We report the total structure of Au(38)(SC(2)H(4)Ph)(24) nanoparticles determined by single crystal X-ray crystallography. This nanoparticle is based upon a face-fused Au(23) biicosahedral core, which is further capped by three monomeric Au(SR)(2) staples at the waist of the Au(23) rod and six dimeric staples with three on the top icosahedron and other three on the bottom icosahedron. The six Au(2)(SR)(3) staples are arranged in a staggered configuration, and the Au(38)S(24) framework has a C(3) rotation axis.

We report a facile, high yielding synthetic method for preparing truly monodisperse Au(38)(SC(2)H(4)Ph)(24) nanoclusters. The synthetic approach involves two main steps: first, glutathionate (-SG) protected polydisperse Au(n) clusters (n ranging from 38 to approximately 102) are synthesized by reducing Au(I)-SG in acetone; subsequently, the size-mixed Au(n) clusters react with excess phenylethylthiol (PhC(2)H(4)SH) for approximately 40 h at 80 degrees C, which leads to Au(38)(SC(2)H(4)Ph)(24) clusters of molecular purity. Detailed studies by mass spectrometry and UV-vis spectroscopy explicitly show a gradual size-focusing process occurred in the thermal etching-induced growth process. The formula and molecular purity of Au(38)(SC(2)H(4)Ph)(24) clusters are confirmed by electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry, and size-exclusion chromatography. The optical and electrochemical properties of Au(38)(SC(2)H(4)Ph)(24) clusters show molecule-like behavior and the HOMO-LUMO gap of the cluster was determined to be approximately 0.9 eV. The size focusing growth process is particularly interesting and may be exploited to synthesize other robust gold thiolate clusters.

Since Faraday's pioneering work on gold colloids, tremendous scientific research on plasmonic gold nanoparticles has been carried out, but no atomically precise Au nanocrystals have been achieved. This work reports the first example of gold nanocrystal molecules. Mass spectrometry analysis has determined its formula to be Au 333 ðSRÞ 79 (R ¼ CH 2 CH 2 Ph). This magic sized nanocrystal molecule exhibits fcc-crystallinity and surface plasmon resonance at approximately 520 nm, hence, a metallic nanomolecule. Simulations have revealed that atomic shell closing largely contributes to the particular robustness of Au 333 ðSRÞ 79 , albeit the number of free electrons (i.e., 333 − 79 ¼ 254) is also consistent with electron shell closing based on calculations using a confined free electron model. Guided by the atomic shell closing growth mode, we have also found the next larger size of extraordinarily stability to be Au ∼530 ðSRÞ ∼100 after a size-focusing selection-which selects the robust size available in the starting polydisperse nanoparticles. This work clearly demonstrates that atomically precise nanocrystal molecules are achievable and that the factor of atomic shell closing contributes to their extraordinary stability compared to other sizes. Overall, this work opens up new opportunities for investigating many fundamental issues of nanocrystals, such as the formation of metallic state, and will have potential impact on condensed matter physics, nanochemistry, and catalysis as well.atomic precision | face-centered cubic | nanomolecule | plasmonic excitation N oble metal nanocrystals have attracted significant interest in both fundamental research and technological applications due primarily to their elegant surface plasmon resonance properties (1-6). Scientific studies on gold nanocrystals date back to Faraday's time in the nineteenth century (7). A classic procedure for the synthesis of gold nanocrystals is the citrate method, which produces quite uniform approximately 10-100 nm diameter nanocrystals with size tunable by controlling the ratio of sodium citrate to gold precursor (8, 9). Compared to the citrate-stabilized Au nanocrystals, thiolate-protected Au nanoparticles are more robust due to strong Au-SR bonds and have found important applications in biomedicine and many other fields (10-18). From the synthetic point of view, in all the previous synthetic works the obtained Au nanocrystals are more or less polydispersed, even the best quality Au nanocrystals achievable thus far-which still has a size dispersity of around 5-10%. Thus, it has long been a dream of nano-chemists to synthesize atomically precise, plasmonic nanocrystals for fundamental studies. Herein, we report the first example of atomically precise gold nanocrystals. Mass spectrometric analyses, in conjunction with other characterization, have determined its molecular formula to be Au 333 ðSRÞ 79 (where SR ¼ SCH 2 CH 2 Ph). This giant gold nanomolecule exhibits face-centered cubic (fcc) structure and surface plasmon resonance at approximately 520 ...

A golden opportunity: A mechanism has been proposed to account for the chemoselective hydrogenation of α,β‐unsaturated ketones (or aldehydes) to unsaturated alcohols catalyzed by monodisperse Au25(SR)18 particles (see picture). Now that the structure of these nanoparticles is known, structure–activity correlations can be drawn.

