33 research outputs found
Probing Intermolecular Interactions within the Amyloid Ī² Trimer Using a Tethered Polymer Nanoarray
Amyloid
oligomers are considered the most neurotoxic species of amyloid aggregates.
Spontaneous assembly of amyloids into aggregates is recognized as
a major molecular mechanism behind Alzheimerās disease and
other neurodegenerative disorders involving protein aggregation. Characterization
of such oligomers is extremely challenging but complicated by their
transient nature. Previously, we introduced a flexible nanoarray (FNA)
method enabling us to probe dimers assembled by the amyloid Ī²
(14-23) [AĪ² (14-23)] peptide. The study presented herein modifies
and enhances this approach to assemble and probe trimers of AĪ²
(14-23). A metal-free click chemistry approach was used, in which
dibenzocyclooctyne (DBCO) groups were incorporated at selected sites
within the FNA template to click AĪ² (14-23) monomers at their
terminal azide groups. Atomic force microscopy (AFM) force spectroscopy
was employed to characterize the assemblies. The force measurement
data demonstrate that the dissociation of the trimer undergoes a stepwise
pattern, in which the first monomer dissociates at the rupture force
ā¼48 Ā± 2.4 pN. The remaining dimer ruptures at the second
step at a slightly larger rupture force (ā¼53 Ā± 3.2 pN).
The assembled trimer was found to be quite dynamic, and transient
species of this inherently dynamic process were identified
Molecular Mechanism of Misfolding and Aggregation of AĪ²(13ā23)
The
misfolding and self-assembly of the amyloid-beta (AĪ²)
peptide into aggregates is a molecular signature of the development
of Alzheimerās disease, but molecular mechanisms of the peptide
aggregation remain unknown. Here, we combined Atomic Force Microscopy
(AFM) and Molecular Dynamics (MD) simulations to characterize the
misfolding process of an AĪ² peptide. Dynamic force spectroscopy
AFM analysis showed that the peptide forms stable dimers with a lifetime
of ā¼1 s. During MD simulations, isolated monomers gradually
adopt essentially similar nonstructured conformations independent
from the initial structure. However, when two monomers approach their
structure changes dramatically, and the conformational space for the
two monomers become restricted. The arrangement of monomers in antiparallel
orientation leads to the cooperative formation of Ī²-sheet conformation.
Interactions, including hydrogen bonds, salt bridges, and weakly polar
interactions of side chains stabilize the structure of the dimer.
Under the applied force, the dimer, as during the AFM experiments,
dissociates in a cooperative manner. Thus, misfolding of the AĪ²
peptide proceeds via the loss of conformational flexibility and formation
of stable dimers suggesting their key role in the subsequent AĪ²
aggregation process
Physicochemically Tunable Polyfunctionalized RNA Square Architecture with Fluorogenic and Ribozymatic Properties
Recent advances in RNA nanotechnology allow the rational design of various nanoarchitectures. Previous methods utilized conserved angles from natural RNA motifs to form geometries with specific sizes. However, the feasibility of producing RNA architecture with variable sizes using native motifs featuring fixed sizes and angles is limited. It would be advantageous to display RNA nanoparticles of diverse shape and size derived from a given primary sequence. Here, we report an approach to construct RNA nanoparticles with tunable size and stability. Multifunctional RNA squares with a 90Ā° angle were constructed by tuning the 60Ā° angle of the three-way junction (3WJ) motif from the packaging RNA (pRNA) of the bacteriophage phi29 DNA packaging motor. The physicochemical properties and size of the RNA square were also easily tuned by modulating the ācoreā strand and adjusting the length of the sides of the square <i>via</i> predictable design. Squares of 5, 10, and 20 nm were constructed, each showing diverse thermodynamic and chemical stabilities. Four āarmsā extending from the corners of the square were used to incorporate siRNA, ribozyme, and fluorogenic RNA motifs. Unique intramolecular contact using the pre-existing intricacy of the 3WJ avoids relatively weaker intermolecular interactions <i>via</i> kissing loops or sticky ends. Utilizing the 3WJ motif, we have employed a modular design technique to construct variable-size RNA squares with controllable properties and functionalities for diverse and versatile applications with engineering, pharmaceutical, and medical potential. This technique for simple design to finely tune physicochemical properties adds a new angle to RNA nanotechnology
Specificity of Binding of Single-Stranded DNA-Binding Protein to Its Target
Single-stranded DNA-binding proteins (SSBs) bind single-stranded
DNA (ssDNA) and participate in all genetic processes involving ssDNA,
such as replication, recombination, and repair. Here we applied atomic
force microscopy to directly image SSBāDNA complexes under
various conditions. We used the hybrid DNA construct methodology in
which the ssDNA segment is conjugated to the DNA duplex. The duplex
part of the construct plays the role of a marker, allowing unambiguous
identification of specific and nonspecific SSBāDNA complexes.
