Science Advances,
Journal Year:
2023,
Volume and Issue:
9(8)
Published: Feb. 22, 2023
White
spot
syndrome
virus
(WSSV)
is
one
of
the
largest
DNA
viruses
and
major
pathogen
responsible
for
white
in
crustaceans.
The
WSSV
capsid
critical
genome
encapsulation
ejection
exhibits
rod-shaped
oval-shaped
structures
during
viral
life
cycle.
However,
detailed
architecture
structural
transition
mechanism
remain
unclear.
Here,
using
cryo-electron
microscopy
(cryo-EM),
we
obtained
a
cryo-EM
model
were
able
to
characterize
its
ring-stacked
assembly
mechanism.
Furthermore,
identified
an
from
intact
virions
analyzed
capsids
induced
by
high
salinity.
These
transitions,
which
decrease
internal
pressure,
always
accompany
release
mostly
eliminate
infection
host
cells.
Our
results
demonstrate
unusual
offer
insights
into
pressure-driven
release.
Nature Communications,
Journal Year:
2023,
Volume and Issue:
14(1)
Published: Feb. 7, 2023
Abstract
Conjugation
is
a
major
mechanism
of
horizontal
gene
transfer
promoting
the
spread
antibiotic
resistance
among
human
pathogens.
It
involves
establishing
junction
between
donor
and
recipient
cell
via
an
extracellular
appendage
known
as
mating
pilus.
In
bacteria,
conjugation
machinery
encoded
by
plasmids
or
transposons
typically
mediates
cognate
mobile
genetic
elements.
Much
less
about
in
archaea.
Here,
we
determine
atomic
structures
cryo-electron
microscopy
three
conjugative
pili,
two
from
hyperthermophilic
archaea
(
Aeropyrum
pernix
Pyrobaculum
calidifontis
)
one
Ti
plasmid
bacterium
Agrobacterium
tumefaciens
,
show
that
archaeal
pili
are
homologous
to
bacterial
pili.
However,
machinery,
Ced,
has
been
‘domesticated’,
is,
genes
for
on
chromosome
rather
than
elements,
cellular
DNA.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: Jan. 26, 2024
A
contractile
sheath
and
rigid
tube
assembly
is
a
widespread
apparatus
used
by
bacteriophages,
tailocins,
the
bacterial
type
VI
secretion
system
to
penetrate
cell
membranes.
In
this
mechanism,
contraction
of
an
external
powers
motion
inner
through
membrane.
The
structure,
energetics,
mechanism
machinery
imply
rigidity
straightness.
tail
Agrobacterium
tumefaciens
bacteriophage
Milano
flexible
bent
varying
degrees,
which
sets
it
apart
from
other
tail-like
systems.
Here,
we
report
structures
including
sheath-tube
complex,
baseplate,
putative
receptor-binding
proteins.
flexible-to-rigid
transformation
upon
can
be
explained
unique
electrostatic
properties
sheath.
All
components
tail,
subunits,
are
crosslinked
disulfides,
some
must
reduced
for
occur.
complex
contains
tailspike,
fiber,
at
least
two
small
proteins
that
form
garland
around
distal
ends
tailspikes
fibers.
Despite
being
flagellotropic,
lacks
thread-like
filaments
wrap
flagellum,
thus
likely
employ
different
binding
mechanism.
Proceedings of the National Academy of Sciences,
Journal Year:
2022,
Volume and Issue:
119(26)
Published: June 21, 2022
While
biofilms
formed
by
bacteria
have
received
great
attention
due
to
their
importance
in
pathogenesis,
much
less
research
has
been
focused
on
the
archaea.
It
known
that
extracellular
filaments
archaea,
such
as
type
IV
pili,
hami,
and
cannulae,
play
a
part
formation
of
archaeal
biofilms.
We
used
cryo-electron
microscopy
determine
atomic
structure
previously
uncharacterized
class
surface
from
hyperthermophilic
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: June 14, 2024
Abstract
Type
IV
pili
(T4P)
represent
one
of
the
most
common
varieties
surface
appendages
in
archaea.
These
filaments,
assembled
from
small
pilin
proteins,
can
be
many
microns
long
and
serve
diverse
functions,
including
adhesion,
biofilm
formation,
motility,
intercellular
communication.
