The origin of esterase activity of Parkinson's disease causative factor DJ-1 implied by evolutionary trace analysis of its prokaryotic homolog HchA.

DJ-1, a causative gene for hereditary recessive Parkinsonism, is evolutionarily conserved across eukaryotes and prokaryotes. Structural analyses of DJ-1 and its homologs suggested the 106th Cys is a nucleophilic cysteine functioning as the catalytic center of hydratase or hydrolase activity. Indeed, DJ-1 and its homologs can convert highly electrophilic α-oxoaldehydes such as methylglyoxal into α-hydroxy acids as hydratase in vitro, and oxidation-dependent ester hydrolase (esterase) activity has also been reported for DJ-1. The mechanism underlying such plural activities, however, has not been fully characterized. To address this knowledge gap, we conducted a series of biochemical assays assessing the enzymatic activity of DJ-1 and its homologs. We found no evidence for esterase activity in any of the Escherichia coli DJ-1 homologs. Furthermore, contrary to previous reports, we found that oxidation inactivated rather than facilitated DJ-1 esterase activity. The E. coli DJ-1 homolog HchA possesses phenylglyoxalase and methylglyoxalase activities but lacks esterase activity. Since evolutionary trace analysis identified the 186th H as a candidate residue involved in functional differentiation between HchA and DJ-1, we focused on H186 of HchA and found that an esterase activity was acquired by H186A mutation. Introduction of reverse mutations into the equivalent position in DJ-1 (A107H) selectively eliminated its esterase activity without compromising α-oxoaldehyde hydratase activity. The obtained results suggest that differences in the amino acid sequences near the active site contributed to acquisition of esterase activity in vitro, and provide an important clue to the origin and significance of DJ-1 esterase activity.

Effect of Condensed Water at an Alumina/Epoxy Resin Interface on Curing Reaction.

The adhesion of epoxy adhesives to aluminum materials is an important issue in assembling parts for lightweight mobility. Aluminum surfaces typically possess an oxide layer, which readily adsorbs water. In this study, the aggregation states of water and its effect on the curing reaction were examined by placing a water layer between an amorphous alumina surface and a mixture of epoxy and amine components. This study used molecular dynamics simulations and density functional theory calculations. Before the reaction, water molecules strongly adsorbed onto the alumina surface, aggregating excess water. Some water diffused into the epoxy/amine mixture, accelerating the diffusion of unreacted substances. This led to faster reaction kinetics, particularly in proximity to the alumina surface. The adsorption of water molecules onto the alumina surface and the aggregation of excess water were similarly observed even after the curing process. Subsequently, the interaction between the alumina surface and various functional groups of the epoxy/amine mixture was evaluated before and after the reaction. Epoxy monomers had little interaction with the alumina surface before the reaction, whereas hydroxy groups formed by the ring-opening reaction of epoxy groups exhibited notable interaction. Conversely, sulfonyl and amino groups in amine compounds formed hydrogen bonds with OH groups on the alumina surface before the reaction. However, after the reaction, amino groups weakened their interaction with the alumina OH groups as they transformed from primary to tertiary during the curing reaction. Both epoxy and amine monomers/fragments similarly interacted with water molecules, both before and after the reaction. The insights gained from this study are expected to contribute to a better understanding of the impact of moisture absorption on the application of epoxy resins.

Exploring the Impact of Molecular Structure on Curing Kinetics: A Comparative Study of Diglycidyl Ether of Bisphenol A and F Epoxy Resins.

Epoxy resins are essential for various applications, and their properties depend on the curing reactions during which epoxy and amine compounds form the network structure. We here focus on how the presence or absence of two methyl groups in common epoxy bases, diglycidyl ether of bisphenol A and F (4,4'-DGEBA and 4,4'-DGEBF), affects the curing kinetics. The chemical reactions of both 4,4'-DGEBA and 4,4'-DGEBF, when cured with the same amine, were monitored by Fourier-transform infrared (FT-IR) spectroscopy and differential scanning calorimetry (DSC). Despite no difference in the reactivity of epoxy groups between 4,4'-DGEBA and 4,4'-DGEBF, the initial curing reaction was slower for the latter. This delay for the 4,4'-DGEBF system was attributed to intermolecular stacking, which hindered the approach of unreacted epoxy groups to amino groups and vice versa. This conclusion was drawn from the results obtained through ultraviolet (UV) spectroscopy, wide-angle X-ray scattering (WAXS), density functional theory (DFT) calculation, and all-atom molecular dynamics (MD) simulation.