Here we demonstrate that domain A by itself has the phosphatase activity both in vitro and in vivo. This phosphatase activity is Mg 2؉ dependent but is not activated by ADP, ATP, or adenosine 5-[␤,␥-imido]triphosphate (AMPPNP), each of which may serve as a cofactor for the EnvZ phosphatase activity. Domain B showed a small but distinct effect on the domain A phosphatase activity only in the presence of ADP or AMPPNP. However, when domain B was covalently linked to domain A, dramatic cofactordependent enhancement of the phosphatase activity was observed. Extending domain A for another 75 residues at the C terminus or 44 residues at the N terminus did not enhance its phosphatase activity. Substitution mutations at His-243, the autophosphorylation site, demonstrate that the His residue plays an essential role in the phosphatase activity. The so-called X-region mutant L288P that is known to specifically abolish the phosphatase activity in EnvZ had no effect on the domain A phosphatase function. We propose that the EnvZ phosphatase activity is regulated by relative positioning of domains A and B, which is controlled by external signals. We also propose that the His-243 residue participates in both kinase and phosphatase reactions. In prokaryotes the histidyl-aspartyl (His-Asp) phosphorelay signal transduction system plays a major role in cellular adaptation to various environmental stresses and growth conditions (1). EnvZ, the osmosensor in Escherichia coli, is a transmembrane histidine kinase consisting of 450 amino acid residues, of which the C-terminal cytoplasmic kinase domain possesses highly conserved regions (H box, N box, G1 box, F box, and G2 box) unique in histidine kinases (2, 3). OmpR, the cognate response regulator, is phosphorylated at Asp-55 by EnvZ. The phosphorylated product, OmpR-P, functions as a transcription factor and regulates the expression of the genes for porin proteins OmpF and OmpC. Most histidine kinases, including EnvZ, are bifunctional having both kinase and phosphatase activities (4-6). EnvZ, thus, has the OmpR kinase activity as well as OmpR-P phosphatase activity. It has been proposed that the cellular level of OmpR-P is regulated by the OmpR-P phosphatase activity, whereas the OmpR kinase activity is maintained at a constant level (7).EnvZ consists of the periplasmic putative receptor domain (residues 48-162), two transmembrane regions (TM1, residues 16-47; TM2, residues 163-179), the linker region (residues 180-222), and the cytoplasmic kinase domain (residues 223-450) (8, 9). The kinase domain possesses both kinase and phosphatase function as the full-length EnvZ and can be further dissected into two distinct functional domains: A (residues 223-289) and B (residues 290-450) (10). It has been demonstrated that domain A, containing the autophosphorylation site His-243, forms a stable dimer and can be phosphorylated in the presence of ATP by domain B that exists as a monomer. The phosphorylated domain A subsequently transfers the highenergy phosphoryl group to OmpR. Because of their ...

With the explosive growth of biological sequences generated in the post-genomic era, one of the most challenging problems in bioinformatics and computational biology is to computationally characterize sequences, structures and functions in an efficient, accurate and high-throughput manner. A number of online web servers and stand-alone tools have been developed to address this to date; however, all these tools have their limitations and drawbacks in terms of their effectiveness, user-friendliness and capacity. Here, we present iLearn, a comprehensive and versatile Python-based toolkit, integrating the functionality of feature extraction, clustering, normalization, selection, dimensionality reduction, predictor construction, best descriptor/model selection, ensemble learning and results visualization for DNA, RNA and protein sequences. iLearn was designed for users that only want to upload their data set and select the functions they need calculated from it, while all necessary procedures and optimal settings are completed automatically by the software. iLearn includes a variety of descriptors for DNA, RNA and proteins, and four feature output formats are supported so as to facilitate direct output usage or communication with other computational tools. In total, iLearn encompasses 16 different types of feature clustering, selection, normalization and dimensionality reduction algorithms, and five commonly used machine-learning algorithms, thereby greatly facilitating feature analysis and predictor construction. iLearn is made freely available via an online web server and a stand-alone toolkit.

We report a facile conversion of polydisperse Au nanoparticles (1−3.5 nm) into well-defined monodisperse 25-atom (Au25) nanorods and nanospheres via one-phase and two-phase thiol etching, respectively. Our method involves two main steps: first, small Au nanoparticles (polydisperse, predominantly 1−3.5 nm) were prepared by NaBH4 reduction of Au(III) salt in the presence of triphenylphosphine; subsequently, these polydisperse Au nanoparticles were used as a common precursor for shape-controlled synthesis of Au25 nanorods and nanospheres following one-phase and two-phase thiol etching, respectively. Our results demonstrate that the Au25 particle shape can be conveniently controlled by using different types of thiol ligands in the second step of thiol etching. These ultrasmall Au25 nanoparticles do not support surface plasmons as do their larger counterparts (i.e., Au nanocrystals); instead, they exhibit molecular-like optical absorption behavior. This conversion process is striking in two features, size focusing and shape control, and may be extendable to the synthesis of other robust well-defined Au nanoclusters.

SummaryThe second messenger cyclic-di-adenosine monophosphate (c-di-AMP) plays important roles in growth, virulence, cell wall homeostasis, potassium transport and affects resistance to antibiotics, heat and osmotic stress. Most Firmicutes contain only one c-di-AMP synthesizing diadenylate cyclase (CdaA); however, little is known about signals and effectors controlling CdaA activity and c-di-AMP levels. In this study, a genetic screen was employed to identify components which affect the c-di-AMP level in Lactococcus. We characterized suppressor mutations that restored osmoresistance to spontaneous c-di-AMP phosphodiesterase gdpP mutants, which contain high c-di-AMP levels. Loss-of-function and gain-of-function mutations were identified in the cdaA and gdpP genes, respectively, which led to lower c-di-AMP levels. A mutation was also identified in the phosphoglucosamine mutase gene glmM, which is commonly located within the cdaA operon in bacteria. The glmM I154F mutation resulted in a lowering of the c-di-AMP level and a reduction in the key peptidoglycan precursor UDP-N-acetylglucosamine in L. lactis. C-di-AMP synthesis by CdaA was shown to be inhibited by GlmM I154F more than GlmM and GlmM I154F was found to bind more strongly to CdaA than GlmM. These findings identify GlmM as a c-di-AMP level modulating protein and provide a direct connection between c-di-AMP synthesis and peptidoglycan biosynthesis.