA
found
in
wastewater
from
numerous
regions
different
countries
due
fecal
shedding
infected
individuals,
there
is
still
little
information
available
regarding
how
prevalent
it
other
water
matrices
especially
groundwater,
where
some
areas
rely
on
supply
drinking
water,
irrigation
farmlands,
purposes.
This
study
attempted
assess
presence
this
virus
genome
groundwater
samples
Tehran,
Iran.
These
were
collected
seasonally
12
sites
over
years
period
(2021–2023).
At
first,
a
adsorption-elution
(VIRADEL)
concentration
procedure
was
tested
utilizing
an
avian
coronavirus
(infectious
bronchitis
virus,
IBV)
process
control
followed
extraction.
Subsequently,
quantified
using
reverse
transcription-quantitative
polymerase
chain
reaction
(RT-qPCR)
detect
E
S
genes.
As
result,
detected
1
out
96
with
2/53
×
103
3/16
copies/l
for
genes,
respectively.
Furthermore,
positive
sample
subjected
semi-nested
PCR
targeting
partial
gene,
direct
sequencing,
phylogenetic
mutation
analysis.
BA.1
Omicron
only
identified
variant
during
study.
findings
show
important
water-based
epidemiology
monitor
at
community-level
subsequent
exposure,
even
when
prevalence
low.
medRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Oct. 26, 2023
Acute
kidney
injury
(AKI)
is
common
in
hospitalized
patients
with
SARS-CoV2
infection
despite
vaccination
and
leads
to
long-term
dysfunction.
However,
peripheral
blood
molecular
signatures
AKI
from
COVID-19
their
association
dysfunction
are
yet
unexplored.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Aug. 21, 2024
Abstract
Antibody
dependent
enhancement
(ADE)
is
a
serious
concern
in
vaccine
development.
The
canonical
ADE
pathways
are
on
the
fragment
crystallizable
(Fc)
region
of
antibody.
In
SARS-CoV-2
several
antibodies
have
been
discovered
that
inflict
vitro.
These
target
N-terminal
domain
(NTD)
spike
protein.
We
previously
proposed
these
NTD-targeting
infection-enhancing
(NIEAs)
cross-link
neighboring
proteins
via
their
NTDs,
and
this
results
decoupling
between
NTD
receptor
binding
(RBD),
facilitating
“RBD
down”
to
“up”
transition.
study
we
present
combination
molecular
dynamics
simulations
cryogenic
electron
microscopy
data
that,
together,
demonstrate
NIEAs
indeed
able
proteins,
cross-linking
RBD
domains.
findings
provide
support
for
an
Fc
independent
pathway
not
only
relevant
but
also
other
viruses
which
undergo
conformational
change
upon
host
cell
entry.
Royal Society of Chemistry eBooks,
Journal Year:
2024,
Volume and Issue:
unknown, P. 300 - 314
Published: Oct. 16, 2024
Glycosylation
is
one
of
the
most
common
and
complex
post-translational
modifications
proteins,
rendering
many
proteins
evasive
to
structural
analysis.
The
intrinsic
heterogeneity
flexibility
pose
major
challenges
for
traditional
elucidation
tools.
Hydrogen/deuterium
exchange
coupled
mass
spectrometry
(HDX–MS)
an
increasingly
widespread
tool
monitoring
protein
dynamics,
including
glycoproteins
their
interactions
in
fully
glycosylated
states.
Recent
advances
have
largely
alleviated
historical
applying
HDX–MS
enable
in-depth
characterization
even
pinpoint
local
effects
glycosylation.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: June 15, 2023
Hydrogen/deuterium
exchange
mass
spectrometry
(HDX-MS)
can
provide
precise
analysis
of
a
protein’s
conformational
dynamics
across
varied
states,
such
as
heat-denatured
vs.
native
protein
structures,
localizing
regions
that
are
specifically
affected
by
conditional
changes.
Maximizing
sequence
coverage
provides
high
confidence
interest
were
located
HDX-MS,
but
one
challenge
for
complete
is
N-glycosylation
sites.
The
deuteration
glycopeptides
has
not
always
been
identified
in
previous
reports
HDX-MS
analyses,
causing
significant
gaps
heavily
glycosylated
proteins
and
uncertainty
structural
many
throughout
glycoprotein.
We
report
the
SARS-CoV-2
spike
ectodomain
its
trimeric
pre-fusion
form,
which
22
predicted
sites
per
monomer,
with
without
heat
treatment.
calculated
their
isotopic
shifts
from
deuteration.
Inclusion
deu-terated
increased
76%
to
84%,
demonstrated
had
deuterated,
improved
results
re-arrangements.
deuterated
improves
glycoproteins
viral
surface
antigens
cellular
receptors.
Abstract
Figure
