Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI.

Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.

Melatonin inhibits the formation of chemically induced experimental encapsulating peritoneal sclerosis through modulation of T cell differentiation by suppressing of NF-κB activation in dendritic cells.

Encapsulating peritoneal sclerosis (EPS) is a severe complication of peritoneal dialysis (PD). Surgery is a therapeutic strategy for the treatment of complete intestinal obstruction. However, complete intestinal obstruction in long-term PD results in high mortality and morbidity rates after surgery. Immunopathogenesis participates in EPS formation: CD8, Th1, and Th17 cell numbers increased during the formation of EPS. The anti-inflammatory and immunomodulatory effects of melatonin may have beneficial effects on this EPS. In the present study, we determined that melatonin treatment significantly decreases the Th1 and Th17 cell populations in mice with EPS, decreases the production of IL-1ß, TNF-α, IL-6, and IFN-γ, and increases the production of IL-10. The suppression of Th1 and Th17 cell differentiation by melatonin occurs through the inhibition of dendritic cell (DC) activation by affecting the initiation of the NF-κB signaling pathway in DCs. Our study suggests that melatonin has preventive potential against the formation of EPS in patients with PD.

Beta Amyloid Oligomers with Higher Cytotoxicity have Higher Sidechain Dynamics.

The underlying biophysical principle governing the cytotoxicity of the oligomeric aggregates of ß-amyloid (Aß) peptides has long been an enigma. Here we show that the size of Aß40 oligomers can be actively controlled by incubating the peptides in reverse micelles. Our approach allowed for the first time a detailed comparison of the structures and dynamics of two Aß40 oligomers of different sizes, viz., 10 and 23 nm, by solid-state NMR. From the chemical shift data, we infer that the conformation and/or the chemical environments of the residues from K16 to K28 are different between the 10-nm and 23-nm oligomers. We find that the 10-nm oligomers are more cytotoxic, and the molecular motion of the sidechain of its charged residue K16 is more dynamic. Interestingly, the residue A21 exhibits unusually high structural rigidity. Our data raise an interesting possibility that the cytotoxicity of Aß40 oligomers could also be correlated to the motional dynamics of the sidechains.

Lewis Acid Probe for Basicity of Sulfide Electrolytes Investigated by 11B Solid-State NMR.

Sulfide-based solid-state lithium-ion batteries (SSLIB) have attracted a lot of interest globally in the past few years for their high safety and high energy density over the traditional lithium-ion batteries. However, sulfide electrolytes (SEs) are moisture-sensitive which pose significant challenges in the material preparation and cell manufacturing. To the best of our knowledge, there is no tool available to probe the types and the strength of the basic sites in sulfide electrolytes, which is crucial for understanding the moisture stability of sulfide electrolytes. Herein, we propose a new spectral probe with the Lewis base indicator BBr3 to probe the strength of Lewis basic sites on various sulfide electrolytes by 11B solid-state NMR spectroscopy (11B-NMR). The active sulfur sites and the corresponding strength of the sulfide electrolytes are successfully evaluated by the proposed Lewis base probe. The probed strength of the active sulfur sites of a sulfide electrolyte is consistent with the results of DFT (density functional theory) calculation and correlated with the H2S generation rate when the electrolyte was exposed in moisture atmosphere. This work paves a new way to investigate the basicity and moisture stability of the sulfide electrolytes.

Fast Water Transport in UTSA-280 via a Knock-Off Mechanism.

