Molecular Biology of the Cell,
Год журнала:
2023,
Номер
34(6)
Опубликована: Март 15, 2023
Protein
phase
transitions
broadly
govern
protein
function
and
dysfunction.
However,
analyzing
the
consequences
of
specific
in
cells
is
hindered
by
low
throughput
limited
resolution
fluorescence
microscopy,
this
problem
compounded
for
proteins
with
complex
behavior
such
as
those
implicated
age-associated
neurodegenerative
diseases.
As
one
solution
to
problem,
we
incorporated
an
orthogonally
proxy
total
expression
adjust
effective
cell
volume
differences
a
flow
cytometric
assay
self-association-Distributed
Amphifluoric
FRET
(DAmFRET)-thereby
allowing
intracellular
saturating
concentrations
different
be
precisely
compared
single
experiments.
We
further
found
that
decreased
experiencing
proteotoxicity,
which
provided
simple
way
assign
toxicity
phases
ectopically
expressed
proteins.
Scientific Reports,
Год журнала:
2022,
Номер
12(1)
Опубликована: Июнь 23, 2022
AlphaFold
2
(AF2)
has
placed
Molecular
Biology
in
a
new
era
where
we
can
visualize,
analyze
and
interpret
the
structures
functions
of
all
proteins
solely
from
their
primary
sequences.
We
performed
AF2
structure
predictions
for
various
protein
systems,
including
globular
proteins,
multi-domain
protein,
an
intrinsically
disordered
(IDP),
randomized
two
larger
(>
1000
AA),
heterodimer
homodimer
complex.
Our
results
show
that
along
with
three
dimensional
(3D)
structures,
also
decodes
sequences
into
residue
flexibilities
via
both
predicted
local
distance
difference
test
(pLDDT)
scores
models,
aligned
error
(PAE)
maps.
PAE
maps
are
correlated
variation
(DV)
matrices
molecular
dynamics
(MD)
simulations,
which
reveals
predict
dynamical
nature
residues.
Here,
introduce
AF2-scores,
simply
derived
pLDDT
range
[0,
1].
found
most
large
complexes,
AF2-scores
highly
root
mean
square
fluctuations
(RMSF)
calculated
MD
simulations.
However,
IDP
do
not
correlate
RMSF
MD,
especially
IDP.
indicate
by
convey
information
flexibility,
i.e.,
dynamics.
Chemical Reviews,
Год журнала:
2022,
Номер
122(17), С. 14055 - 14065
Опубликована: Фев. 8, 2022
While
the
application
of
cryogenic
electron
microscopy
(cryo-EM)
to
helical
polymers
in
biology
has
a
long
history,
due
huge
number
macromolecular
assemblies
viruses,
bacteria,
archaea,
and
eukaryotes,
use
cryo-EM
study
synthetic
soft
matter
noncovalent
been
much
more
limited.
This
mainly
lack
familiarity
with
materials
science
chemistry
communities,
contrast
fact
that
was
developed
as
biological
technique.
Nevertheless,
relatively
few
structures
self-assembled
peptide
nanotubes
ribbons
solved
at
near-atomic
resolution
by
have
demonstrated
should
be
method
choice
for
structural
analysis
filaments.
In
addition,
also
self-assembly
enormous
potential
polymorphism,
something
may
obscured
techniques
such
scattering
spectroscopy.
These
revealed
how
far
we
currently
are
from
being
able
predict
structure
these
their
chaotic
behavior.
Angewandte Chemie International Edition,
Год журнала:
2023,
Номер
62(25)
Опубликована: Март 6, 2023
The
accumulation
of
the
amyloid-β
peptides
(Aβ)
is
central
to
development
Alzheimer's
disease.
mechanism
by
which
Aβ
triggers
a
cascade
events
that
leads
dementia
topic
intense
investigation.
self-associates
into
series
complex
assemblies
with
different
structural
and
biophysical
properties.
It
interaction
these
oligomeric,
protofibril
fibrillar
lipid
membranes,
or
membrane
receptors,
results
in
permeability
loss
cellular
homeostasis,
key
event
disease
pathology.
can
have
an
array
impacts
on
reports
included:
carpeting
effect;
detergent
ion-channel
pore
formation.
Recent
advances
imaging
interactions
are
providing
clearer
picture
induced
disruption.
Understanding
relationship
between
structures
will
inform
therapeutics
targeting
cytotoxicity.
Cell,
Год журнала:
2023,
Номер
186(26), С. 5798 - 5811.e26
Опубликована: Дек. 1, 2023
Cryoelectron
microscopy
(cryo-EM)
has
provided
unprecedented
insights
into
amyloid
fibril
structures,
including
those
associated
with
disease.
However,
these
structures
represent
the
endpoints
of
long
assembly
processes,
and
their
relationship
to
fibrils
formed
early
in
is
unknown.
Consequently,
whether
different
architectures,
potentially
pathological
properties,
form
during
remains
Here,
we
used
cryo-EM
determine
at
times
vitro
fibrillation
a
disease-related
variant
human
islet
polypeptide
(IAPP-S20G).
Strikingly,
lag,
growth,
plateau
phases
have
new
forms
appearing
others
disappearing
as
proceeds.
A
time
course
wild-type
hIAPP
also
shows
changing
time,
suggesting
that
this
general
property
IAPP
assembly.
The
observation
transiently
populated
implications
for
understanding
mechanisms
potential
progression
Journal of Molecular Biology,
Год журнала:
2022,
Номер
434(7), С. 167466 - 167466
Опубликована: Янв. 22, 2022
The
presence
of
amyloid
fibrils
is
a
hallmark
more
than
50
human
disorders,
including
neurodegenerative
diseases
and
systemic
amyloidoses.
