[Cu36H10(PET)24(PPh3)6Cl2] Reveals Surface Vacancy Defects in Ligand-Stabilized Metal Nanoclusters.

Precise identification and in-depth understanding of defects in nanomaterials can aid in rationally modulating defect-induced functionalities. However, few studies have explored vacancy defects in ligand-stabilized metal nanoclusters with well-defined structures, owing to the substantial challenge of synthesizing and isolating such defective metal nanoclusters. Herein, a novel defective copper hydride nanocluster, [Cu36H10(PET)24(PPh3)6Cl2] (Cu36; PET: phenylethanethiolate; PPh3: triphenylphosphine), is successfully synthesized at the gram scale via a simple one-pot reduction method. Structural analysis reveals that Cu36 is a distorted half cubic nanocluster, evolved from the perfect Nichol's half cube. The two surface copper vacancies in Cu36 are found to be the principal imperfections, which result in some structural adjustments, including copper atom reconstruction near the vacancies as well as ligand modifications (e.g., substitution, migration, and exfoliation). Density functional theory calculations imply that the above-mentioned defects have a considerable influence on the electronic structure and properties. The modeling suggests that the formation of defective Cu36 rather than the perfect half cube is driven by the enlargement of the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital of the nanocluster. The structural evolution induced by the surface copper atom vacancies provides atomically precise insights into the defect-induced readjustment of the local structure and introduces new avenues for understanding the chemistry of defects in nanomaterials.

H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing.

As an environment-dependent pleiotropic gene regulator in Gram-negative bacteria, the H-NS protein is crucial for adaptation and toxicity control of human pathogens such as Salmonella, Vibrio cholerae or enterohaemorrhagic Escherichia coli. Changes in temperature affect the capacity of H-NS to form multimers that condense DNA and restrict gene expression. However, the molecular mechanism through which H-NS senses temperature and other physiochemical parameters remains unclear and controversial. Combining structural, biophysical and computational analyses, we show that human body temperature promotes unfolding of the central dimerization domain, breaking up H-NS multimers. This unfolding event enables an autoinhibitory compact H-NS conformation that blocks DNA binding. Our integrative approach provides the molecular basis for H-NS-mediated environment-sensing and may open new avenues for the control of pathogenic multi-drug resistant bacteria.

Structural basis for specific inhibition of the highly sensitive ShHTL7 receptor.

Striga hermonthica is a root parasitic plant that infests cereals, decimating yields, particularly in sub-Saharan Africa. For germination, Striga seeds require host-released strigolactones that are perceived by the family of HYPOSENSITIVE to LIGHT (ShHTL) receptors. Inhibiting seed germination would thus be a promising approach for combating Striga However, there are currently no strigolactone antagonists that specifically block ShHTLs and do not bind to DWARF14, the homologous strigolactone receptor of the host. Here, we show that the octyl phenol ethoxylate Triton X-100 inhibits S. hermonthica seed germination without affecting host plants. High-resolution X-ray structures reveal that Triton X-100 specifically plugs the catalytic pocket of ShHTL7. ShHTL7-specific inhibition by Triton X-100 demonstrates the dominant role of this particular ShHTL receptor for Striga germination. Our structural analysis provides a rationale for the broad specificity and high sensitivity of ShHTL7, and reveals that strigolactones trigger structural changes in ShHTL7 that are required for downstream signaling. Our findings identify Triton and the related 2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]acetic acid as promising lead compounds for the rational design of efficient Striga-specific herbicides.

Thielavins W-Z7, New Antifouling Thielavins from the Marine-Derived Fungus Thielavia sp. UST030930-004.

Eleven new depsides-thielavins W-Z (1-4) and thielavins Z1-Z7 (5-11)-and also four known thielavins-A, H, J, and K (12-15)-were isolated from the ethyl acetate extract of a marine-derived fungal strain Thielavia sp UST030930-004. All of these compounds were evaluated for antifouling activity against cyprids of the barnacle Balanus (=Amphibalanus) amphitrite. The results showed that compounds 1-3 and 6-13 were active, with EC50 values ranging from 2.95 ± 0.59 to 69.19 ± 9.51 µM, respectively. The inhibitive effect of compounds 1-3 and 7 was reversible. This is the first description of the antifouling activity of thielavins against barnacle cyprids.