Water and other small molecules frequently coordinate within metal-organic frameworks (MOFs). These coordinated molecules may actively engage in mass transfer, moving together with the transport molecules, but this phenomenon has yet to be examined. In this study, we explore a unique water transfer mechanism in UTSA-280, where an incoming water molecule can displace a coordinated molecule for mass transfer. We refer to this process as the "knock-off" mechanism. Despite UTSA-280 possessing one-dimensional channels, the knock-off transport enables water movement along the other two axes, effectively simulating a pseudo-three-dimensional mass transfer. Even with a relatively narrow pore width, the knock-off mechanism enables a high water flux in the UTSA-280 membrane. The knock-off mechanism also renders UTSA-280 superior water/ethanol diffusion selectivity for pervaporation. To validate this unique mechanism, we conducted 1 H and 2 H solid-state NMR on UTSA-280 after the adsorption of deuterated water. We also derived potential energy diagrams from the density functional theory to gain atomic-level insight into the knock-off and the direct-hopping mechanisms. The simulation findings reveal that the energy barrier of the knock-off mechanism is marginally lower than the direct-hopping pathway, implying its potential role in enhancing water diffusion in UTSA-280.

Wood cellulose microfibrils have a 24-chain core-shell nanostructure in seed plants.

Wood cellulose microfibril (CMF) is the most abundant organic substance on Earth but its nanostructure remains poorly understood. There are controversies regarding the glucan chain number (N) of CMFs during initial synthesis and whether they become fused afterward. Here, we combined small-angle X-ray scattering, solid-state nuclear magnetic resonance and X-ray diffraction analyses to resolve CMF nanostructures in native wood. We developed small-angle X-ray scattering measurement methods for the cross-section aspect ratio and area of the crystalline-ordered CMF core, which has a higher scattering length density than the semidisordered shell zone. The 1:1 aspect ratio suggested that CMFs remain mostly segregated, not fused. The area measurement reflected the chain number in the core zone (Ncore). To measure the ratio of ordered cellulose over total cellulose (Roc) by solid-state nuclear magnetic resonance, we developed a method termed global iterative fitting of T1ρ-edited decay (GIFTED), in addition to the conventional proton spin relaxation editing method. Using the formula N = Ncore/Roc, most wood CMFs were found to contain 24 glucan chains, conserved between gymnosperm and angiosperm trees. The average CMF has a crystalline-ordered core of ~2.2 nm diameter and a semidisordered shell of ~0.5 nm thickness. In naturally and artificially aged wood, we observed only CMF aggregation (contact without crystalline continuity) but not fusion (forming a conjoined crystalline unit). This further argued against the existence of partially fused CMFs in new wood, overturning the recently proposed 18-chain fusion hypothesis. Our findings are important for advancing wood structural knowledge and more efficient use of wood resources in sustainable bio-economies.

Interleukin 26 Induces Macrophage IL-9 Expression in Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is an autoimmune disease with chronic inflammation, bone erosion, and joint deformation. Synovial tissue in RA patients is full of proinflammatory cytokines and infiltrated immune cells, such as T help (Th) 9, Th17, macrophages, and osteoclasts. Recent reports emphasized a new member of the interleukin (IL)-10 family, IL-26, an inducer of IL-17A that is overexpressed in RA patients. Our previous works found that IL-26 inhibits osteoclastogenesis and conducts monocyte differentiation toward M1 macrophages. In this study, we aimed to clarify the effect of IL-26 on macrophages linking to Th9 and Th17 in IL-9 and IL-17 expression and downstream signal transduction. Murine and human macrophage cell lines and primary culture cells were used and stimulated by IL26. Cytokines expressions were evaluated by flow cytometry. Signal transduction and transcription factors expression were detected by Western blot and real time-PCR. Our results show that IL-26 and IL-9 colocalized in macrophage in RA synovium. IL-26 directly induces macrophage inflammatory cytokines IL-9 and IL-17A expression. IL-26 increases the IL-9 and IL-17A upstream mechanisms IRF4 and RelB expression. Moreover, the AKT-FoxO1 pathway is also activated by IL-26 in IL-9 and IL-17A expressing macrophage. Blockage of AKT phosphorylation enhances IL-26 stimulating IL-9-producing macrophage cells. In conclusion, our results support that IL-26 promotes IL-9- and IL-17-expressing macrophage and might initiate IL-9- and IL-17-related adaptive immunity in rheumatoid arthritis. Targeting IL-26 may a potential therapeutic strategy for rheumatoid arthritis or other IL-9 plus IL-17 dominant diseases.