A
key
unresolved
challenge
in
understanding
the
involvement
disease
to
explain
relationship
between
individual
structural
polymorphs
fibrils,
potentially
mixed
populations,
specific
pathologies
with
which
they
are
associated.
Although
cryo-electron
microscopy
(cryo-EM)
solid-state
nuclear
magnetic
resonance
(ssNMR)
spectroscopy
methods
have
been
successfully
employed
recent
years
determine
structures
high
resolution
detail,
rely
on
ensemble
averaging
fibril
entire
sample
or
significant
subpopulations.
Here,
we
report
method
for
identification
imaged
by
atomic
force
(AFM)
integration
high-resolution
maps
determined
cryo-EM
comparative
AFM
image
analysis.
This
approach
was
demonstrated
using
hitherto
structurally
formed
vitro
from
fragment
tau
(297–391),
termed
‘dGAE’.
Our
established
unequivocally
that
dGAE
bear
no
heparin-induced
vitro.
Furthermore,
our
analysis
resulted
prediction
closely
related
paired
helical
filaments
(PHFs)
isolated
Alzheimer’s
(AD)
brain
tissue
characterised
cryo-EM.
These
results
show
utility
particle
AFM,
provide
workflow
how
data
can
be
incorporated
into
facilitate
an
integrated
polymorphism.
Chemical Society Reviews,
Год журнала:
2023,
Номер
52(14), С. 4603 - 4631
Опубликована: Янв. 1, 2023
This
review
highlights
the
design
principles
for
functional
amyloid
fibrillar
assemblies
from
an
engineering
perspective
as
well
through
lens
of
structural
insights.
ACS Chemical Neuroscience,
Год журнала:
2024,
Номер
15(5), С. 898 - 908
Опубликована: Фев. 26, 2024
Protein
misfolding
has
been
extensively
studied
in
the
context
of
neurodegenerative
disorders
and
systemic
amyloidoses.
Due
to
aggregation
proteins
being
highly
heterogeneous
generating
a
variety
structures,
growing
body
evidence
illustrates
numerous
ways
how
aggregates
contribute
progression
diseases
such
as
Alzheimer's
disease,
Parkinson's
prion
disorders.
Different
misfolded
species
same
protein,
commonly
referred
strains,
appear
play
significant
role
shaping
disease
clinical
phenotype
progression.
The
distinct
toxicity
profiles
various
underscore
their
importance.
Current
diagnostics
struggle
differentiate
among
these
strains
early
course.
This
review
explores
potential
spectral
fluorescence
approaches
illuminate
complexities
protein
pathology
discusses
applications
advanced
methods
detection
characterization
By
examining
spectrally
variable
probes,
current
data
analysis
approaches,
important
considerations
for
use
techniques,
this
aims
provide
an
overview
progress
made
field
highlights
directions
future
research.
Research Square (Research Square),
Год журнала:
2022,
Номер
unknown
Опубликована: Май 18, 2022
Abstract
AlphaFold
2
(AF2)
has
placed
Molecular
Biology
in
a
new
era
where
we
can
visualize,
analyze
and
interpret
the
structures
functions
of
all
proteins
solely
from
their
primary
sequences.
We
performed
AF2
structure
predictions
for
various
protein
systems,
including
globular
proteins,
multi-domain
protein,
an
intrinsically
disordered
(IDP),
randomized
two
larger
(>
1000
AA),
heterodimer
homodimer
complex.
Our
results
show
that
along
with
three
dimensional
(3D)
structures,
also
decodes
sequences
into
residue
flexibilities
via
both
predicted
local
distance
difference
test
(pLDDT)
scores
models,
aligned
error
(PAE)
maps.
PAE
maps
are
correlated
variation
(DV)
matrices
molecular
dynamics
(MD)
simulations,
which
reveals
predict
dynamical
nature
residues.
Here,
introduce
AF2-scores,
simply
derived
pLDDT
range
[0,
1].
found
good
multisequence
alignment
(MSA)
depths,
large
complexes,
AF2-scores
highly
root
mean
square
fluctuations
(RMSF)
calculated
MD
simulations.
For
little
or
no
MSA
hits
(the
IDP
protein),
do
not
correlate
RMSF
MD,
especially
(IDPs).
indicate
by
convey
information
flexibility,
i.e.,
dynamics.
Frontiers in Molecular Biosciences,
Год журнала:
2023,
Номер
10
Опубликована: Март 29, 2023
Aberrant
aggregation
of
the
transactive
response
DNA-binding
protein
(TDP-43)
is
associated
with
several
lethal
neurodegenerative
diseases,
including
amyotrophic
lateral
sclerosis
and
frontotemporal
dementia.
Cytoplasmic
neuronal
inclusions
TDP-43
are
enriched
in
various
fragments
low-complexity
C-terminal
domain
different
neurotoxicity.
Here
we
dissect
structural
basis
polymorphism
using
magic-angle
spinning
solid-state
NMR
spectroscopy
combination
electron
microscopy
Fourier-transform
infrared
spectroscopy.
We
demonstrate
that
fragments,
namely
TDP-13
(TDP-43300-414),
TDP-11
(TDP-43300-399),
TDP-10
(TDP-43314-414),
adopt
distinct
polymorphic
structures
their
amyloid
fibrillar
state.
Our
work
demonstrates
removal
less
than
10%
sequence
at
N-
C-termini
generates
fibrils
comparable
macroscopic
features
but
local
arrangement.
It
highlights
assembly
mechanism
TDP-43,
addition
to
hydrophobic
region,
also
driven
by
complex
interactions
involving
aggregation-prone
segments
a
potential
source
polymorphism.