Nature Communications,
Год журнала:
2023,
Номер
14(1)
Опубликована: Янв. 24, 2023
Abstract
The
Zrt-/Irt-like
protein
(ZIP)
family
consists
of
ubiquitously
expressed
divalent
metal
transporters
critically
involved
in
maintaining
systemic
and
cellular
homeostasis
zinc,
iron,
manganese.
Here,
we
present
a
study
on
prokaryotic
ZIP
from
Bordetella
bronchiseptica
(BbZIP)
by
combining
structural
biology,
evolutionary
covariance,
computational
modeling,
variety
biochemical
assays
to
tackle
the
issue
transport
mechanism
which
has
not
been
established
for
family.
apo
state
structure
an
inward-facing
conformation
revealed
disassembled
site,
altered
inter-helical
interactions,
importantly,
rigid
body
movement
4-transmembrane
helix
(TM)
bundle
relative
other
TMs.
computationally
generated
biochemically
validated
outward-facing
model
slide
4-TM
bundle,
carries
site(s),
approximately
8
Å
toward
extracellular
side
against
static
TMs
mediate
dimerization.
These
findings
allow
us
conclude
that
BbZIP
is
elevator-type
transporter.
Annual Review of Biochemistry,
Год журнала:
2020,
Номер
89(1), С. 605 - 636
Опубликована: Июнь 20, 2020
ATP-binding
cassette
(ABC)
transporters
constitute
one
of
the
largest
and
most
ancient
protein
superfamilies
found
in
all
living
organisms.
They
function
as
molecular
machines
by
coupling
ATP
binding,
hydrolysis,
phosphate
release
to
translocation
diverse
substrates
across
membranes.
The
range
from
vitamins,
steroids,
lipids,
ions
peptides,
proteins,
polysaccharides,
xenobiotics.
ABC
undergo
substantial
conformational
changes
during
substrate
translocation.
A
comprehensive
understanding
their
inner
workings
thus
requires
linking
these
structural
rearrangements
different
functional
state
transitions.
Recent
advances
single-particle
cryogenic
electron
microscopy
have
not
only
delivered
crucial
information
on
architecture
several
medically
relevant
supramolecular
assemblies,
including
ATP-sensitive
potassium
channel
peptide-loading
complex,
but
also
made
it
possible
explore
entire
space
nanomachines
under
turnover
conditions
thereby
gain
detailed
mechanistic
insights
into
mode
action.
Biologics,
Год журнала:
2021,
Номер
Volume 15, С. 353 - 361
Опубликована: Авг. 1, 2021
Abstract:
Clustered
regularly
interspaced
short
palindromic
repeat
(CRISPR)
and
their
associated
protein
(Cas-9)
is
the
most
effective,
efficient,
accurate
method
of
genome
editing
tool
in
all
living
cells
utilized
many
applied
disciplines.
Guide
RNA
(gRNA)
CRISPR-associated
proteins
are
two
essential
components
CRISPR/Cas-9
system.
The
mechanism
contains
three
steps,
recognition,
cleavage,
repair.
designed
sgRNA
recognizes
target
sequence
gene
interest
through
a
complementary
base
pair.
While
Cas-9
nuclease
makes
double-stranded
breaks
at
site
3
pair
upstream
to
protospacer
adjacent
motif,
then
break
repaired
by
either
non-homologous
end
joining
or
homology-directed
repair
cellular
mechanisms.
genome-editing
has
wide
number
applications
areas
including
medicine,
agriculture,
biotechnology.
In
it
could
help
design
new
grains
improve
nutritional
value.
being
investigated
for
cancers,
HIV,
therapy
such
as
sickle
cell
disease,
cystic
fibrosis,
Duchenne
muscular
dystrophy.
technology
also
regulation
specific
genes
advanced
modification
protein.
However,
immunogenicity,
effective
delivery
systems,
off-target
effect,
ethical
issues
have
been
major
barriers
extend
clinical
applications.
Although
becomes
era
molecular
biology
countless
roles
ranging
from
basic
researches
applications,
there
still
challenges
rub
practical
various
improvements
needed
overcome
obstacles.
Keywords:
CRISPR,
Cas-9,
sgRNA,
gene-editing,
mechanism,
Cell,
Год журнала:
2022,
Номер
185(1), С. 158 - 168.e11
Опубликована: Янв. 1, 2022
Small
molecule
chaperones
have
been
exploited
as
therapeutics
for
the
hundreds
of
diseases
caused
by
protein
misfolding.
The
most
successful
examples
are
CFTR
correctors,
which
transformed
cystic
fibrosis
therapy.
These
molecules
revert
folding
defects
ΔF508
mutant
and
widely
used
to
treat
patients.