Diagonal Interactions between Glutamate and Arginine Analogs with Varying Side-Chain Lengths in a ß-Hairpin.

Cross-strand interactions are important for the stability of ß-sheet structures. Accordingly, cross-strand diagonal interactions between glutamate and arginine analogs with varying side-chain lengths were studied in a series of ß-hairpin peptides. The peptides were analyzed by homonuclear two-dimensional nuclear magnetic resonance methods. The fraction folded population and folding free energy of the peptides were derived from the chemical shift data. The fraction folded population trends could be rationalized using the strand propensity of the constituting residues, which was not the case for the peptides with lysine analogs, highlighting the difference between the arginine analogs and lysine analogs. Double-mutant cycle analysis was used to derive the diagonal ion-pairing interaction energetics. The most stabilizing diagonal cross-strand interaction was between the shortest residues (i.e., Asp2-Agp9), most likely due to the least side-chain conformational penalty for ion-pair formation. The diagonal interaction energetics in this study involving the arginine analogs appears to be consistent with and extend beyond our understanding of diagonal ion-pairing interactions involving lysine analogs. The results should be useful for designing ß-strand-containing molecules to affect biological processes such as amyloid formation and protein-protein interactions.

Breast Tumor Classification using Short-ResNet with Pixel-based Tumor Probability Map in Ultrasound Images.

Breast cancer is the most common form of cancer and is still the second leading cause of death for women in the world. Early detection and treatment of breast cancer can reduce mortality rates. Breast ultrasound is always used to detect and diagnose breast cancer. The accurate breast segmentation and diagnosis as benign or malignant is still a challenging task in the ultrasound image. In this paper, we proposed a classification model as short-ResNet with DC-UNet to solve the segmentation and diagnosis challenge to find the tumor and classify benign or malignant with breast ultrasonic images. The proposed model has a dice coefficient of 83% for segmentation and achieves an accuracy of 90% for classification with breast tumors. In the experiment, we have compared with segmentation task and classification result in different datasets to prove that the proposed model is more general and demonstrates better results. The deep learning model using short-ResNet to classify tumor whether benign or malignant, that combine DC-UNet of segmentation task to assist in improving the classification results.

A molecular basis for tetramer destabilization and aggregation of transthyretin Ala97Ser.

Transthyretin (TTR)-related amyloidosis (ATTR) is a syndrome of diseases characterized by the extracellular deposition of fibrillar materials containing TTR variants. Ala97Ser (A97S) is the major mutation reported in Taiwanese ATTR patients. Here, we combine atomic resolution structural information together with the biochemical data to demonstrate that substitution of polar Ser for a small hydrophobic side chain of Ala at residue 97 of TTR largely influences the local packing density of the FG-loop, thus leading to the conformational instability of native tetramer, the increased monomeric species, and thus the enhanced amyloidogenicity of apo-A97S. Based on calorimetric studies, the tetramer destabilization of A97S can be substantially altered by interacting with native stabilizers via similarly energetic patterns compared to that of wild-type (WT) TTR; however, stabilizer binding partially rearranges the networks of hydrogen bonding in TTR variants while FG-loops of tetrameric A97S still remain relatively flexible. Moreover, TTR in complexed with holo-retinol binding protein 4 is slightly influenced by the structural and dynamic changes of FG-loop caused by A97S substitution with an approximately five-fold difference in binding affinity. Collectively, our findings suggest that the amyloidogenic A97S mutation destabilizes TTR by increasing the flexibility of the FG-loop in the monomer, thus modulating the rate of amyloid fibrillization.

Hydrogen phosphates play a critical structural role in amorphous calcium phosphates.

