bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Авг. 7, 2024
Cross-linking
mass
spectrometry
(XL-MS)
is
a
powerful
technology
for
mapping
protein-protein
interactions
(PPIs)
at
the
systems-level.
By
covalently
connecting
pairs
of
proximal
residues,
cross-linking
reagents
provide
distance
restraints
to
infer
protein
conformations
and
interaction
interfaces.
While
binary
cross-links
have
been
remarkably
informative,
multimeric
can
offer
enhanced
spatial
resolution
facilitate
characterization
dynamic
heterogeneous
complexes.
However,
identification
remains
extremely
challenging
due
fragmentation
complexity
vast
expansion
database
search
space.
Here,
we
present
novel
trioxane-based
MS-cleavable
homotrifunctional
cross-linker
TSTO,
which
target
three
lysine
residues
simultaneously.
Owing
its
unique
structure
MS-cleavability,
TSTO
enables
fast
unambiguous
cross-linked
peptides
using
LC-MS
Mass Spectrometry Reviews,
Год журнала:
2024,
Номер
unknown
Опубликована: Май 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.
Abstract
Increasing
insights
into
how
sequence
motifs
in
intrinsically
disordered
regions
(IDRs)
provide
functions
underscore
the
need
for
systematic
motif
detection.
Contrary
to
structured
where
can
be
readily
identified
from
alignments,
rapid
evolution
of
IDRs
limits
usage
alignment‐based
tools
reliably
detecting
within.
Here,
we
developed
SHARK‐capture,
an
alignment‐free
detection
tool
designed
difficult‐to‐align
regions.
SHARK‐capture
innovates
on
word‐based
methods
by
flexibly
incorporating
amino
acid
physicochemistry
assess
similarity
without
requiring
rigid
definitions
equivalency
groups.
offers
consistently
strong
performance
a
benchmark,
with
superior
residue‐level
performance.
known
functional
across
orthologs
microtubule‐associated
zinc
finger
protein
BuGZ.
We
also
short
IDR
S.
cerevisiae
RNA
helicase
Ded1p,
which
experimentally
verified
capable
promoting
ATPase
activity.
Our
improved
allows
us
systematically
calculate
10,889
2695
yeast
and
it
as
resource.
most
precise
yet
identification
conserved
is
freely
available
Python
package
(
https://pypi.org/project/bio-shark/
)
https://git.mpi-cbg.de/tothpetroczylab/shark
.
Chemical Reviews,
Год журнала:
2024,
Номер
124(15), С. 9113 - 9135
Опубликована: Июль 15, 2024
The
incorporation
of
noncanonical
amino
acids
into
proteins
and
protein-based
materials
has
significantly
expanded
the
repertoire
available
protein
structures
chemistries.
Through
residue-specific
incorporation,
properties
can
be
globally
modified,
resulting
in
creation
novel
with
diverse
tailored
characteristics.
In
this
review,
we
highlight
recent
advancements
techniques
as
well
applications
engineered
materials.
Specifically,
discuss
their
utility
bio-orthogonal
acid
tagging
(BONCAT),
fluorescent
(FUNCAT),
threonine-derived
(THRONCAT),
cross-linking,
fluorination,
enzyme
engineering.
This
review
underscores
importance
a
tool
for
development
to
meet
research
industrial
needs.
European Journal of Cell Biology,
Год журнала:
2024,
Номер
103(2), С. 151393 - 151393
Опубликована: Янв. 24, 2024
The
ability
of
a
pathogen
to
survive
and
cause
an
infection
is
often
determined
by
specific
interactions
between
the
host
proteins.
Such
can
be
both
intra-
extracellular
may
define
outcome
infection.
There
are
range
innovative
biochemical,
biophysical
bioinformatic
techniques
currently
available
identify
protein-protein
(PPI)
pathogen.
However,
complexity
diversity
host-pathogen
PPIs
has
led
development
several
high
throughput
(HT)
that
enable
study
multiple
at
once
and/or
screen
samples
same
time,
in
unbiased
manner.
We
review
here
major
HT
laboratory-based
technologies
employed
for
host-bacterial
interaction
studies.
Journal of Proteome Research,
Год журнала:
2024,
Номер
23(7), С. 2332 - 2342
Опубликована: Май 24, 2024
Here,
we
present
FLiPPR,
or
FragPipe
LiP
(limited
proteolysis)
Processor,
a
tool
that
facilitates
the
analysis
of
data
from
limited
proteolysis
mass
spectrometry
(LiP-MS)
experiments
following
primary
search
and
quantification
in
FragPipe.
LiP-MS
has
emerged
as
method
can
provide
proteome-wide
information
on
protein
structure
been
applied
to
range
biological
biophysical
questions.
Although
be
carried
out
with
standard
laboratory
reagents
spectrometers,
analyzing
slow
poses
unique
challenges
compared
typical
quantitative
proteomics
workflows.
To
address
this,
leverage
then
process
its
output
FLiPPR.
FLiPPR
formalizes
specific
imputation
heuristic
carefully
uses
missing
report
most
significant
structural
changes.
Moreover,
introduces
merging
scheme
protein-centric
multiple
hypothesis
correction
scheme,
enabling
processed
sets
more
robust
less
redundant.
These
improvements
strengthen
statistical
trends
when
previously
published
are
reanalyzed
FragPipe/FLiPPR
workflow.
We
hope
will
lower
barrier
for
users
adopt
LiP-MS,
standardize
procedures
analysis,
systematize
facilitate
eventual
larger-scale
integration
data.
Journal of Proteome Research,
Год журнала:
2024,
Номер
23(8), С. 3269 - 3279
Опубликована: Фев. 9, 2024
Protein–protein
interactions
(PPIs)
are
fundamental
to
understanding
biological
systems
as
protein
complexes
the
active
molecular
modules
critical
for
carrying
out
cellular
functions.
Dysfunctional
PPIs
have
been
associated
with
various
diseases
including
cancer.
Systems-wide
PPI
analysis
not
only
sheds
light
on
pathological
mechanisms,
but
also
represents
a
paradigm
in
identifying
potential
therapeutic
targets.
In
recent
years,
cross-linking
mass
spectrometry
(XL-MS)
has
emerged
powerful
tool
defining
endogenous
of
networks.
While
proteome-wide
studies
performed
cell
lysates,
intact
cells
and
tissues,
applications
XL-MS
clinical
samples
reported.
this
study,
we
adopted
DSBSO-based
vivo
platform
map
interaction
landscapes
from
two
breast
cancer
patient-derived
xenograft
(PDX)
models.
As
result,
generated
PDX
network
comprising
2,557
human
proteins
identified
unique
subtypes.
Interestingly,
most
observed
differences
correlated
well
abundance
changes
determined
by
TMT-based
proteome
quantitation.
Collectively,
work
demonstrated
feasibility
samples,
established
an
analytical
workflow
tissue
that
can
be
generalized
mapping
patient
future
dissect
disease-relevant