To
investigate
molecular
mechanism
their
action,
we
determined
cryo-electron
microscopy
structures
in
complex
with
FDA-approved
correctors
lumacaftor
or
tezacaftor.
Both
drugs
insert
into
a
hydrophobic
pocket
first
transmembrane
domain
(TMD1),
linking
together
four
helices
that
thermodynamically
unstable.
Mutating
residues
at
binding
site
rendered
ΔF508-CFTR
insensitive
tezacaftor,
underscoring
functional
significance
structural
discovery.
results
support
stabilize
TMD1
an
early
stage
biogenesis,
prevent
its
premature
degradation,
thereby
allosterically
rescuing
many
disease-causing
mutations.
Science,
Год журнала:
2022,
Номер
378(6617), С. 284 - 290
Опубликована: Окт. 20, 2022
The
predominant
mutation
causing
cystic
fibrosis,
a
deletion
of
phenylalanine
508
(Δ508)
in
the
fibrosis
transmembrane
conductance
regulator
(CFTR),
leads
to
severe
defects
CFTR
biogenesis
and
function.
advanced
therapy
Trikafta
combines
folding
corrector
tezacaftor
(VX-661),
channel
potentiator
ivacaftor
(VX-770),
dual-function
modulator
elexacaftor
(VX-445).
However,
it
is
unclear
how
exerts
its
effects,
part
because
structure
Δ508
unknown.
Here,
we
present
cryo-electron
microscopy
structures
absence
presence
modulators.
When
used
alone,
partially
rectified
interdomain
assembly
CFTR,
but
when
combined
with
type
I
corrector,
did
so
fully.
These
data
illustrate
different
modulators
synergistically
rescue
Cellular and Molecular Life Sciences,
Год журнала:
2022,
Номер
79(1)
Опубликована: Янв. 1, 2022
Transmembrane
(TM)
proteins
are
major
drug
targets,
but
their
structure
determination,
a
prerequisite
for
rational
design,
remains
challenging.
Recently,
the
DeepMind's
AlphaFold2
machine
learning
method
greatly
expanded
structural
coverage
of
sequences
with
high
accuracy.
Since
employed
algorithm
did
not
take
specific
properties
TM
into
account,
reliability
generated
structures
should
be
assessed.
Therefore,
we
quantitatively
investigated
quality
at
genome
scales,
level
ABC
protein
superfamily
folds
and
membrane
(e.g.
dimer
modeling
stability
in
molecular
dynamics
simulations).
We
tested
template-free
prediction
challenging
CASP14
target
several
published
after
training.
Our
results
suggest
that
performs
well
case
its
neural
network
is
overfitted.
conclude
cautious
applications
models
will
advance
protein-associated
studies
an
unexpected
level.
Nature,
Год журнала:
2023,
Номер
616(7957), С. 606 - 614
Опубликована: Март 22, 2023
Abstract
The
cystic
fibrosis
transmembrane
conductance
regulator
(CFTR)
is
an
anion
channel
that
regulates
salt
and
fluid
homeostasis
across
epithelial
membranes
1
.
Alterations
in
CFTR
cause
fibrosis,
a
fatal
disease
without
cure
2,3
Electrophysiological
properties
of
have
been
analysed
for
decades
4–6
structure
CFTR,
determined
two
globally
distinct
conformations,
underscores
its
evolutionary
relationship
with
other
ATP-binding
cassette
transporters.
However,
direct
correlations
between
the
essential
functions
extant
structures
are
lacking
at
present.
Here
we
combine
ensemble
functional
measurements,
single-molecule
fluorescence
resonance
energy
transfer,
electrophysiology
kinetic
simulations
to
show
nucleotide-binding
domains
(NBDs)
human
dimerize
before
opening.
exhibits
allosteric
gating
mechanism
which
conformational
changes
within
NBD-dimerized
channel,
governed
by
ATP
hydrolysis,
regulate
chloride
conductance.
potentiators
ivacaftor
GLPG1837
enhance
activity
increasing
pore
opening
while
NBDs
dimerized.
Disease-causing
substitutions
proximal
(G551D)
or
distal
(L927P)
ATPase
site
both
reduce
efficiency
NBD
dimerization.
These
findings
collectively
enable
framing
informs
on
search
more
efficacious
clinical
therapies.
Abstract
Single
amino
acid
substitutions
can
profoundly
affect
protein
folding,
dynamics,
and
function.
The
ability
to
discern
between
benign
pathogenic
is
pivotal
for
therapeutic
interventions
research
directions.
Given
the
limitations
in
experimental
examination
of
these
variants,
AlphaMissense
has
emerged
as
a
promising
predictor
pathogenicity
missense
variants.