Amorphous calcium phosphate (ACP) is an intriguing mineral phase of calcium phosphate in its own right, in addition to its relevance in biomineralization. We hereby demonstrate that ACPs prepared by different synthetic routes such as the crosslinking of inorganic oligomers and polymer-induced liquid precursors have distinctive relative compositions of orthophosphate and hydrogen phosphate, and the extent of their hydrogen bonding with water. For all the ACPs or ACP-derived materials studied in this work, the species of hydrogen phosphate is the most important structural element. Depending on the synthetic pathways, orthophosphate and water, as well as their associated hydrogen bonds, may also play a role in the structural formation of ACPs.

Site specific NMR characterization of abeta-40 oligomers cross seeded by abeta-42 oligomers.

Extracellular accumulation of ß amyloid peptides of 40 (Aß40) and 42 residues (Aß42) has been considered as one of the hallmarks in the pathology of Alzheimer's disease. In this work, we are able to prepare oligomeric aggregates of Aß with uniform size and monomorphic structure. Our experimental design is to incubate Aß peptides in reverse micelles (RMs) so that the peptides could aggregate only through a single nucleation process and the size of the oligomers is confined by the physical dimension of the reverse micelles. The hence obtained Aß oligomers (AßOs) are 23 nm in diameter and they belong to the category of high molecular-weight (MW) oligomers. The solid-state NMR data revealed that Aß40Os adopt the structural motif of ß-loop-ß but the chemical shifts manifested that they may be structurally different from low-MW AßOs and mature fibrils. From the thioflavin-T results, we found that high-MW Aß42Os can accelerate the fibrillization of Aß40 monomers. Our protocol allows performing cross-seeding experiments among oligomeric species. By comparing the chemical shifts of Aß40Os cross seeded by Aß42Os and those of Aß40Os prepared in the absence of Aß42Os, we observed that the chemical states of E11, K16, and E22 were altered, whereas the backbone conformation of the ß-sheet region near the C-terminus was structurally invariant. The use of reverse micelles allows hitherto the most detailed characterization of the structural variability of Aß40Os.

The Effects of Charged Amino Acid Side-Chain Length on Diagonal Cross-Strand Interactions between Carboxylate- and Ammonium-Containing Residues in a ß-Hairpin.

The ß-sheet is one of the common protein secondary structures, and the aberrant aggregation of ß-sheets is implicated in various neurodegenerative diseases. Cross-strand interactions are an important determinant of ß-sheet stability. Accordingly, both diagonal and lateral cross-strand interactions have been studied. Surprisingly, diagonal cross-strand ion-pairing interactions have yet to be investigated. Herein, we present a systematic study on the effects of charged amino acid side-chain length on a diagonal ion-pairing interaction between carboxylate- and ammonium-containing residues in a ß-hairpin. To this end, 2D-NMR was used to investigate the conformation of the peptides. The fraction folded population and the folding free energy were derived from the chemical shift data. The fraction folded population for these peptides with potential diagonal ion pairs was mostly lower compared to the corresponding peptide with a potential lateral ion pair. The diagonal ion-pairing interaction energy was derived using double mutant cycle analysis. The Asp2-Dab9 (Asp: one methylene; Dab: two methylenes) interaction was the most stabilizing (-0.79 ± 0.14 kcal/mol), most likely representing an optimal balance between the entropic penalty to enable the ion-pairing interaction and the number of side-chain conformations that can accommodate the interaction. These results should be useful for designing ß-sheet containing molecular entities for various applications.

Direct investigation of the reorientational dynamics of A-site cations in 2D organic-inorganic hybrid perovskite by solid-state NMR.