Electronic Interaction of Epoxy Resin with Copper at the Adhered Interface.

A better understanding of the aggregation states of adhesive molecules in the interfacial region with an adherend is crucial for controlling the adhesion strength and is of great inherent academic interest. The adhesion mechanism has been described through four theories: adsorption, mechanical, diffusion, and electronic. While interfacial characterization techniques have been developed to validate the aforementioned theories, that related to the electronic theory has not yet been thoroughly studied. We here directly detected the electronic interaction between a commonly used thermosetting adhesive, cured epoxy of diglycidyl ether of bisphenol A (DGEBA) and 4,4'-diaminodiphenylmethane (DDM), and copper (Cu). This study used a combination of density functional theory (DFT) calculations and femtosecond transient absorption spectroscopic (TAS) measurements as this epoxy adhesive-Cu pairing is extensively used in electronic device packaging. The DFT calculations predicted that π electrons in a DDM molecule adsorbed onto the Cu surface flowed out onto the Cu surface, resulting in a positive charge on the DDM. TAS measurements for the Cu/epoxy multilayer film, a model sample containing many metal/adhesive interfaces, revealed that the electronic states of excited DDM moieties at the Cu interface were different from those in the bulk region. These results were in good accordance with the prediction by DFT calculations. Thus, it can be concluded that TAS is applicable to characterize the electronic interaction of adhesives with metal adherends in a nondestructive manner.

Changes in brain proteasome dynamics associated with aging.

In the nervous system, proteasomes are important for proteolysis and cellular homeostasis of neurons and glial cells and for brain health. Proteasome function declines with age in many tissues, including the nervous system, and this decline affects many of the nervous system processes important to brain health and may be related to age-related cognitive decline. Therefore, we analyzed the factors that contribute to this decline in function using the brain of mice from different months of life. Peptidase activity of proteasomes in crude extracts decreased with aging, while ubiquitinated proteins increased with aging. Additionally, there was a tendency for the number of subunits that form proteasomes to decrease slightly with age. On the other hand, ump1, which is required for proteasome formation, accumulated with age. Therefore, analysis of proteasome dynamics in each month revealed that proteasome formation decreased with aging. This study suggests that with aging, not only 20S proteasome function but also 26 proteasome function decreases, the decline in proteasome function is due to the lack of proteasome formation, the PA28-20S-PA700 complex, which is involved in immunity, increases in the brain, and one factor in this lack of proteasome formation is that the proteins called UMP1.

Mapping causal links between prefrontal cortical regions and intra-individual behavioral variability.

Intra-individual behavioral variability is significantly heightened by aging or neuropsychological disorders, however it is unknown which brain regions are causally linked to such variabilities. We examine response time (RT) variability in 21 macaque monkeys performing a rule-guided decision-making task. In monkeys with selective-bilateral lesions in the anterior cingulate cortex (ACC) or in the dorsolateral prefrontal cortex, cognitive flexibility is impaired, but the RT variability is significantly diminished. Bilateral lesions within the frontopolar cortex or within the mid-dorsolateral prefrontal cortex, has no significant effect on cognitive flexibility or RT variability. In monkeys with lesions in the posterior cingulate cortex, the RT variability significantly increases without any deficit in cognitive flexibility. The effect of lesions in the orbitofrontal cortex (OFC) is unique in that it leads to deficits in cognitive flexibility and a significant increase in RT variability. Our findings indicate remarkable dissociations in contribution of frontal cortical regions to behavioral variability. They suggest that the altered variability in OFC-lesioned monkeys is related to deficits in assessing and accumulating evidence to inform a rule-guided decision, whereas in ACC-lesioned monkeys it results from a non-adaptive decrease in decision threshold and consequently immature impulsive responses.

