Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 18, 2025
Abstract
Accurate
biomolecular
structure
prediction
enables
the
of
mutational
effects,
speculation
function
based
on
predicted
structural
homology,
analysis
ligand
binding
modes,
experimental
model
building
and
many
other
applications.
Such
algorithms
to
predict
essential
functional
features
remain
out
reach
for
biomolecular.
Here,
we
report
quantitative
qualitative
evaluation
nucleic
acid
structures
CASP16
blind
challenge
by
12
groups
who
provided
targets.
Blind
predictions
accurately
secondary
some
aspects
tertiary
structure,
including
reasonable
global
folds
complex
RNAs,
however,
often
lack
accuracy
in
regions
highest
importance.
All
models
have
inaccuracies
non-canonical
where,
e.g.,
nucleic-acid
backbone
bends
or
a
base
forms
non-standard
hydrogen
bond.
These
interactions
are
integral
form
functionally
important
such
as
RNA
enzymatic
active
sites.
Additionally,
modeling
conserved
interfaces
between
acids
ligands,
proteins,
remains
poor.
For
targets,
may
not
represent
only
occupies
solution
its
life-cycle,
posing
future
community.
Язык: Английский
Molecular Origami: Designing Functional Molecules of the Future
Molecules,
Год журнала:
2025,
Номер
30(2), С. 242 - 242
Опубликована: Янв. 9, 2025
In
the
field
of
chemical
biology,
DNA
origami
has
been
actively
researched.
This
technique,
which
involves
folding
strands
like
to
assemble
them
into
desired
shapes,
made
it
possible
create
complex
nanometer-sized
structures,
marking
a
major
breakthrough
in
nanotechnology.
On
other
hand,
controlling
mechanisms
and
folded
structures
proteins
or
shorter
peptides
challenging.
However,
recent
advances
techniques
such
as
protein
origami,
peptide
de
novo
design
have
construct
various
nanoscale
functional
molecules.
These
approaches
suggest
emergence
new
molecular
principles,
can
be
termed
"molecular
origami".
this
review,
we
provide
an
overview
research
trends
protein/peptide
DNA/RNA
explore
potential
future
applications
technologies
electrochemical
biosensors.
Язык: Английский
Structural analyses of apolipoprotein A-IV polymorphisms Q360H and T347S elucidate the inhibitory effect against thrombosis
Journal of Biological Chemistry,
Год журнала:
2025,
Номер
unknown, С. 108392 - 108392
Опубликована: Март 1, 2025
Язык: Английский
Interactions of Ligand, Aptamer, and Complementary Oligonucleotide: Studying Impacts of Na+ and Mg2+ Cations on Sensitive FRET-Based Detection of Aflatoxin B1
Molecules,
Год журнала:
2025,
Номер
30(10), С. 2125 - 2125
Опубликована: Май 11, 2025
The
effects
of
magnesium
and
sodium
on
the
interactions
between
aptamer,
its
specific
ligand,
short
complementary
oligonucleotides
(cDNAs)
differing
in
affinity
their
binding
with
aptamer
were
studied.
Aflatoxin
B1
(AFB1)
AFB1-binding
used
study.
Dependencies
for
fluorophore-labeled
AFB1
under
varied
concentrations
cations
obtained
using
fluorescence
anisotropy
measurements.
increase
to
presence
was
demonstrated
isothermal
calorimetry.
collected
data
indicate
that
300
mM
Mg2+
(significantly
more
than
range
commonly
sensors)
provides
best
(16.5
±
2.2
nM)
aptamer–AFB1
complexation.
Sodium
decreases
Mg2+-modulated
at
some
Na+/Mg2+
ratios.
cDNAs
increases
concentration
cations,
but
not
same
way
as
AFB1.
Based
characterized
conditions
bimolecular
interactions,
ligand-induced
displacement
studied
registration
Forster
energy
transfer
(FRET).
most
sensitive
revealing
(IC10%
3.2
0.3
this
three-compound
FRET
system
cDNA
having
an
equilibrium
constant
close
reaction.
Язык: Английский