Here,
we
determine
atomic
structures
two
distinct
adhesive
T4P
Saccharolobus
islandicus
via
cryo-electron
microscopy
(cryo-EM).
Unexpectedly,
both
were
same
polypeptide
but
under
different
growth
conditions.
One
filament,
denoted
mono-pilus,
conforms
to
canonical
archaeal
where
all
subunits
are
equivalent,
whereas
other
tri-pilus,
exists
three
conformations.
The
conformations
tri-pilus
very
single
conformation
found
involve
orientations
outer
immunoglobulin-like
domains,
mediated
by
a
flexible
linker.
Remarkably,
domains
rotate
nearly
180°
between
mono-
Both
forms
require
ATPase
TadC-like
membrane
pore
for
assembly,
indicating
that
secretion
system
produce
structurally
filaments.
Our
results
show
appear
less
constrained
rigid
than
those
homologous
flagellar
filaments
as
helical
propellers.
Cell,
Journal Year:
2024,
Volume and Issue:
187(20), P. 5604 - 5619.e14
Published: Aug. 28, 2024
We
use
cryoelectron
microscopy
(cryo-EM)
as
a
sequence-
and
culture-independent
diagnostic
tool
to
identify
the
etiological
agent
of
an
agricultural
pandemic.
For
past
4
years,
American
insect-rearing
facilities
have
experienced
distinctive
larval
pathology
colony
collapse
farmed
Zophobas
morio
(superworm).
By
means
cryo-EM,
we
discovered
causative
agent:
densovirus
that
named
black
wasting
virus
(ZmBWV).
confirmed
etiology
disease
by
fulfilling
Koch's
postulates
characterizing
strains
from
across
United
States.
ZmBWV
is
member
family
Parvoviridae
with
5,542
nt
genome,
describe
intersubunit
interactions
explaining
its
expanded
internal
volume
relative
human
parvoviruses.
Cryo-EM
structures
at
resolutions
up
2.1
Å
revealed
single-strand
DNA
(ssDNA)
ordering
capsid
inner
surface
pinned
base-binding
pockets
in
surface.
Also,
demonstrated
prophylactic
potential
non-pathogenic
provide
cross-protection
vivo.
Micromachines,
Journal Year:
2023,
Volume and Issue:
14(9), P. 1674 - 1674
Published: Aug. 27, 2023
Single
particle
cryo-electron
microscopy
(cryo-EM)
has
emerged
as
the
prevailing
method
for
near-atomic
structure
determination,
shedding
light
on
important
molecular
mechanisms
of
biological
macromolecules.
However,
inherent
dynamics
and
structural
variability
complexes
coupled
with
large
number
experimental
images
generated
by
a
cryo-EM
experiment
make
data
processing
nontrivial.
In
particular,
ab
initio
reconstruction
atomic
model
building
remain
major
bottlenecks
that
demand
substantial
computational
resources
manual
intervention.
Approaches
utilizing
recent
innovations
in
artificial
intelligence
(AI)
technology,
particularly
deep
learning,
have
potential
to
overcome
limitations
cannot
be
adequately
addressed
traditional
image
approaches.
Here,
we
review
newly
proposed
AI-based
methods
volume
generation,
heterogeneous
3D
reconstruction,
building.
We
highlight
advancements
made
implementation
AI
methods,
well
discuss
remaining
areas
future
development.
Communications Biology,
Journal Year:
2023,
Volume and Issue:
6(1)
Published: Sept. 8, 2023
Abstract
Large
gaps
exist
in
our
understanding
of
how
bacteriophages,
the
most
abundant
biological
entities
on
Earth,
assemble
and
function.
The
structure
“neck”
region,
where
DNA-filled
capsid
is
connected
to
host-recognizing
tail
remains
poorly
understood.
We
describe
cryo-EM
structures
neck,
neck-capsid
neck-tail
junctions,
Agrobacterium
phage
Milano.
Milano
neck
1
protein
connects
12-fold
symmetrical
a
5-fold
vertex
icosahedral
capsid.
