An Optimized Deep-Forest Algorithm Using a Modified Differential Evolution Optimization Algorithm: A Case of Host-Pathogen Protein-Protein Interaction Prediction.
Computational and Structural Biotechnology Journal,
Год журнала:
2025,
Номер
unknown
Опубликована: Янв. 1, 2025
Язык: Английский
Peptides En Route from Prebiotic to Biotic Catalysis
Accounts of Chemical Research,
Год журнала:
2024,
Номер
57(15), С. 2027 - 2037
Опубликована: Июль 17, 2024
ConspectusIn
the
quest
to
understand
prebiotic
catalysis,
different
molecular
entities,
mainly
minerals,
metal
ions,
organic
cofactors,
and
ribozymes,
have
been
implied
as
key
players.
Of
these,
inorganic
cofactors
gained
attention
for
their
ability
catalyze
a
wide
array
of
reactions
central
modern
metabolism
frequently
participate
in
these
within
enzymes.
Nevertheless,
bridging
gap
between
remains
fundamental
question
origins
life.In
this
Account,
peptides
are
investigated
potential
bridge
linking
catalysis
by
minerals/cofactors
enzymes
that
dominate
life's
chemical
reactions.
Before
ribosomal
synthesis
emerged,
random
sequences
were
plausible
on
early
Earth.
This
was
made
possible
sources
amino
acid
delivery
synthesis,
well
condensation
under
variety
conditions.
Early
proteins
probably
exhibited
distinct
compositions,
enriched
small
aliphatic
acidic
residues.
An
increase
abundance
acids
with
larger
side
chains
canonical
basic
groups
most
likely
dependent
emergence
more
challenging
(bio)synthesis.
Pressing
questions
thus
arise:
how
did
composition
influence
peptide
properties,
what
extent
could
they
contribute
metabolism?Recent
research
from
our
group
colleagues
shows
highly
peptides/proteins
comprising
only
presumably
"early"
fact
competent
at
secondary
structure
formation
even
possess
adaptive
folding
characteristics
such
spontaneous
refoldability
chaperone
independence
achieve
soluble
structures.
Moreover,
we
showed
can
still
bind
RNA
utilizing
ions
carboxylate
phosphoester
functional
groups.
And
finally,
ancient
shown
be
capable
binding
considered
prebiotically
plausible,
supporting
properties
providing
groups,
which
would
nominate
them
catalytic
hubs
great
relevance.These
findings
underscore
biochemical
plausibility
an
peptide/protein
world
devoid
complex
yet
collaborating
other
species.
Drawing
mechanistic
protein-cofactor
it
is
speculated
here
peptide/protein-cofactor
ensemble
facilitate
similar
range
reactions,
albeit
lower
rates.
hypothesis
invites
systematic
experimental
test.Nonetheless,
Account
does
not
exclude
scenarios
prebiotic-to-biotic
or
prioritize
any
specific
pathways
syntheses.
The
objective
examine
availability,
composition,
among
various
factors
involved
life.
Язык: Английский
Navigating the archaeal frontier: insights and projections from bioinformatic pipelines
Frontiers in Microbiology,
Год журнала:
2024,
Номер
15
Опубликована: Сен. 23, 2024
Archaea
continues
to
be
one
of
the
least
investigated
domains
life,
and
in
recent
years,
advent
metagenomics
has
led
discovery
many
new
lineages
at
phylum
level.
For
majority,
only
automatic
genomic
annotations
can
provide
information
regarding
their
metabolic
potential
role
environment.
Here,
data
from
2,978
archaeal
genomes
was
used
perform
using
bioinformatics
tools,
alongside
synteny
analysis.
These
classifications
were
done
assess
how
good
these
different
tools
relation
data.
Our
study
revealed
that
even
with
lowered
cutoffs,
several
functional
models
do
not
capture
recently
discovered
diversity.
Moreover,
our
investigation
a
significant
portion
genomes,
approximately
42%,
remain
uncharacterized.
In
comparison,
within
3,235
bacterial
diverse
range
unclassified
proteins
is
obtained,
well-studied
organisms
like
Escherichia
coli
having
substantially
lower
proportion
uncharacterized
regions,
ranging
<5
25%,
less
studied
being
comparable
archaea
35-40%
regions.
Leveraging
this
analysis,
we
able
identify
protein
markers,
thereby
providing
insights
into
metabolism
dataset.
findings
underscore
substantial
gap
between
classification
comprehensive
mapping
metabolism.
Despite
advances
computational
approaches,
remains
unexplored,
highlighting
need
for
extensive
experimental
validation
domain,
as
well
more
refined
annotation
methods.
This
contributes
better
understanding
underscores
importance
further
research
elucidating
genomes.
Язык: Английский
The dinucleotide structure of NAD enables specific reduction on mineral surfaces
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Окт. 13, 2024
Abstract
Nucleotide-derived
cofactors
could
function
as
a
missing
link
between
the
informational
and
metabolic
part
at
life’s
emergence.
One
well-known
example
is
nicotinamide
dinucleotide
(NAD),
one
of
evolutionarily
most
conserved
redox
found
in
metabolism.
Here,
we
propose
that
role
these
even
extend
to
links
geo-
biochemistry.
We
show
NAD
+
can
be
reduced
under
close-to
nature
conditions
with
nickel-iron-alloys
water-rock-interaction
settings
rich
hydrogen
(serpentinizing
systems)
mononucleotide
(NMN),
precursor
molecule
NAD,
has
different
properties
regarding
reduction
specificity
sensitivity
than
NAD.
The
additional
adenosine
monophosphate
(AMP)
“tail”
dinucleotide,
shared
trait
many
organic
cofactors,
seems
play
crucial
mechanistic
preventing
overreduction
nicotinamide-bearing
nucleotide.
This
also
connected
used
transition
metals.
While
combination
nickel
iron
promotes
1,4-NADH
efficiently,
case
NMN,
presence
leads
accumulation
products.
Testing
reducing
abilities
both
NADH
NMNH
abiotic
showed
molecules
act
equally
effective,
soluble
hydride
donors
non-enzymatic,
proto-metabolic
stages
Язык: Английский