An automated framework for NMR resonance assignment through simultaneous slice picking and spin system forming.

Despite significant advances in automated nuclear magnetic resonance-based protein structure determination, the high numbers of false positives and false negatives among the peaks selected by fully automated methods remain a problem. These false positives and negatives impair the performance of resonance assignment methods. One of the main reasons for this problem is that the computational research community often considers peak picking and resonance assignment to be two separate problems, whereas spectroscopists use expert knowledge to pick peaks and assign their resonances at the same time. We propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems, to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from the existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on 'slices', which are one-dimensional vectors in three-dimensional spectra that correspond to certain ([Formula: see text]) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods while using a less number of spectra than those methods. Our method is freely available at http://sfb.kaust.edu.sa/Pages/Software.aspx.

Caspase-3-dependent apoptosis of citreamicin ε-induced HeLa cells is associated with reactive oxygen species generation.

Citreamicins, members of the polycyclic xanthone family, are promising antitumor agents that are produced by Streptomyces species. Two diastereomers, citreamicin ε A (1) and B (2), were isolated from a marine-derived Streptomyces species. The relative configurations of these two diastereomers were determined using NMR spectroscopy and successful crystallization of citreamicin ε A (1). Both diastereomers showed potent cytotoxic activity against HeLa (cervical cancer) and HepG2 (hepatic carcinoma) cells with IC50 values ranging from 30 to 100 nM. The terminal deoxynucleotidyl transferase dUTP nick-end labeling assay confirmed that citreamicin ε A (1) induced cellular apoptosis, and Western blot analysis showed that apoptosis occurred via activation of caspase-3. The 2,7-dichlorofluorescein diacetate assay indicated that citreamicin ε substantially increased the intracellular concentration of reactive oxygen species (ROS). To confirm the hypothesis that citreamicin ε induced apoptosis through an increase in the intracellular ROS concentration, the oxidized products, oxicitreamicin ε A (3) and B (4), were obtained from a one-step reaction catalyzed by Ag2O. These products, with a reduced capacity to increase the intracellular ROS concentration, exhibited a significantly weakened cytotoxicity in both HeLa and HepG2 cells compared with that of citreamicin ε A (1) and B (2).

Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases.

Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper-binding, cell-surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP(C)) and a disease-associated isoform (PrP(Sc)). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP(C) into PrP(Sc). The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins.

Optimized Charge Storage in Aza-Based Covalent Organic Frameworks by Tuning Electrolyte Proton Activity.

Proton activity in electrolytes plays a crucial role in deciding the electrochemical performance of aqueous batteries. On the one hand, it can influence the capacity and rate performance of host materials because of the high redox activity of protons. On the other hand, it can also cause a severe hydrogen evolution reaction (HER) when the protons are aggregated near the electrode/electrolyte interface. The HER dramatically limits the potential window and the cycling stability of the electrodes. Therefore, it is critical to clarify the impact of electrolyte proton activity on the battery macro-electrochemical performance. In this work, using an aza-based covalent organic framework (COF) as a representative host material, we studied the effect of electrolyte proton activity on the potential window, storage capacity, rate performance, and cycle stability in various electrolytes. A tradeoff relationship between proton redox reactions and the HER in the COF host is revealed by utilizing various in situ and ex situ characterizations. Moreover, the origin of proton activity in near-neutral electrolytes is discussed in detail and is confirmed to be related to the hydrated water molecules in the first solvation shell. A detailed analysis of the charge storage process in the COFs is presented. These understandings can be of importance for utilizing the electrolyte proton activity to build high-energy aqueous batteries.

mTOR complex 2 activation by reconstituted high-density lipoprotein prevents senescence in circulating angiogenic cells.