USP8 prevents aberrant NF-κB and Nrf2 activation by counteracting ubiquitin signals from endosomes.

K63-linked ubiquitin chains attached to plasma membrane proteins serve as tags for endocytosis and endosome-to-lysosome sorting. USP8 is an essential deubiquitinase for the maintenance of endosomal functions. Prolonged depletion of USP8 leads to cell death, but the major effects on cellular signaling pathways are poorly understood. Here, we show that USP8 depletion causes aberrant accumulation of K63-linked ubiquitin chains on endosomes and induces immune and stress responses. Upon USP8 depletion, two different decoders for K63-linked ubiquitin chains, TAB2/3 and p62, were recruited to endosomes and activated the TAK1-NF-κB and Keap1-Nrf2 pathways, respectively. Oxidative stress, an environmental stimulus that potentially suppresses USP8 activity, induced accumulation of K63-linked ubiquitin chains on endosomes, recruitment of TAB2, and expression of the inflammatory cytokine. The results demonstrate that USP8 is a gatekeeper of misdirected ubiquitin signals and inhibits immune and stress response pathways by removing K63-linked ubiquitin chains from endosomes.

Optineurin provides a mitophagy contact site for TBK1 activation.

Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase that is involved in many intracellular processes, such as innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating the autophagy adaptors that mediate the selective autophagic removal of damaged mitochondria. However, the mechanism by which PINK1-Parkin-mediated mitophagy activates TBK1 remains largely unknown. Here, we show that the autophagy adaptor optineurin (OPTN) provides a unique platform for TBK1 activation. Both the OPTN-ubiquitin and the OPTN-pre-autophagosomal structure (PAS) interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact sites between damaged mitochondria and the autophagosome formation sites. At this assembly point, a positive feedback loop for TBK1 activation is initiated that accelerates hetero-autophosphorylation of the protein. Expression of monobodies engineered here to bind OPTN impaired OPTN accumulation at contact sites, as well as the subsequent activation of TBK1, thereby inhibiting mitochondrial degradation. Taken together, these data show that a positive and reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.

Absolute local conformation of poly(methyl methacrylate) chains adsorbed on a quartz surface.

Polymer chains at a buried interface with an inorganic solid play a critical role in the performance of polymer nanocomposites and adhesives. Sum frequency generation (SFG) vibrational spectroscopy with a sub-nanometer depth resolution provides valuable information regarding the orientation angle of functional groups at interfaces. However, in the case of conventional SFG, since the signal intensity is proportional to the square of the second-order nonlinear optical susceptibility and thereby loses phase information, it cannot be unambiguously determined whether the functional groups face upward or downward. This problem can be solved by phase-sensitive SFG (ps-SFG). We here applied ps-SFG to poly(methyl methacrylate) (PMMA) chains in direct contact with a quartz surface, shedding light on the local conformation of chains adsorbed onto the solid surface. The measurements made it possible to determine the absolute orientation of the ester methyl groups of PMMA, which were oriented toward the quartz interface. Combining ps-SFG with all-atomistic molecular dynamics simulation, the distribution of the local conformation and the driving force are also discussed.

Enhanced ionic conductivity in block copolymer electrolytes through interfacial passivation using mixed ionic liquids.

We present a strategic approach for enhancing the ionic conductivity of block copolymer electrolytes. This was achieved by introducing mixed ionic liquids (ILs) with varying molar ratios, wherein the imidazolium cation was paired with either tetrafluoroborate (BF4) anion or bis(trifluoromethylsulfonyl)imide (TFSI) anion. Two polymer matrices, poly(4-styrenesulfonate)-b-polymethylbutylene (SSMB) and poly(4-styrenesulfonyl (trifluoromethanesulfonyl)imide)-b-polymethylbutylene (STMB), were synthesized for this purpose. All the SSMB and STMB containing mixed ILs showed hexagonal cylindrical structures, but the type of tethered acid group significantly influenced the interfacial properties. STMB electrolytes demonstrated enhanced segregation strength, which was attributed to strengthened Coulomb and hydrogen bonding interactions in the ionic domains, where the ILs were uniformly distributed. In contrast, the SSMB electrolytes exhibited increased concentration fluctuations because the BF4 anions were selectively sequestered at the block interfaces. This resulted in the effective confinement of imidazolium TFSI along the ionic domains, thereby preventing ion trapping in dead zones and facilitating rapid ion diffusion. Consequently, the SSMB electrolytes with mixed ILs demonstrated significantly improved ionic conductivities, surpassing the expected values based on the arithmetic average of the conductivities of each IL, whereas the ionic conductivity of the STMB was aligned with the expected average. The methodology explored in this study holds great promise for the development of solid-state polymer electrolytes.