Since
heterogenous
performance
on
different
types
proteins
be
expected,
we
assessed
efficacy
across
several
groups
(e.g.
soluble,
transmembrane,
mitochondrial
proteins)
regions
intramembrane,
membrane
interacting,
high
confidence
AlphaFold
segments)
using
ClinVar
data
validation.
Our
comprehensive
evaluation
showed
that
delivers
outstanding
performance,
with
MCC
scores
predominantly
0.6
0.74.
We
observed
low
disordered
datasets
related
CFTR
ABC
protein.
However,
superior
was
shown
when
benchmarked
against
quality
CFTR2
database.
results
emphasizes
AlphaMissense’s
potential
pinpointing
functional
hot
spots,
its
likely
surpassing
benchmarks
calculated
from
ProteinGym
datasets.
International Journal of Molecular Sciences,
Год журнала:
2020,
Номер
21(11), С. 3837 - 3837
Опубликована: Май 28, 2020
Transient
Receptor
Potential
(TRP)
channels
are
a
family
of
ion
whose
members
distributed
among
all
kinds
animals,
from
invertebrates
to
vertebrates.
The
importance
these
molecules
is
exemplified
by
the
variety
physiological
roles
they
play.
Perhaps,
most
extensively
studied
member
this
TRPV1
channel;
nonetheless,
activity
TRPV4
has
been
associated
several
physio
and
pathophysiological
processes,
its
dysfunction
can
lead
severe
consequences.
Several
lines
evidence
derived
animal
models
even
clinical
trials
in
humans
highlight
as
therapeutic
target
protein
that
will
receive
more
attention
near
future,
be
reviewed
here.
Genes,
Год журнала:
2019,
Номер
10(3), С. 183 - 183
Опубликована: Фев. 26, 2019
Genetic
defects
in
cystic
fibrosis
(CF)
transmembrane
conductance
regulator
(CFTR)
gene
cause
CF.
Infants
with
CFTR
mutations
show
a
peribronchial
neutrophil
infiltration
prior
to
the
establishment
of
infection
their
lung.
The
inflammatory
response
progressively
increases
children
that
include
both
upper
and
lower
airways.
Infectious
leads
an
increase
mucus
viscosity
plugging
small
medium-size
bronchioles.
Eventually,
neutrophils
chronically
infiltrate
airways
biofilm
or
chronic
bacterial
infection.
Perpetual
airway
inflammation
destroy
lungs,
which
increased
morbidity
eventual
mortality
most
patients
Studies
have
now
established
cytotoxins,
extracellular
DNA,
traps
(NETs)
are
associated
clogging
lung
injury
In
addition
opportunistic
pathogens,
various
aspects
CF
milieux
(e.g.,
pH,
salt
concentration,
phenotypes)
influence
NETotic
capacity
neutrophils.
milieu
may
promote
survival
pro-inflammatory
aberrant
NETosis,
rather
than
anti-inflammatory
apoptotic
death
these
cells.
Degrading
NETs
helps
manage
disease;
since
DNAse
treatment
release
cytotoxins
from
NETs,
further
improvements
needed
degrade
maximal
positive
effects.
Neutrophil-T
cell
interactions
be
important
regulating
viral
infection-mediated
pulmonary
exacerbations
infections.
Therefore,
clarifying
role
disease
identifying
therapies
preserve
effects
neutrophils,
while
reducing
detrimental
cytotoxic
components,
essential
achieving
innovative
therapeutic
advances.
ATP-binding
cassette
(ABC)
transporters
are
molecular
pumps
ubiquitous
across
all
kingdoms
of
life.
While
their
structures
have
been
widely
reported,
the
kinetics
governing
transport
cycles
remain
largely
unexplored.
Multidrug
resistance
protein
1
(MRP1)
is
an
ABC
exporter
that
extrudes
a
variety
chemotherapeutic
agents
and
native
substrates.
Previously,
MRP1
were
determined
in
inward-facing
(IF)
or
outward-facing
(OF)
conformation.
Here,
we
used
single-molecule
fluorescence
spectroscopy
to
track
conformational
changes
bovine
(bMRP1)
real
time.
We
also
structure
bMRP1
under
active
turnover
conditions.
Our
results
show
substrate
stimulates
ATP
hydrolysis
by
accelerating
IF-to-OF
transition.
The
rate-limiting
step
cycle
dissociation
nucleotide-binding-domain
dimer,
while
per
se
does
not
reset
resting
state.
combination
structural
kinetic
data
illustrates
how
different
conformations
temporally
linked
alter
dynamics
achieve
transport.