Limited methods are available for investigating the reorientational dynamics of A-site cations in two-dimensional organic-inorganic hybrid perovskites (2D OIHPs), which play a pivotal role in determining their physical properties. Here, we describe an approach to study the dynamics of A-site cations using solid-state NMR and stable isotope labelling. 2H NMR of 2D OIHPs incorporating methyl-d3-ammonium cations (d3-MA) reveals the existence of multiple modes of reorientational motions of MA. Rotational-echo double resonance (REDOR) NMR of 2D OIHPs incorporating 15N- and ¹³C-labeled methylammonium cations (13C,15N-MA) reflects the averaged dipolar coupling between the C and N nuclei undergoing different modes of motions. Our study reveals the interplay between the A-site cation dynamics and the structural rigidity of the organic spacers, so providing a molecular-level insight into the design of 2D OIHPs.

Alpha-Lipoic Acid Inhibits Spontaneous Diabetes and Autoimmune Recurrence in Non-Obese Diabetic Mice by Enhancing Differentiation of Regulatory T Cells and Showed Potential for Use in Cell Therapies for the Treatment of Type 1 Diabetes.

Type 1 diabetes (T1D) is caused by the destruction of ß cells in pancreatic islets by autoimmune T cells. Islet transplantation has been established as an effective treatment for T1D. However, the survival of islet grafts is often disrupted by recurrent autoimmunity. Alpha-lipoic acid (ALA) has been reported to have immunomodulatory effects and, therefore, may have therapeutic potential in the treatment of T1D. In this study, we investigated the therapeutic potential of ALA in autoimmunity inhibition. We treated non-obese diabetic (NOD) mice with spontaneous diabetes and islet-transplantation mice with ALA. The onset of diabetes was decreased and survival of the islet grafts was extended. The populations of Th1 cells decreased, and regulatory T cells (Tregs) increased in ALA-treated mice. The in vitro Treg differentiation was significantly increased by treatment with ALA. The adoptive transfer of ALA-differentiated Tregs into NOD recipients improved the outcome of the islet grafts. Our results showed that in vivo ALA treatment suppressed spontaneous diabetes and autoimmune recurrence in NOD mice by inhibiting the Th1 immune response and inducing the differentiation of Tregs. Our study also demonstrated the therapeutic potential of ALA in Treg-based cell therapies and islet transplantation used in the treatment of T1D.

Cholesterol Modulates the Interaction between HIV-1 Viral Protein R and Membrane.

Being a major metabolite for maintaining cellular homeostasis, as well as an important structural component in lipid membrane, cholesterol also plays critical roles in the life cycles of some viruses, including human immunodeficiency virus-1 (HIV-1). The involvement of cholesterol in HIV-1 infectivity, assembly and budding has made it an important research target. Viral protein R (Vpr) is an accessory protein of HIV-1, which is involved in many major events in the life cycle of HIV-1. In addition to its multi-functional roles in the HIV-1 life cycle, it is shown to interact with lipid membrane and form a cation-selective channel. In this work, we examined the effect of cholesterol on the interaction of Vpr and lipid membrane. Using calcein release assay, we found that the membrane permeability induced by the membrane binding of Vpr was significantly reduced in the presence of cholesterol in membrane. In addition, using solid-state NMR (ssNMR) spectroscopy, Vpr was shown to experience multiple chemical environments in lipid membrane, as indicated by the broad line shape of carbonyl 13C resonance of Cys-76 residue ranging from 165-178 ppm, which can be attributed to the existence of complex Vpr-membrane environments. We further showed that the presence of cholesterol in membrane will alter the distribution of Vpr in the complex membrane environments, which may explain the change of the Vpr induced membrane permeability in the presence of cholesterol.

Formation and Near-Infrared Emission of CsPbI3 Nanoparticles Embedded in Cs4PbI6 Crystals.