OBJECTIVE: Circulating angiogenic cells (CACs) participate in neovascularization and arterial repair. Although high-density lipoprotein (HDL) is known to enhance the functional activity of CACs, the mechanisms underlying this regulation are poorly understood. Here, we examined the mechanism(s) by which reconstituted HDL (rHDL) affects CAC senescence. METHODS AND RESULTS: CACs isolated from human peripheral blood and treated with rHDL displayed reduced senescence, as measured by acidic ß-galactosidase staining. This protective effect was blocked by the mammalian target of rapamycin (mTOR) inhibitor (rapamycin). According to Western blot analysis and immunoprecipitation results, rHDL promoted mTOR phosphorylation, mTOR-rictor complex formation, and mTOR-rictor-dependent Akt activation, which were accompanied by increased nuclear translocation of human telomerase reverse transcriptase and enhanced nuclear telomerase activity. Suppression of rictor gene expression with a small interfering RNA blocked mTOR-rictor complex formation and Akt activation. The suppression also abolished the rHDL-induced inhibition of CAC senescence and promotion of nuclear telomerase activity. Treatment of aged mice with rHDL attenuated spleen-derived CAC senescence. In CACs isolated from rHDL-treated aged mice, the phosphorylated mTOR and Akt levels were significantly enhanced. CONCLUSION: rHDL stimulates sustained mTOR phosphorylation and mTOR-rictor complex formation and inhibits senescence onset in CACs through mTOR complex 2 pathway activation.

Four new antibacterial xanthones from the marine-derived actinomycetes Streptomyces caelestis.

Four new polycyclic antibiotics, citreamicin θ A (1), citreamicin θ B (2), citreaglycon A (3), and dehydrocitreaglycon A (4), were isolated from marine-derived Streptomyces caelestis. The structures of these compounds were elucidated by 1D and 2D NMR spectra. All four compounds displayed antibacterial activity against Staphylococcus haemolyticus, Staphylococcus aureus, and Bacillus subtillis. Citreamicin θ A (1), citreamicin θ B (2) and citreaglycon A (3) also exhibited low MIC values of 0.25, 0.25, and 8.0 µg/mL, respectively, against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300.

Hitherto Unknown Solvent and Anion Pairs in Solvation Structures Reveal New Insights into High-Performance Lithium-Ion Batteries.

Solvent-solvent and solvent-anion pairings in battery electrolytes have been identified for the first time by nuclear magnetic resonance spectroscopy. These hitherto unknown interactions are enabled by the hydrogen bonding induced by the strong Lewis acid Li+ , and exist between the electron-deficient hydrogen (δ+ H) present in the solvent molecules and either other solvent molecules or negatively-charged anions. Complementary with the well-established strong but short-ranged Coulombic interactions between cation and solvent molecules, such weaker but longer-ranged hydrogen-bonding casts the formation of an extended liquid structure in electrolytes that is influenced by their components (solvents, additives, salts, and concentration), which in turn dictates the ion transport within bulk electrolytes and across the electrolyte-electrode interfaces. The discovery of this new inter-component force completes the picture of how electrolyte components interact and arrange themselves, sets the foundation to design better electrolytes on the fundamental level, and probes battery performances.

NMR studies on binding sites and aggregation-disassociation of fluorinated surfactant sodium perfluorooctanoate on protein ubiquitin.

The fluorinated surfactant sodium perfluorooctanoate (SPFO) could bind onto ubiquitin (UBQ) and induce the unfolding of UBQ. By using (15)N-edited heteronuclear single-quantum coherence (HSQC) NMR and (19)F NMR to monitor (15)N-labeled UBQ and SPFO, respectively, the binding sites and the aggregation process of SPFO on UBQ at various SPFO concentrations were observed. A detailed process from specific binding to cooperative binding of SPFO on UBQ, and a detailed structure change of UBQ upon the increase of SPFO concentration were obtained. The refolding of UBQ in UBQ-SPFO complex was carried out by adding cationic surfactant. It was shown that added cationic surfactants formed mixed micelles with SPFO and resulted in the dissociation of the UBQ-SPFO complex, and consequently, most ubiquitin could be refolded to its native state.

