Yuan-Chih Chang

Crystal structure of the left-handed archaeal RadA helical filament: identification of a functional motif for controlling quaternary structures and enzymatic functions of RecA family proteins

The RecA family of proteins mediates homologous recombination, an evolutionarily conserved pathway that maintains genomic stability by protecting against DNA double strand breaks. RecA proteins are thought to facilitate DNA strand exchange reactions as closed-rings or as right-handed helical filaments. Here, we report the crystal structure of a left-handed Sulfolobus solfataricus RadA helical filament. Each protomer in this left-handed filament is linked to its neighbour via interactions of a β-strand polymerization motif with the neighbouring ATPase domain. Immediately following the polymerization motif, we identified an evolutionarily conserved hinge region (a subunit rotation motif) in which a 360° clockwise axial rotation accompanies stepwise structural transitions from a closed ring to the AMP–PNP right-handed filament, then to an overwound right-handed filament and finally to the left-handed filament. Additional structural and functional analyses of wild-type and mutant proteins confirmed that the subunit rotation motif is crucial for enzymatic functions of RecA family proteins. These observations support the hypothesis that RecA family protein filaments may function as rotary motors.

Calcium Ion Promotes Yeast Dmc1 Activity via Formation of Long and Fine Helical Filaments with Single-stranded DNA

Dmc1 is specifically required for homologous recombination during meiosis. Here we report that the calcium ion enabled Dmc1 from budding yeast to form regular helical filaments on single-stranded DNA (ssDNA) and activate its strand assimilation activity. Relative to magnesium, calcium increased the affinity of Dmc1 for ATP and but reduces its DNA-dependent ATPase activity. These effects, together with previous studies of other RecA-like recombinases, support the view that ATP binding to Dmc1 protomers is required for functional filament structure. The helical pitch of the Saccharomyces cerevisiae Dmc1-ssDNA helical filament was estimated to be 13.4 ± 2.5 nm. Analysis of apparently “complete” Dmc1-ssDNA filaments indicated a stoichiometry of 24 ± 2 nucleotides per turn of the Dmc1 helix. This finding suggests that the number or protomers per helical turn and/or the number of nucleotides bound per Dmc1 protomer differs from that reported previously for Rad51 and RecA filaments. Our data support the view that the active form of Dmc1 protein is a helical filament rather than a ring. We speculate that Ca2+ plays a significant role in regulating meiotic recombination.

Drug-loaded bubbles with matched focused ultrasound excitation for concurrent blood–brain barrier opening and brain-tumor drug delivery

Focused ultrasound (FUS) with microbubbles has been used to achieve local blood-brain barrier opening (BBB opening) and increase the penetration of therapeutic drugs into brain tumors. However, inertial cavitation of microbubbles during FUS-induced BBB opening causes intracerebral hemorrhaging (ICH), leading to acute and chronic brain injury and limiting the efficiency of drug delivery. Here we investigated whether induction of drug (1,3-bis(2-chloroethyl)-1-nitrosourea, BCNU)-loaded bubbles (BCNU bubbles) to oscillate at their resonant frequency would reduce inertial cavitation during BBB opening, thereby eliminating ICH and enhancing drug delivery in a rat brain model. FUS was tested at 1 and 10 MHz, over a wide range of pressure (mechanical index ranging from 0.16 to 1.42) in the presence of BCNU bubbles. Excitation of BCNU bubbles by resonance frequency-matched FUS (10 MHz) resulted in predominantly stable cavitation and significantly reduced the occurrence of potential hazards of exposure to biological tissues during the BBB opening process. In addition, the drug release process could be monitored by acoustic emission obtained from ultrasound imaging. In tumor-bearing animals, BCNU bubbles with FUS showed significant control of tumor progression and improved maximum survival from 26 to 35 days. This study provides useful advancements toward the goal of successfully translating FUS theranostic bubble-enhanced brain drug delivery into clinical use.

Noninvasive, Targeted, and Non-Viral Ultrasound-Mediated GDNF-Plasmid Delivery for Treatment of Parkinson's Disease.

