Journal of Cell Science,
Journal Year:
2023,
Volume and Issue:
136(5)
Published: Jan. 12, 2023
ABSTRACT
The
dynein-2
complex
must
be
transported
anterogradely
within
cilia
to
then
drive
retrograde
trafficking
of
the
intraflagellar
transport
(IFT)
machinery
containing
IFT-A
and
IFT-B
complexes.
Here,
we
screened
for
potential
interactions
between
complexes
found
multiple
among
subunits.
In
particular,
WDR60
(also
known
as
DYNC2I1)
DYNC2H1–DYNC2LI1
dimer
from
dynein-2,
IFT54
TRAF3IP1)
IFT57
contribute
dynein-2–IFT-B
interactions.
interacts
with
via
a
conserved
region
N-terminal
its
light
chain-binding
regions.
Expression
constructs
in
WDR60-knockout
(KO)
cells
revealed
that
truncation
mutants
lacking
IFT54-binding
site
fail
rescue
abnormal
phenotypes
WDR60-KO
cells,
such
aberrant
accumulation
IFT
around
ciliary
tip
on
distal
side
transition
zone.
However,
construct
specifically
just
substantially
restored
defects.
line
current
docking
model
anterograde
trains,
these
results
indicate
extensive
involving
subunits
participate
their
connection.
Bioinformatics Advances,
Journal Year:
2024,
Volume and Issue:
4(1)
Published: Jan. 1, 2024
Abstract
Summary
Network
biology
is
an
interdisciplinary
field
bridging
computational
and
biological
sciences
that
has
proved
pivotal
in
advancing
the
understanding
of
cellular
functions
diseases
across
systems
scales.
Although
been
around
for
two
decades,
it
remains
nascent.
It
witnessed
rapid
evolution,
accompanied
by
emerging
challenges.
These
stem
from
various
factors,
notably
growing
complexity
volume
data
together
with
increased
diversity
types
describing
different
tiers
organization.
We
discuss
prevailing
research
directions
network
biology,
focusing
on
molecular/cellular
networks
but
also
other
such
as
biomedical
knowledge
graphs,
patient
similarity
networks,
brain
social/contact
relevant
to
disease
spread.
In
more
detail,
we
highlight
areas
inference
comparison
multimodal
integration
heterogeneous
higher-order
analysis,
machine
learning
network-based
personalized
medicine.
Following
overview
recent
breakthroughs
these
five
areas,
offer
a
perspective
future
biology.
Additionally,
scientific
communities,
educational
initiatives,
importance
fostering
within
field.
This
article
establishes
roadmap
immediate
long-term
vision
Availability
implementation
Not
applicable.
PROTEOMICS,
Journal Year:
2022,
Volume and Issue:
22(19-20)
Published: June 10, 2022
Mass
spectrometry
(MS)
has
emerged
at
the
forefront
of
quantitative
proteomic
techniques.
Liquid
chromatography-mass
(LC-MS)
can
be
used
to
determine
abundances
proteins
and
peptides
in
complex
biological
samples.
Several
methods
have
been
developed
adapted
for
accurate
quantification
based
on
chemical
isotopic
labeling.
Among
various
labeling
techniques,
isobaric
tagging
approaches
rely
analysis
from
MS2-based
rather
than
MS1-based
quantification.
In
this
review,
we
will
provide
an
overview
several
tags
along
with
some
recent
developments
including
complementary
ion
tags,
improvements
sensitive
quantitation
analytes
lower
abundance,
strategies
increase
multiplexing
capabilities,
targeted
strategies.
We
also
discuss
limitations
alleviate
these
restrictions
through
bioinformatic
tools
data
acquisition
methods.
This
review
highlight
applications
biomarker
discovery
validation,
thermal
proteome
profiling,
cross-linking
structural
investigations,
single-cell
analysis,
top-down
proteomics,
different
molecules
neuropeptides,
glycans,
metabolites,
lipids,
while
providing
considerations
evaluations
each
application.
Essays in Biochemistry,
Journal Year:
2023,
Volume and Issue:
67(2), P. 215 - 228
Published: Feb. 3, 2023
Cross-linking
mass
spectrometry
has
become
an
established
technology
to
provide
structural
information
on
the
topology
and
dynamics
of
protein
complexes.