Comparison
homologs
leads
four
proposed
classes,
likely
evolved
from
simplest
one
siphophages
more
complex
ones
myo-
podophages.
surrounded
by
atypical
collar,
which
covalently
crosslinks
sheath
1.
decorated
with
three
types
proteins,
minor
(mCP)
two
linking
proteins
crosslinking
mCP
major
protein.
extensive
network
disulfide
bonds
within
between
provides
an
exceptional
structural
stability
Antibodies
are
a
major
component
of
adaptive
immunity
against
invading
pathogens.
Here,
we
explore
possibilities
for
an
analytical
approach
to
characterize
the
antigen-specific
antibody
repertoire
directly
from
secreted
proteins
in
convalescent
serum.
This
aims
perform
simultaneous
sequencing
and
epitope
mapping
using
combination
single
particle
cryo-electron
microscopy
(cryoEM)
bottom-up
proteomics
techniques
based
on
mass
spectrometry
(LC-MS/MS).
We
evaluate
performance
deep-learning
tool
ModelAngelo
determining
de
novo
sequences
reconstructed
3D
volumes
antibody-antigen
complexes.
demonstrate
that
while
map
quality
is
critical
bottleneck,
it
possible
sequence
variable
domains
cryoEM
reconstructions
with
accuracies
up
80-90%.
While
rate
errors
exceeds
typical
levels
somatic
hypermutation,
show
ModelAngelo-derived
can
be
used
assign
V-genes.
provides
functional
guide
assemble
peptides
LC-MS/MS
data
more
accurately
improves
tolerance
background
polyclonal
sequences.
Following
this
proof-of-principle,
discuss
feasibility
future
directions
repertoires.
Antibodies
are
a
major
component
of
adaptive
immunity
against
invading
pathogens.
Here
we
explore
possibilities
for
an
analytical
approach
to
characterize
the
antigen-specific
antibody
repertoire
directly
from
secreted
proteins
in
convalescent
serum.
This
aims
perform
simultaneous
sequencing
and
epitope
mapping
using
combination
single
particle
cryo-electron
microscopy
(cryoEM)
bottom-up
proteomics
techniques
based
on
mass
spectrometry
(LC-MS/MS).
We
evaluate
performance
deep-learning
tool
ModelAngelo
determining
de
novo
sequences
reconstructed
3D
volumes
antibody-antigen
complexes.
demonstrate
that
while
map
quality
is
critical
bottleneck,
it
possible
sequence
variable
domains
cryoEM
reconstructions
with
accuracies
up
80-90%.
While
rate
errors
exceeds
typical
levels
somatic
hypermutation,
show
ModelAngelo-derived
can
be
used
assign
V-genes.
provides
functional
guide
assemble
peptides
LC-MS/MS
data
more
accurately
improves
tolerance
background
polyclonal
sequences.
Following
this
proof-of-principle,
discuss
feasibility
future
directions
repertoires.
QRB Discovery,
Journal Year:
2025,
Volume and Issue:
6
Published: Jan. 1, 2025
Abstract
Integrative
modeling
enables
structure
determination
for
large
macromolecular
assemblies
by
combining
data
from
multiple
experiments
with
theoretical
and
computational
predictions.
Recent
advancements
in
AI-based
prediction
cryo
electron-microscopy
have
sparked
renewed
enthusiasm
integrative
modeling;
structures
methods
can
be
integrated
situ
maps
to
characterize
assemblies.
This
approach
previously
allowed
us
others
determine
the
architectures
of
diverse
assemblies,
such
as
nuclear
pore
complexes,
chromatin
remodelers,
cell–cell
junctions.
Experimental
spanning
several
scales
was
used
these
studies,
ranging
high-resolution
data,
X-ray
crystallography
AlphaFold
structure,
low-resolution
cryo-electron
tomography
co-immunoprecipitation
experiments.
Two
recurrent
challenges
emerged
across
a
range
studies.
First,
contained
significant
fractions
disordered
regions,
necessitating
development
new
regions
context
ordered
regions.
Second,
needed
developed
utilize
information
tomography,
timely
challenge
structural
biology
is
increasingly
moving
towards
characterization.
Here,
we
recapitulate
recent
developments
proteins
analysis
highlight
other
opportunities
method
modeling.