Glial cell line-derived neurotrophic factor (GDNF) supports the growth and survival of dopaminergic neurons. CNS gene delivery currently relies on invasive intracerebral injection to transit the blood-brain barrier. Non-viral gene delivery via systematic transvascular route is an attractive alternative because it is non-invasive, but a high-yield and targeted gene-expressed method is still lacking. In this study, we propose a novel non-viral gene delivery approach to achieve targeted gene transfection. Cationic microbubbles as gene carriers were developed to allow the stable formation of a bubble-GDNF gene complex, and transcranial focused ultrasound (FUS) exposure concurrently interacting with the bubble-gene complex allowed transient gene permeation and induced local GDNF expression. We demonstrate that the focused ultrasound-triggered GDNFp-loaded cationic microbubbles platform can achieve non-viral targeted gene delivery via a noninvasive administration route, outperform intracerebral injection in terms of targeted GDNF delivery of high-titer GDNF genes, and has a neuroprotection effect in Parkinson’s disease (PD) animal models to successfully block PD syndrome progression and to restore behavioral function. This study explores the potential of using FUS and bubble-gene complexes to achieve noninvasive and targeted gene delivery for the treatment of neurodegenerative disease.

The T4 Phage DNA Mimic Protein Arn Inhibits the DNA Binding Activity of the Bacterial Histone-like Protein H-NS

Background: DNA mimic proteins prevent DNA-binding proteins from binding to DNA. Results: T4 phage DNA mimic protein Arn disrupts H-NS·DNA binding and neutralizes the gene-silencing effect of H-NS. Conclusion: Arn participates in viral anti-host defense system by its DNA mimicking properties. Significance: This anti-H-NS function of Arn represents a novel battle mechanism between phage and bacteria. The T4 phage protein Arn (Anti restriction nuclease) was identified as an inhibitor of the restriction enzyme McrBC. However, until now its molecular mechanism remained unclear. In the present study we used structural approaches to investigate biological properties of Arn. A structural analysis of Arn revealed that its shape and negative charge distribution are similar to dsDNA, suggesting that this protein could act as a DNA mimic. In a subsequent proteomic analysis, we found that the bacterial histone-like protein H-NS interacts with Arn, implying a new function. An electrophoretic mobility shift assay showed that Arn prevents H-NS from binding to the Escherichia coli hns and T4 p8.1 promoters. In vitro gene expression and electron microscopy analyses also indicated that Arn counteracts the gene-silencing effect of H-NS on a reporter gene. Because McrBC and H-NS both participate in the host defense system, our findings suggest that T4 Arn might knock down these mechanisms using its DNA mimicking properties.

Superhydrophobic silica nanoparticles as ultrasound contrast agents

Microbubbles have been widely studied as ultrasound contrast agents for diagnosis and as drug/gene carriers for therapy. However, their size and stability (lifetime of 5-12min) limited their applications. The development of stable nanoscale ultrasound contrast agents would therefore benefit both. Generating bubbles persistently in situ would be one of the promising solutions to the problem of short lifetime. We hypothesized that bubbles could be generated in situ by providing stable air nuclei since it has been found that the interfacial nanobubbles on a hydrophobic surface have a much longer lifetime (orders of days). Mesoporous silica nanoparticles (MSNs) with large surface areas and different levels of hydrophobicity were prepared to test our hypothesis. It is clear that the superhydrophobic and porous nanoparticles exhibited a significant and strong contrast intensity compared with other nanoparticles. The bubbles generated from superhydrophobic nanoparticles sustained for at least 30min at a MI of 1.0, while lipid microbubble lasted for about 5min at the same settings. In summary MSNs have been transformed into reliable bubble precursors by making simple superhydrophobic modification, and made into a promising contrast agent with the potentials to serve as theranostic agents that are sensitive to ultrasound stimulation.