We designed hybrid DNA substrates with 5ā²- and 3ā²-ssDNA
termini to clarify the role of ssDNA polarity on SSB loading. The
hybrid substrates, in which two duplexes are connected with ssDNA,
were the models for gapped DNA substrates. We demonstrated that <i>Escherichia coli</i> SSB binds to ssDNA ends and internal ssDNA
regions with the same efficiency. However, the specific recognition
by ssDNA requires the presence of Mg<sup>2+</sup> cations or a high
ionic strength. In the absence of Mg<sup>2+</sup> cations and under
low-salt conditions, the protein is capable of binding DNA duplexes.
In addition, the number of interprotein interactions increases, resulting
in the formation of clusters on double-stranded DNA. This finding
suggests that the protein adopts different conformations depending
on ionic strength, and specific recognition of ssDNA by SSB requires
a high ionic strength or the presence of Mg<sup>2+</sup> cations
Specificity of Binding of Single-Stranded DNA-Binding Protein to Its Target
Single-stranded DNA-binding proteins (SSBs) bind single-stranded
DNA (ssDNA) and participate in all genetic processes involving ssDNA,
such as replication, recombination, and repair. Here we applied atomic
force microscopy to directly image SSBāDNA complexes under
various conditions. We used the hybrid DNA construct methodology in
which the ssDNA segment is conjugated to the DNA duplex. The duplex
part of the construct plays the role of a marker, allowing unambiguous
identification of specific and nonspecific SSBāDNA complexes.
We designed hybrid DNA substrates with 5ā²- and 3ā²-ssDNA
termini to clarify the role of ssDNA polarity on SSB loading. The
hybrid substrates, in which two duplexes are connected with ssDNA,
were the models for gapped DNA substrates. We demonstrated that <i>Escherichia coli</i> SSB binds to ssDNA ends and internal ssDNA
regions with the same efficiency. However, the specific recognition
by ssDNA requires the presence of Mg<sup>2+</sup> cations or a high
ionic strength. In the absence of Mg<sup>2+</sup> cations and under
low-salt conditions, the protein is capable of binding DNA duplexes.
In addition, the number of interprotein interactions increases, resulting
in the formation of clusters on double-stranded DNA. This finding
suggests that the protein adopts different conformations depending
on ionic strength, and specific recognition of ssDNA by SSB requires
a high ionic strength or the presence of Mg<sup>2+</sup> cations
Specificity of Binding of Single-Stranded DNA-Binding Protein to Its Target
Single-stranded DNA-binding proteins (SSBs) bind single-stranded
DNA (ssDNA) and participate in all genetic processes involving ssDNA,
such as replication, recombination, and repair. Here we applied atomic
force microscopy to directly image SSBāDNA complexes under
various conditions. We used the hybrid DNA construct methodology in
which the ssDNA segment is conjugated to the DNA duplex. The duplex
part of the construct plays the role of a marker, allowing unambiguous
identification of specific and nonspecific SSBāDNA complexes.