Readily
accessible
workflows
can
detailed
data
simplified
systems,
such
as
purified
However,
using
this
study
structure
complexes
in
situ,
organelles,
cells,
even
tissues,
is
still
a
technological
frontier.
The
complexity
these
systems
remains
considerable
challenge,
but
there
have
been
dramatic
improvements
sample
handling,
acquisition,
processing.
Here,
we
summarise
developments
describe
paths
towards
comprehensive
comparative
interactomes
by
cross-linking
spectrometry.
Molecular & Cellular Proteomics,
Journal Year:
2024,
Volume and Issue:
23(3), P. 100724 - 100724
Published: Jan. 22, 2024
We
propose
a
pipeline
that
combines
AlphaFold2
(AF2)
and
crosslinking
mass
spectrometry
(XL-MS)
to
model
the
structure
of
proteins
with
multiple
conformations.
The
consists
two
main
steps:
ensemble
generation
using
AF2
conformer
selection
XL-MS
data.
For
selection,
we
developed
scores—the
monolink
probability
score
(MP)
crosslink
(XLP)—both
which
are
based
on
residue
depth
from
protein
surface.
benchmarked
MP
XLP
large
dataset
decoy
structures
showed
our
scores
outperform
previously
scores.
then
tested
methodology
three
having
an
open
closed
conformation
in
Protein
Data
Bank:
Complement
component
3
(C3),
luciferase,
glutamine-binding
periplasmic
protein,
first
generating
ensembles
AF2,
were
screened
for
conformations
experimental
In
five
out
six
cases,
most
accurate
within
ensembles—or
1
Å
this
model—was
identified
crosslinks,
as
assessed
through
score.
remaining
case,
only
monolinks
(assessed
score)
successfully
these
results
further
improved
by
including
"occupancy"
monolinks.
This
serves
compelling
proof-of-concept
effectiveness
contrast,
assessment
was
able
identify
cases.
Our
highlight
complementarity
methods
like
XL-MS,
providing
reliable
metrics
assess
quality
predicted
models.
scoring
functions
mentioned
above
available
at
https://gitlab.com/topf-lab/xlms-tools.
Mass Spectrometry Reviews,
Journal Year:
2024,
Volume and Issue:
unknown
Published: May 14, 2024
Abstract
Protein–protein
interactions
(PPIs)
are
essential
for
numerous
biological
activities,
including
signal
transduction,
transcription
control,
and
metabolism.
They
play
a
pivotal
role
in
the
organization
function
of
proteome,
their
perturbation
is
associated
with
various
diseases,
such
as
cancer,
neurodegeneration,
infectious
diseases.
Recent
advances
mass
spectrometry
(MS)‐based
protein
interactomics
have
significantly
expanded
our
understanding
PPIs
cells,
techniques
that
continue
to
improve
terms
sensitivity,
specificity
providing
new
opportunities
study
diverse
systems.
These
differ
depending
on
type
interaction
being
studied,
each
approach
having
its
set
advantages,
disadvantages,
applicability.
This
review
highlights
recent
enrichment
methodologies
interactomes
before
MS
analysis
compares
unique
features
specifications.
It
emphasizes
prospects
further
improvement
potential
applications
advancing
knowledge
contexts.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Feb. 26, 2024
Abstract
Crimean-Congo
hemorrhagic
fever
virus
(CCHFV)
is
a
WHO
priority
pathogen.
Antibody-based
medical
countermeasures
offer
an
important
strategy
to
mitigate
severe
disease
caused
by
CCHFV.
Most
efforts
have
focused
on
targeting
the
viral
glycoproteins.
However,
glycoproteins
are
poorly
conserved
among
strains.
The
CCHFV
nucleocapsid
protein
(NP)
highly
between
Here,
we
investigate
protective
efficacy
of
monoclonal
antibody
NP.
We
find
that
anti-NP
(mAb-9D5)
protected
female
mice
against
lethal
infection
or
resulted
in
significant
delay
mean
time-to-death
succumbed
compared
isotype
control
animals.
Antibody
protection
independent
Fc-receptor
functionality
and
complement
activity.
bound
NP
from
several
strains
exhibited
robust
cross-protection
heterologous
strain
Afg09-2990.
Our
work
demonstrates
viable
target
for
antibody-based
therapeutics,
providing
another
direction
developing
immunotherapeutics
