Analytical Chemistry,
Год журнала:
2024,
Номер
96(45), С. 18195 - 18203
Опубликована: Ноя. 1, 2024
Mitochondrial
complex
activity
controls
a
multitude
of
physiological
processes
by
regulating
the
cellular
metabolism.
Current
methods
for
evaluating
mitochondrial
mainly
focus
on
single
metabolic
reactions
within
mitochondria.
These
often
require
fresh
samples
in
large
quantities
mitochondria
purification
or
intact
membranes
real-time
monitoring.
Confronting
these
limitations,
we
shifted
analytical
perspective
toward
interactive
networks
at
whole-cell
level
to
reflect
activity.
To
this
end,
compiled
panel
respiratory
chain-mapped
metabolites
(MRCMs),
whose
perturbations
theoretically
provide
an
overall
reflection
By
introducing
N-dimethyl-p-phenylenediamine
and
Fine-tuning
of
protein-protein
interactions
occurs
naturally
through
coevolution,
but
this
process
is
difficult
to
recapitulate
in
the
laboratory.
We
describe
a
platform
for
synthetic
coevolution
that
can
isolate
matched
pairs
interacting
muteins
from
complex
libraries.
This
large
dataset
coevolved
complexes
drove
systems-level
analysis
molecular
recognition
between
Z
domain–affibody
spanning
wide
range
structures,
affinities,
cross-reactivities,
and
orthogonalities,
captured
broad
spectrum
coevolutionary
networks.
Furthermore,
we
harnessed
pretrained
protein
language
models
expand,
silico,
amino
acid
diversity
our
screen,
predicting
remodeled
interfaces
beyond
reach
experimental
library.
The
integration
these
approaches
provides
means
simulating
generating
with
diverse
properties
biotechnology
biology.
The Journal of Immunology,
Год журнала:
2024,
Номер
212(2), С. 235 - 243
Опубликована: Янв. 2, 2024
Abstract
Abs
are
versatile
molecules
with
the
potential
to
achieve
exceptional
binding
target
Ags,
while
also
possessing
biophysical
properties
suitable
for
therapeutic
drug
development.
Protein
display
and
directed
evolution
systems
have
transformed
synthetic
Ab
discovery,
engineering,
optimization,
vastly
expanding
number
of
clones
able
be
experimentally
screened
binding.
Moreover,
burgeoning
integration
high-throughput
screening,
deep
sequencing,
machine
learning
has
further
augmented
in
vitro
promising
accelerate
design
process
massively
expand
sequence
space
interrogated.
In
this
Brief
Review,
we
discuss
experimental
computational
tools
employed
engineering
optimization.
We
explore
challenges
posed
by
developing
infectious
diseases,
prospects
leveraging
learning–guided
protein
prospectively
resistant
viral
escape.
Drug Discovery Today,
Год журнала:
2024,
Номер
29(7), С. 104025 - 104025
Опубликована: Май 17, 2024
In
the
past
40
years,
therapeutic
antibody
discovery
and
development
have
advanced
considerably,
with
machine
learning
(ML)
offering
a
promising
way
to
speed
up
process
by
reducing
costs
number
of
experiments
required.
Recent
progress
in
ML-guided
design
(D&D)
has
been
hindered
diversity
data
sets
evaluation
methods,
which
makes
it
difficult
conduct
comparisons
assess
utility.
Establishing
standards
guidelines
will
be
crucial
for
wider
adoption
ML
advancement
field.
This
perspective
critically
reviews
current
practices,
highlights
common
pitfalls
proposes
method
various
ML-based
techniques
D&D.
Addressing
challenges
across
process,
best
practices
are
recommended
each
stage
enhance
reproducibility
progress.
Proceedings of the National Academy of Sciences,
Год журнала:
2024,
Номер
121(34)
Опубликована: Авг. 12, 2024
Mutations
in
protein
active
sites
can
dramatically
improve
function.
The
site,
however,
is
densely
packed
and
extremely
sensitive
to
mutations.
Therefore,
some
mutations
may
only
be
tolerated
combination
with
others
a
phenomenon
known
as
epistasis.
Epistasis
reduces
the
likelihood
of
obtaining
improved
functional
variants
slows
natural
lab
evolutionary
processes.
Research
has
shed
light
on
molecular
origins
epistasis
its
role
shaping
trajectories
outcomes.
In
addition,
sequence-
AI-based
strategies
that
infer
epistatic
relationships
from
mutational
patterns
or
experimental
evolution
data
have
been
used
design
variants.
recent
years,
combinations
such
approaches
atomistic
calculations
successfully
predicted
highly
combinatorial
sites.
These
were
thousands
active-site
variants,
demonstrating
that,
while
our
understanding
remains
incomplete,
determinants
are
critical
for
accurate
now
sufficiently
understood.
We
conclude
space
explored
by
expanded
enhance
activities
discover
new
ones.
Furthermore,
opens
way
systematically
exploring
sequence
structure
impacts
function,
deepening
control
over
activity.
Reactive
oxygen
species
(ROS)
are
produced
during
cellular
metabolism
and
in
response
to
environmental
stress.
While
low
levels
of
ROS
play
essential
physiological
roles,
excess
can
damage
components,
leading
cell
death
or
transformation.
also
regulate
protein
interactions
cancer
cells,
thereby
affecting
processes
such
as
growth,
migration,
angiogenesis.
Dysregulated
occur
via
various
mechanisms,
including
amino
acid
modifications,
conformational
changes,
alterations
complex
stability.
Understanding
ROS-mediated
changes
is
crucial
for
targeted
therapies.
In
this
review,
we
examine
the
role
that
mechanisms
regulating
pathways
through
protein-protein
interactions.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 29, 2025
Abstract
Linking
sequence
variation
to
phenotypic
effects
is
critical
for
efficient
exploitation
of
large
genomic
datasets.
Here
we
present
a
novel
approach
combining
directed
evolution
with
protein
language
modeling
characterize
naturally-evolved
variants
rice
immune
receptor.
Using
high-throughput
evolution,
engineered
the
receptor
Pik-1
bind
and
recognize
fungal
proteins
Avr-PikC
Avr-PikF,
which
evade
detection
by
currently
characterized
alleles.
A
model
was
fine-tuned
on
this
data
correlate
ligand
binding
behavior.
This
then
used
found
in
3,000
Rice
Genomes
Project
dataset.
Two
scored
highly
against
Avr-PikC,
vitro
analyses
confirmed
their
improved
over
wild-type
Overall,
machine
learning
identified
promising
sources
disease
resistance
shows
potential
utility
exploring
other
interest.
ACS Synthetic Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 15, 2025
The
subunit
dissociation
of
oligomeric
enzymes
is
a
major
challenge
that
limits
their
practical
applications.
In
this
study,
yeast-surface-displayed
tetrameric
β-glucuronidase
with
C-terminal
anchor
protein
fusion
was
found
partially
dissociated
into
dimers.
coexpression
free
and
anchored
subunits
significantly
improved
the
display
efficiency
catalytic
activity.
Given
may
adopt
non-native
conformation
on
cell
surface,
interfaces
surface-displayed
were
in
situ
characterized
using
Förster
resonance
energy
transfer
(FRET)
strategy,
structure
well
maintained
coexpressed
β-glucuronidases.
Finally,
strategy
applied
to
cellulases,
enhancing
activities
endoglucanase
dimeric
β-glucosidase
concentration
cellulosic
ethanol
for
two-enzyme
codisplaying
strain.
This
work
provides
insights
structure-activity
relationship
efficient
utilization
enzymes.