Effect of segmental motion on hydrolytic degradation of polyglycolide in electro-spun fiber mats.

Recently, environmentally degradable polymers have received great attention from the perspective of sustaining the aquatic environment. To control the degradation behavior of solid polymer materials in an aqueous phase, it is crucial to better understand the thermal molecular motion of polymer chains in water. We herein focus on polyglycolide (PGA), which is one of the representative aliphatic polyesters that are hydrolytically degradable. Three kinds of fiber mats of PGA with different fiber diameters and comparable crystallinities were prepared using an electrospinning method. Our choice of fiber mats was because the ratio of the surface area, where the hydrolytic degradation starts to occur, to the volume was larger than that for the films. Dynamic mechanical analysis (DMA) enabled us to gain direct access to the dynamic glass transition temperature (Tgα) of PGA in the fiber mats both in dry gaseous nitrogen and liquid water. The Tgα value varied not only with the presence of water molecules, but also with the fiber diameter, or the specific surface area. The degradation behavior of PGA fiber mats was examined by immersing the samples in phosphate-buffered saline at various temperatures. When the segmental motion of PGA in the fiber mats was released, the apparent crystallinity of the mats increased, meaning that PGA amorphous chains were cleaved and thus partially eluted into the aqueous phase. It was also shown that partially cleaved chains crystallized.

Insights into Mechanical Dynamics of Nanoscale Interfaces in Epoxy Composites Using Nanorheology Atomic Force Microscopy.

Interfacial polymer layers with nanoscale size play critical roles in dissipating the strain energy around cracks and defects in structural nanocomposites, thereby enhancing the material's fracture toughness. However, understanding how the intrinsic mechanical dynamics of the interfacial layer determine the toughening and reinforcement mechanisms in various polymer nanocomposites remains a major challenge. Here, by means of a recently developed nanorheology atomic force microscopy method, also known as nanoscale dynamic mechanical analysis (nDMA), we report direct mapping of dynamic mechanical responses at the interface of a model epoxy nanocomposite under the transition from a glassy to a rubbery state. We demonstrate a significant deviation in the dynamic moduli of the interface from matrix behavior. Interestingly, the sign of the deviation is observed to be reversed when the polymer changes from a glassy to a rubbery state, which provides an excellent explanation for the difference in the modulus reinforcement between glassy and rubbery epoxy nanocomposites. More importantly, nDMA loss tangent images unambiguously show an enhanced viscoelastic response at the interface compared to the bulk matrix in the glassy state. This observation can therefore provide important insights into the nanoscale toughening mechanism that occurs in epoxy nanocomposites due to viscoelastic energy dissipation at the interface.

Neutron Reflectometry Analysis of Condensed Water Layer Formation at a Solid Interface of Epoxy Resins Under High Humidity.

Water absorbed by epoxy resins from a humid atmosphere considerably influences their structure and properties. Examining the effects of absorbed water on epoxy resins at their interfaces with solid substrates is crucial because of their adhesive applications in various fields. The spatial distribution of absorbed water in epoxy resin thin films under high humidity was investigated in this study by neutron reflectometry. Water molecules were found to accumulate at the SiO2/epoxy resin interface after exposure at a relative humidity of 85% for 8 h. The formation of an ∼1-nm-thick condensed water layer was observed, and the thickness of this layer varied with curing conditions of epoxy systems. Furthermore, water accumulation at the interface was noted to be affected by high-temperature and high-humidity environments. The formation of the condensed water layer is presumed to be related to the features of the polymer layer near the interface. The construction of the interface layer of epoxy resin would be affected by the interface constraint effect on the cross-linked polymer chain during the curing reaction. This study provides essential information for understanding the factors influencing the accumulation of water at the interface in epoxy resins. In practical applications, the process of improving the construction of epoxy resins near the interface would be a reasonable solution to resist water accumulation in the interface.

