bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 16, 2024
Abstract
Electron
cryomicroscopy
(cryo-EM)
has
recently
allowed
determination
of
near-atomic
resolution
structures
membrane
proteins
and
protein
complexes
embedded
in
lipid
vesicles.
However,
particle
selection
from
electron
micrographs
these
vesicles
can
be
challenging
due
to
the
strong
signal
contributed
bilayer.
This
challenge
often
requires
iterative
laborious
workflows
generate
a
dataset
high-quality
images
for
subsequent
analysis.
Here
we
present
Vesicle
Picker,
an
open-source
program
built
on
Segment
Anything
model.
Picker
enables
automatic
identification
cryo-EM
with
high
recall
precision.
It
then
exhaustively
selects
all
potential
locations,
either
at
perimeter
or
uniformly
over
surface
projection
vesicle.
The
is
designed
interface
cryoSPARC,
which
performs
both
upstream
micrograph
processing
downstream
single
image
We
demonstrate
Picker’s
utility
by
determining
high-resolution
map
vacuolar-type
ATPase
native
synaptic
(SVs)
identifying
additional
complex
SV
membrane.
ACS Applied Bio Materials,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 1, 2025
In-situ
fabrication
of
nucleic
acid
molecular
machines
in
biological
environments
is
desirable
for
smart
theranostic
applications.
However,
given
the
complex
nature
environments,
integration
multiple
functional
modules
into
a
coordinated
machine
remains
challenging.
Recent
advances
nanotechnology
offer
solutions
to
these
challenges.
Here,
we
outline
design
principles
acid–based
tailored
physiological
conditions,
drawing
on
recent
examples.
We
review
cutting-edge
technologies
that
facilitate
their
functionalization
settings,
particularly
presynthesis
modifications
using
unnatural
bases
and
postsynthesis
via
bioorthogonal
chemistry
noncovalent
interactions.
discuss
advantages
limitations
suggest
future
directions
overcome
existing
Biomolecules,
Journal Year:
2025,
Volume and Issue:
15(4), P. 525 - 525
Published: April 3, 2025
The
vacuolar-type
ATPase
(V-ATPase)
is
a
multi-subunit
enzyme
complex
that
maintains
lysosomal
acidification,
critical
process
for
cellular
homeostasis.
By
controlling
the
pH
within
lysosomes,
V-ATPase
contributes
to
overall
homeostasis,
helping
maintain
balance
between
degradation
and
synthesis
of
components.
Dysfunction
impairs
leading
accumulation
undigested
materials
contributing
various
diseases,
including
cardiovascular
diseases
(CVDs)
like
atherosclerosis
myocardial
disease.
Furthermore,
V-ATPase's
role
in
function
suggests
potential
therapeutic
strategies
targeting
this
mitigate
disease
progression.
Understanding
mechanisms
by
which
influences
pathology
essential
developing
novel
treatments
aimed
at
improving
outcomes
patients
with
heart
vascular
diseases.
Journal of Biological Chemistry,
Journal Year:
2025,
Volume and Issue:
unknown, P. 108381 - 108381
Published: March 1, 2025
V-ATPases
are
highly
conserved
ATP-driven
rotary
proton
pumps
found
widely
among
eukaryotes
that
composed
of
two
subcomplexes:
V1
and
V0.
V-ATPase
activity
is
regulated
in
part
through
reversible
disassembly,
during
which
physically
separates
from
V0
both
subcomplexes
become
inactive.
Reassociation
to
reactivates
the
complex
for
pumping
organelle
acidification.
reassembly
S.
cerevisiae
requires
RAVE
(Rav1,
Rav2,
Skp1)
higher
eukaryotes,
including
humans,
utilize
Rabconnectin-3
complex.
Mammalian
has
subunits:
Rabconnectin-3α
Rabconnectin-3β.
isoforms
homologous
Rav1,
but
there
no
known
Rav2
homolog
molecular
basis
interaction
between
β
subunits
unknown.
We
identified
ROGDI
as
a
novel
subunit.
mutations
cause
Kohlschutter-Tonz
syndrome,
an
epileptic
encephalopathy
with
amelogenesis
imperfecta
parallels
V-ATPase-related
disease.
shares
extensive
structural
homology
yeast
can
functionally
replace
yeast.
binds
N-terminal
domains
α
β,
similar
binding
Rav1.
Molecular
modeling
suggests
may
bridge
subunits.
co-immunoprecipitates
detergent-solubilized
lysates
present
them
immunopurified
lysosomes
mammalian
cells.
In
immunofluorescence
microscopy,
partially
localizes
acidic,
perinuclear
lysosomes.
The
discovery
interactor
sheds
new
light
on
syndrome
mechanisms
behind
regulation.
Proceedings of the National Academy of Sciences,
Journal Year:
2025,
Volume and Issue:
122(13)
Published: March 25, 2025
F-type
ATP
synthase
(F
1
F
O
)
catalyzes
proton
motive
force-driven
synthesis
in
mitochondria,
chloroplasts,
and
bacteria.
Different
from
the
mitochondrial
bacterial
enzymes,
photosynthetic
organisms
have
evolved
diverse
structural
mechanistic
details
to
adapt
light-dependent
reactions.
Although
complete
structure
of
chloroplast
has
been
reported,
no
high-resolution
an
bacteria
available.
Here,
we
report
cryo-EM
structures
intact
functionally
competent
Chloroflexus
aurantiacus
(
Ca
),
a
filamentous
anoxygenic
phototrophic
bacterium
earliest
branch
organisms.
The
its
ADP-free
ADP-bound
forms
for
three
rotational
states
reveal
previously
unrecognized
architecture
synthases.
A
pair
peripheral
stalks
connect
head
through
dimer
δ-subunits,
associate
with
two
membrane-embedded
a-subunits
that
are
asymmetrically
positioned
outside
clamp
’s
c
10
-ring.
constitute
inlets
on
periplasmic
side
outlets
cytoplasmic
side,
endowing
unique
translocation
pathways
allow
more
protons
being
translocated
relative
single
a-subunit
.
Our
findings
deepen
understanding
mechanisms
synthases
suggest
innovative
strategies
modulating
their
activities
by
altering
number
a-subunit.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 9, 2024
Abstract
Imaging
of
endogenous
protein
complexes
in
their
native
membranes
can
reveal
protein-protein
interactions
that
are
lost
upon
detergent
solubilization.
To
investigate
the
mycobacterial
oxidative
phosphorylation
machinery,
we
prepared
inverted
membrane
vesicles
from
Mycobacterium
smegmatis
and
enriched
for
containing
interest
by
affinity
chromatography.
Electron
cryomicroscopy
(cryo-EM)
these
revealed
malate-quinone
oxidoreductase
(Mqo),
an
enzyme
Krebs
cycle,
physically
associates
with
electron
transport
chain
Complex
III
2
IV
(CIII
CIV
)
supercomplex.
Analysis
Mqo:CIII
interaction
shows
CIII
is
necessary
malate-driven,
but
not
NADH-
driven,
activity
oxygen
consumption.
Further,
association
Mqo
enables
transfer
malate
to
millisecond
kinetics.
Together,
findings
indicate
a
connection
between
cycle
respiration
directs
electrons
along
single
branch
chain.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: July 18, 2024
Vacuolar-type
ATPases
(V-ATPases)
are
membrane-embedded
proton
pumps
that
acidify
intracellular
compartments
in
almost
all
eukaryotic
cells.
Homologous
with
ATP
synthases,
these
multi-subunit
enzymes
consist
of
a
soluble
catalytic
V