We designed hybrid DNA substrates with 5ā²- and 3ā²-ssDNA
termini to clarify the role of ssDNA polarity on SSB loading. The
hybrid substrates, in which two duplexes are connected with ssDNA,
were the models for gapped DNA substrates. We demonstrated that <i>Escherichia coli</i> SSB binds to ssDNA ends and internal ssDNA
regions with the same efficiency. However, the specific recognition
by ssDNA requires the presence of Mg<sup>2+</sup> cations or a high
ionic strength. In the absence of Mg<sup>2+</sup> cations and under
low-salt conditions, the protein is capable of binding DNA duplexes.
In addition, the number of interprotein interactions increases, resulting
in the formation of clusters on double-stranded DNA. This finding
suggests that the protein adopts different conformations depending
on ionic strength, and specific recognition of ssDNA by SSB requires
a high ionic strength or the presence of Mg<sup>2+</sup> cations
CIFOR Poverty and Environment Network (PEN)
As a guardian of
the bacterial genome, the RecG DNA helicase repairs
DNA replication and rescues stalled replication. We applied atomic
force microscopy (AFM) to directly visualize dynamics of RecG upon
the interaction with replication fork substrates in the presence and
absence of SSB using high-speed AFM. We directly visualized that RecG
moves back and forth over dozens of base pairs in the presence of
SSB. There is no RecG translocation in the absence of SSB. Computational
modeling was performed to build models of <i>Escherichia coli</i> RecG in a free state and in complex with the fork. The simulations
revealed the formation of complexes of RecG with the fork and identified
conformational transitions that may be responsible for RecG remodeling
that can facilitate RecG translocation along the DNA duplex. Such
complexes do not form with the DNA duplex, which is in line with experimental
data. Overall, our results provide mechanistic insights into the modes
of interaction of RecG with the replication fork, suggesting a novel
role of RecG in the repair of stalled DNA replication forks
Dynamics of the Interaction of RecG Protein with Stalled Replication Forks
As a guardian of
the bacterial genome, the RecG DNA helicase repairs
DNA replication and rescues stalled replication. We applied atomic
force microscopy (AFM) to directly visualize dynamics of RecG upon
the interaction with replication fork substrates in the presence and
absence of SSB using high-speed AFM. We directly visualized that RecG
moves back and forth over dozens of base pairs in the presence of
SSB. There is no RecG translocation in the absence of SSB. Computational
modeling was performed to build models of <i>Escherichia coli</i> RecG in a free state and in complex with the fork. The simulations
revealed the formation of complexes of RecG with the fork and identified
conformational transitions that may be responsible for RecG remodeling
that can facilitate RecG translocation along the DNA duplex. Such
complexes do not form with the DNA duplex, which is in line with experimental
data. Overall, our results provide mechanistic insights into the modes
of interaction of RecG with the replication fork, suggesting a novel
role of RecG in the repair of stalled DNA replication forks
Dynamics of the Interaction of RecG Protein with Stalled Replication Forks
As a guardian of
the bacterial genome, the RecG DNA helicase repairs
DNA replication and rescues stalled replication. We applied atomic
force microscopy (AFM) to directly visualize dynamics of RecG upon
the interaction with replication fork substrates in the presence and
absence of SSB using high-speed AFM. We directly visualized that RecG
moves back and forth over dozens of base pairs in the presence of
SSB. There is no RecG translocation in the absence of SSB. Computational
modeling was performed to build models of <i>Escherichia coli</i> RecG in a free state and in complex with the fork. The simulations
revealed the formation of complexes of RecG with the fork and identified
conformational transitions that may be responsible for RecG remodeling
that can facilitate RecG translocation along the DNA duplex. Such
complexes do not form with the DNA duplex, which is in line with experimental
data. Overall, our results provide mechanistic insights into the modes
of interaction of RecG with the replication fork, suggesting a novel
role of RecG in the repair of stalled DNA replication forks
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L'Auto-vƩlo : automobilisme, cyclisme, athlƩtisme, yachting, aƩrostation, escrime, hippisme / dir. Henri Desgranges
29 janvier 19431943/01/29 (A44,N15335)