Cs4PbI6, as a rarely investigated member of the Cs4PbX6 (X is a halogen element) family, has been successfully synthesized at low temperatures, and the synthetic conditions have been optimized. Metal iodides such as LiI, KI, NiI2, CoI2, and ZnI2, as additives, play an important role in enhancing the formation of the Cs4PbI6 microcrystals. ZnI2 with the lowest dissociation energy is the most efficient additive to supply iodide ions, and its amount of addition has also been optimized. Strong red to near-infrared (NIR) emission properties have been detected, and its optical emission centers have been identified to be numerous embedded perovskite-type α-CsPbI3 nanocrystallites (∼5 nm in diameter) based on investigations of temperature- and pressure-dependent photoluminescent properties. High-resolution transmission electron microscopy was used to detect these hidden nanoparticles, although the material was highly beam-sensitive and confirmed a "raisin bread"-like structure of the Cs4PbI6 crystals. A NIR mini-LED for the biological application has been successfully fabricated using as-synthesized Cs4PbI6 crystals. This work provides information for the future development of infrared fluorescent nanoscale perovskite materials.

Valproic Acid Suppresses Autoimmune Recurrence and Allograft Rejection in Islet Transplantation through Induction of the Differentiation of Regulatory T Cells and Can Be Used in Cell Therapy for Type 1 Diabetes.

Type 1 diabetes mellitus (T1D) results from the destruction of insulin-producing ß cells in the islet of the pancreas by lymphocytes. Non-obese diabetic (NOD) mouse is an animal model frequently used for this disease. It has been considered that T1D is a T cell-mediated autoimmune disease. Both CD4+ and CD8+ T cells are highly responsible for the destruction of ß cells within the pancreatic islets of Langerhans. Previous studies have revealed that regulatory T (Treg) cells play a critical role in the homeostasis of the immune system as well as immune tolerance to autoantigens, thereby preventing autoimmunity. Valproic acid (VPA), a branched short-chain fatty acid, is widely used as an antiepileptic drug and a mood stabilizer. Previous reports have demonstrated that VPA treatment decreases the incidence and severity of collagen-induced arthritis and experimental autoimmune neuritis by increasing the population of Treg cells in these mouse disease models. Given the effect of VPA in the induction of Treg cells' population, we evaluated the therapeutic potential and the protective mechanism of VPA treatment in the suppression of graft autoimmune rejection and immune recurrence in syngeneic or allogenic islet transplantation mouse models. In our study, we found that the treatment of VPA increased the expression of forkhead box P3 (FOXP3), which is a critical transcription factor that controls Treg cells' development and function. Our data revealed that 400 mg/kg VPA treatment in recipients effectively prolonged the survival of syngeneic and allogenic islet grafts. The percentage of Treg cells in splenocytes increased in VPA-treated recipients. We also proved that adoptive transfer of VPA-induced Tregs to the transplanted recipients effectively prolonged the survival of islet grafts. The results of this study provide evidence of the therapeutic potential and the underlying mechanism of VPA treatment in syngeneic islet transplantation for T1D. It also provides experimental evidence for cell therapy by adoptive transferring of in vitro VPA-induced Tregs for the suppression of autoimmune recurrence.

Longer charged amino acids favor ß-strand formation in hairpin peptides.

Interactions between charged amino acids significantly influence the structure and function of proteins. The encoded charged amino acids Asp, Glu, Arg, and Lys have different number of hydrophobic methylenes linking the backbone to the charged functionality. It remains to be fully understood how does this difference in the number of methylenes affect protein structure stability. Protein secondary structures are the fundamental three-dimensional building blocks of protein structures. ß-Sheet structures are particularly interesting, because these structures have been associated with a number of protein misfolding diseases. Herein, we report the effect of charged amino acid side chain length at two ß-strand positions individually on the stability of a ß-hairpin. The charged amino acids include side chains with a carboxylate, an ammonium, or a guanidinium group. The experimental peptides, fully folded reference peptides, and fully unfolded reference peptides were synthesized by solid phase peptide synthesis and analyzed by 2D NMR methods including TOCSY, DQF-COSY, and ROESY. Sequence specific assignments were performed for all peptides. The chemical shift data were used to derive the fraction folded population and the folding free energy for the experimental peptides. Results showed that the fraction folded population increased with increasing charged amino acid side chain length. These results should be useful for developing functional peptides that adopt the ß-conformation.