Inertial cavitation initiated by polytetrafluoroethylene nanoparticles under pulsed ultrasound stimulation

Nanoscale gas bubbles residing on a macroscale hydrophobic surface have a surprising long lifetime (on the order of days) and can serve as cavitation nuclei for initiating inertial cavitation (IC). Whether interfacial nanobubbles (NBs) reside on the infinite surface of a hydrophobic nanoparticle (NP) and could serve as cavitation nuclei is unknown, but this would be very meaningful for the development of sonosensitive NPs. To address this problem, we investigated the IC activity of polytetrafluoroethylene (PTFE) NPs, which are regarded as benchmark superhydrophobic NPs due to their low surface energy caused by the presence of fluorocarbon. Both a passive cavitation detection system and terephthalic dosimetry was applied to quantify the intensity of IC. The IC intensities of the suspension with PTFE NPs were 10.30 and 48.41 times stronger than those of deionized water for peak negative pressures of 2 and 5MPa, respectively. However, the IC activities were nearly completely inhibited when the suspension was degassed or ethanol was used to suspend PTFE NPs, and they were recovered when suspended in saturated water, which may indicates the presence of interfacial NBs on PTFE NPs surfaces. Importantly, these PTFE NPs could sustainably initiate IC for excitation by a sequence of at least 6000 pulses, whereas lipid microbubbles were completely depleted after the application of no more than 50 pulses under the same conditions. The terephthalic dosimetry has shown that much higher hydroxyl yields were achieved when PTFE NPs were present as cavitation nuclei when using ultrasound parameters that otherwise did not produce significant amounts of free radicals. These results show that superhydrophobic NPs may be an outstanding candidate for use in IC-related applications.

Structure of yeast Ape1 and its role in autophagic vesicle formation

In Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the form of a large complex into a Cvt vesicle using autophagic machinery, targeting it into the vacuole (the yeast lysosome) where it is proteolytically processed into its mature form, Ape1, by removal of an amino-terminal 45-amino acid propeptide. prApe1 is thought to serve as a scaffolding cargo critical for the assembly of the Cvt vesicle by presenting the propeptide to mediate higher-ordered complex formation and autophagic receptor recognition. Here we report the X-ray crystal structure of Ape1 at 2.5 Å resolution and reveal its dodecameric architecture consisting of dimeric and trimeric units, which associate to form a large tetrahedron. The propeptide of prApe1 exhibits concentration-dependent oligomerization and forms a stable tetramer. Structure-based mutagenesis demonstrates that disruption of the inter-subunit interface prevents dodecameric assembly and vacuolar targeting in vivo despite the presence of the propeptide. Furthermore, by examining the vacuolar import of propeptide-fused exogenous protein assemblies with different quaternary structures, we found that 3-dimensional spatial distribution of propeptides presented by a scaffolding cargo is essential for the assembly of the Cvt vesicle for vacuolar delivery. This study describes a molecular framework for understanding the mechanism of Cvt or autophagosomal biogenesis in selective macroautophagy.

Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.

RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadAs recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination.

In situ tailoring and manipulation of carbon nanotubes.

Multiwalled carbon nanotubes (MWNTs), with their excellent properties, have long been considered as a model material for realizing the potential of nanotechnology. Several techniques have been developed to tailor and manipulate MWNTs, and they have shown promise in the construction of nanobalances, nanosensors, SPM probes, nanoelectronics, fuel cells, and so on. In order to achieve their full capability, MWNTs need to be modified in length, diameter, and shape to atomic-scale precision. Therefore, the synergy of various techniques and sequential operations in real time is often required. Here we report on an in situ method that combines several tailoring and manipulation techniques using an ultra-high-vacuum transmission electron microscope/scanning tunneling microscope (UHV TEM/STM) system. We demonstrate nanoscale precision in the engineering and fabricating of a MWNT with two examples; a probe for investigating single nanoparticles and a balance with singleatom mass resolution. We carried out our experiments in an ultra-high-vacuum transmission electron microscope (UHV-TEM, JEOL JEM2000V) combined with a scanning tunneling microscope (STM; built inhouse) riding on a nanopositioning system. The nanopositioning system provided coarse mechanical motions in three dimensions and the fine adjustments were performed with a piezo-tube scanner. The MWNTs (Alfa, 3–24 nm in diameter, stock #43197) were first attached to a gold knife edge electrode using the electrophoresis technique (applying a 6 MHz AC voltage of 8 V). The assembly was then loaded into the electron microscope. A pre-inserted gold STM tip was aligned and connected with a chosen MWNT under TEM observation at an operating voltage of 200 kV. The bottom of Figure 1a shows such an initial MWNT with 15 walls and about 1.87 nm inner diameter attached to the STM