Docking of tetra-methyl zirconium to the surface of silica: a well-defined pre-catalyst for conversion of CO2 to cyclic carbonates.

The metal complex (Zr(CH3)4(THF)2) has been fully synthesized, characterized and grafted onto partially dehydroxylated silica to give two surface species [([triple bond, length as m-dash]Si-O-)Zr(CH3)3(THF)2] (minor) and [([triple bond, length as m-dash]Si-O-)2Zr(CH3)2(THF)2] (major) which have been characterized by SS NMR, IR, and elemental analysis. These supported pre-catalysts exhibit the best conversion of CO2 to cyclic carbonates, as compared to the previously reported SOMC catalysts.

De novo design of a beta alpha beta motif.

A designer monomeric protein with a beta alpha beta fold--two parallel beta strands connected by an alpha helix (see structure)--was constructed solely from coded amino acids. The high thermal stability of the structure is due to a large extent to tryptophan-tryptophan interactions between the two beta strands.

A Slice-based 13C-detected NMR Spin System Forming and Resonance Assignment Method.

Nuclear magnetic resonance (NMR) spectroscopy is attracting more attention in the field of computational structural biology. Till recently, 1H-detected experiments are the dominant NMR technique used due to the high sensitivity of 1H nuclei. However, the current availability of high magnetic fields and cryogenically cooled probe heads allow researchers to overcome the low sensitivity of 13C nuclei. Consequently, 13C-detected experiments have become a popular technique in different NMR applications especially resonance assignment and structure determination of large proteins. In this paper, we propose the first spin system forming method for 13C-detected NMR spectra. Our method is able to accurately form spin systems based on as few as two 13C-detected spectra, CBCACON, and CBCANCO. Our method picks slices from the more trusted spectrum and uses them as feedback to direct the slice picking in the less trusted one. This feedback leads to picking the accurate slices that consequently helps to form better spin systems. We tested our method on a real dataset of 'Ubiquitin' and a benchmark simulated dataset consisting of 12 proteins. We fed our spin systems as inputs to a genetic algorithm to generate the chemical shift assignment, and obtained 92 percent correct chemical shift assignment for Ubiquitin. For the simulated dataset, we obtained an average recall of 86 percent and an average precision of 88 percent. Finally, our chemical shift assignment of Ubiquitin was given as an input to CS-ROSETTA server that generated structures close to the experimentally determined structure.

Poly-ethers from Winogradskyella poriferorum: Antifouling potential, time-course study of production and natural abundance.

A sponge-associated bacterium, Winogradskyella poriferorum strain UST030701-295T was cultured up to 100l for extraction of antifouling bioactive compounds. Five poly-ethers were isolated and partially characterized based on nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS); two of them showed inhibitory effects on biofilm formation of marine bacteria and larval settlement of macro-foulers but did not produce any adverse effects on the phenotypes of zebra fish embryos at a concentration of 5µg ml(-1). The effect of culture duration on the production of the poly-ethers and the bioactivity of the relevant extracts was monitored over a period of 12 days. The total crude poly-ether production increased from day 2 to day 5 and the highest bioactivity was observed on day 3. The poly-ethers were found to be localized in the cellular fraction of the extracts, implying their natural occurrence. The potent bioactivity of these poly-ethers together with their high natural abundance in bacteria makes them promising candidates as ingredients in antifouling applications.

The Bacillus subtilis YkuV is a thiol:disulfide oxidoreductase revealed by its redox structures and activity.