Aggregation States and Segmental Dynamics of Poly(methyl methacrylate) in Nanofiber Mats.

Nanofiber mats composed of polymers, having a large surface-to-volume ratio and high porosity, have been widely applied in the environmental and biomedical fields but fundamental knowledge on the polymer chains in the mats seems to be limited. We here report the aggregation states and segmental dynamics of poly(methyl methacrylate)s (PMMAs) with different stereoregularities in electrospun nanofiber mats. Attenuated total reflectance Fourier transform infrared (ATR/FTIR) spectroscopy revealed that, in the case of atactic PMMA (at-PMMA), the population of the trans-trans conformation of the main chain part, which allows carbonyl groups of the side group to interact affirmatively with each other, increased in the electrospun nanofiber mat. On the other hand, in the case of isotactic PMMA (it-PMMA), the skeletal conformation was unchanged even in the nanofiber mat. As a result of the aggregation states of PMMA chains, the glass-transition temperature (Tg) of the electrospun nanofiber mats increased and remained unchanged from the corresponding bulk value for at- and it-PMMA, respectively. These findings should be useful for designing materials and devices composed of electrospun nanofibers.

Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range.

Magnetic resonance imaging (MRI) is a non-invasive neuroimaging technique that is useful for identifying normal developmental and aging processes and for data sharing. Marmosets have a relatively shorter life expectancy than other primates, including humans, because they grow and age faster. Therefore, the common marmoset model is effective in aging research. The current study investigated the aging process of the marmoset brain and provided an open MRI database of marmosets across a wide age range. The Brain/MINDS Marmoset Brain MRI Dataset contains brain MRI information from 216 marmosets ranging in age from 1 and 10 years. At the time of its release, it is the largest public dataset in the world. It also includes multi-contrast MRI images. In addition, 91 of 216 animals have corresponding high-resolution ex vivo MRI datasets. Our MRI database, available at the Brain/MINDS Data Portal, might help to understand the effects of various factors, such as age, sex, body size, and fixation, on the brain. It can also contribute to and accelerate brain science studies worldwide.

Elucidation of ubiquitin-conjugating enzymes that interact with RBR-type ubiquitin ligases using a liquid-liquid phase separation-based method.

RING-between RING (RBR)-type ubiquitin (Ub) ligases (E3s) such as Parkin receive Ub from Ub-conjugating enzymes (E2s) in response to ligase activation. However, the specific E2s that transfer Ub to each RBR-type ligase are largely unknown because of insufficient methods for monitoring their interaction. To address this problem, we have developed a method that detects intracellular interactions between E2s and activated Parkin. Fluorescent homotetramer Azami-Green fused with E2 and oligomeric Ash (Assembly helper) fused with Parkin form a liquid-liquid phase separation (LLPS) in cells only when E2 and Parkin interact. Using this method, we identified multiple E2s interacting with activated Parkin on damaged mitochondria during mitophagy. Combined with in vitro ubiquitination assays and bioinformatics, these findings revealed an underlying consensus sequence for E2 interactions with activated Parkin. Application of this method to other RBR-type E3s including HOIP, HHARI, and TRIAD1 revealed that HOIP forms an LLPS with its substrate NEMO in response to a proinflammatory cytokine and that HHARI and TRIAD1 form a cytosolic LLPS independent of Ub-like protein NEDD8. Since an E2-E3 interaction is a prerequisite for RBR-type E3 activation and subsequent substrate ubiquitination, the method we have established here can be an in-cell tool to elucidate the potentially novel mechanisms involved in RBR-type E3s.

cIAP1-based degraders induce degradation via branched ubiquitin architectures.