The Bacillus subtilis YkuV responds to environmental oxidative stress and plays an important role for the bacteria to adapt to the environment. Bioinformatic analysis suggests that YkuV is a homolog of membrane-anchored proteins and belongs to the thioredoxin-like protein superfamily containing the typical Cys-Xaa-Xaa-Cys active motif. However, the biological function of this protein remains unknown thus far. In order to elucidate the biological function, we have determined the solution structures of both the oxidized and reduced forms of B. subtilis YkuV by NMR spectroscopy and performed biochemical studies. Our results demonstrated that the reduced YkuV has a low midpoint redox potential, allowing it to reduce a variety of protein substrates. The overall structures of both oxidized and reduced forms are similar, with a typical thioredoxin-like fold. However, significant conformational changes in the Cys-Xaa-Xaa-Cys active motif of the tertiary structures are observed between the two forms. In addition, the backbone dynamics provide further insights in understanding the strong redox potential of the reduced YkuV. Furthermore, we demonstrated that YkuV is able to reduce different protein substrates in vitro. Together, our results clearly established that YkuV may function as a general thiol:disulfide oxidoreductase, which acts as an alternative for thioredoxin or thioredoxin reductase to maintain the reducing environment in the cell cytoplasm.

Solution structures and backbone dynamics of a flavodoxin MioC from Escherichia coli in both Apo- and Holo-forms: implications for cofactor binding and electron transfer.

Flavodoxins play central roles in the electron transfer involving various biological processes in microorganisms. The mioC gene of Escherichia coli encodes a 16-kDa flavodoxin and locates next to the chromosomal replication initiation origin (oriC). Extensive researches have been carried out to investigate the relationship between mioC transcription and replication initiation. Recently, the MioC protein was proposed to be essential for the biotin synthase activity in vitro. Nevertheless, the exact role of MioC in biotin synthesis and its physiological function in vivo remain elusive. In order to understand the molecular basis of the biological functions of MioC and the cofactor-binding mechanisms of flavodoxins, we have determined the solution structures of both the apo- and holo-forms of E. coli MioC protein at high resolution by nuclear magnetic resonance spectroscopy. The overall structures of both forms consist of an alpha/beta sandwich, which highly resembles the classical flavodoxin fold. However, significant diversities are observed between the two forms, especially the stabilization of the FMN-binding loops and the notable extension of secondary structures upon FMN binding. Structural comparison reveals fewer negative charged and aromatic residues near the FMN-binding site of MioC, as compared with that of flavodoxin 1 from E. coli, which may affect both the redox potentials and the redox partner interactions. Furthermore, the backbone dynamics studies reveal the conformational flexibility at different time scales for both apo- and holo-forms of MioC, which may play important roles for cofactor binding and electron transfer.

Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases.

The RPB8 subunit is present in all three types of eukaryotic RNA polymerases and is highly conserved during evolution. It is an essential subunit required for the transcription of nuclear genes, but the detailed mechanism including its interactions with different subunits and oligonucleotides remains largely unclear. Herein, we report the three-dimensional structure of human RPB8 (hRPB8) at high resolution determined by NMR spectroscopy. The protein fold comprises an eight-stranded beta-barrel, six short helices, and a large unstructured Omega-loop. The overall structure of hRPB8 is similar to that of yRPB8 from Saccharomyces cerevisiae and belongs to the oligonucleotide/oligosaccharide-binding fold. However, several features of the tertiary structures are notably different between the two proteins. In particular, hRPB8 has a more clustered positively charged binding interface with the largest subunit RPB1 of the RNA polymerases. We employed biochemical methods to detect its interactions with different single-stranded DNA sequences. In addition, single-stranded DNA titration experiments were performed to identify the residues involved in nonspecific binding with different DNA sequences. Furthermore, we characterized the millisecond time scale conformational flexibility of hRPB8 upon its binding to single-stranded DNA. The current results demonstrate that hRPB8 interacts with single-stranded DNA nonspecifically and adopts significant conformational changes, and the hRPB8/single-stranded DNA complex is a fast exchanging system. The solution structure in conjunction with the biochemical and dynamic studies reveal new aspects of this subunit in the molecular assembly and the biological function of the human nuclear RNA polymerases.