Targeted protein degradation through chemical hijacking of E3 ubiquitin ligases is an emerging concept in precision medicine. The ubiquitin code is a critical determinant of the fate of substrates. Although two E3s, CRL2VHL and CRL4CRBN, frequently assemble with proteolysis-targeting chimeras (PROTACs) to attach lysine-48 (K48)-linked ubiquitin chains, the diversity of the ubiquitin code used for chemically induced degradation is largely unknown. Here we show that the efficacy of cIAP1-targeting degraders depends on the K63-specific E2 enzyme UBE2N. UBE2N promotes degradation of cIAP1 induced by cIAP1 ligands and subsequent cancer cell apoptosis. Mechanistically, UBE2N-catalyzed K63-linked ubiquitin chains facilitate assembly of highly complex K48/K63 and K11/K48 branched ubiquitin chains, thereby recruiting p97/VCP, UCH37 and the proteasome. Degradation of neo-substrates directed by cIAP1-recruiting PROTACs also depends on UBE2N. These results reveal an unexpected role for K63-linked ubiquitin chains and UBE2N in degrader-induced proteasomal degradation and demonstrate the diversity of the ubiquitin code used for chemical hijacking.

Direct visualization of cooperative adsorption of a string-like molecule onto a solid.

Natural systems, composite materials, and thin-film devices adsorb macromolecules in different phases onto their surfaces. In general, polymer chains form interfacial layers where their aggregation states and thermal molecular motions differ from the bulk. Here, we visualize well-defined double-stranded DNAs (dsDNAs) using atomic force microscopy and molecular dynamics simulations to clarify the adsorption mechanism of polymer chains onto solid surfaces. Initially, short and long dsDNAs are individually and cooperatively adsorbed, respectively. Cooperative adsorption involves intertwining of multiple chains. The dependence of adsorption on the chain affects the formation of the interfacial layer, realizing different mechanical properties of DNA/filler bulk composites. These findings will contribute to the development of light and durable polymer composites and films for various industrial, biomedical, and environmental applications.

Kinetics of the interfacial curing reaction for an epoxy-amine mixture.

A better understanding of the chemical reaction between epoxy and amine compounds at a solid interface is crucial for the design and fabrication of materials with appropriate adhesive strength. Here, we examined the curing reaction kinetics of epoxy phenol novolac and 4,4'-diaminodiphenyl sulfone at the outermost interface using sum-frequency generation spectroscopy, and X-ray and neutron reflectivity in conjunction with a full atomistic molecular dynamics simulation. The reaction rate constant was much larger at the quartz interface than in the bulk. While the apparent activation energy at the quartz interface obtained from an Arrhenius plot was almost identical to the bulk value, the frequency factor at the quartz interface was greater than that in the bulk. These results could be explained in terms of the densification and orientation of reactants at the interface, facilitating the encounter of the reactants present.

Unraveling Nanoscale Elastic and Adhesive Properties at the Nanoparticle/Epoxy Interface Using Bimodal Atomic Force Microscopy.

The addition of a small fraction of solid nanoparticles to thermosetting polymers can substantially improve their fracture toughness, while maintaining various intrinsic thermomechanical properties. The underlying mechanism is largely related to the debonding process and subsequent formation of nanovoids at a nanoscale nanoparticle/epoxy interface, which is thought to be associated with a change in the structural and mechanical properties of the formed epoxy network at the interface compared with the matrix region. However, a direct characterization of the local physical properties at this nanoscale interface remains significantly challenging. Here, we employ a recently developed bimodal atomic force microscopy technique for the direct mapping of nanoscale elastic and adhesive responses of an amine-cured epoxy resin filled with ∼50 nm diameter silica nanoparticles. The obtained elastic modulus and dissipated energy maps with high spatial resolution evidence the existence of a ∼20-nm-thick interfacial epoxy layer surrounding the nanoparticles, which exhibits a reduced modulus and weaker adhesive response in comparison with the matrix properties. While the presence of such a soft and weak-adhesive interfacial layer is found not to affect the architecture of structural heterogeneities in the epoxy matrix, it conceivably supports the toughening mechanism related to the debonding and plastic nanovoid growth at the silica/epoxy interface. The incorporation of this soft interfacial layer into the Halpin-Tsai model also provides a good explanation for the effect of the silica fraction on the tensile modulus of cured epoxy nanocomposites.