Structural evidence of α-aminoacylated lipoproteins of Staphylococcus aureus.

Bacterial lipoproteins are known to be diacylated or triacylated and activate mammalian immune cells via Toll-like receptor 2/6 or 2/1 heterodimer. Because the genomes of low G+C content gram-positive bacteria, such as Staphylococcus aureus, do not contain Escherichia coli-type apolipoprotein N-acyltransferase, an enzyme converting diacylated lipoproteins into triacylated forms, it has been widely believed that native lipoproteins of S. aureus are diacylated.

Rapid naked-eye detection of mercury ions based on non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles.

Colorimetric detection of mercury ions (Hg(2+)) with the naked eye was accomplished within 1 min by a combination of non-crosslinking aggregation of double-stranded DNA-carrying gold nanoparticles and complex formation of thymine-Hg(2+)-thymine.

Enlightenment of yeast mitochondrial homoplasmy: diversified roles of gene conversion.

Mitochondria have their own genomic DNA. Unlike the nuclear genome, each cell contains hundreds to thousands of copies of mitochondrial DNA (mtDNA). The copies of mtDNA tend to have heterogeneous sequences, due to the high frequency of mutagenesis, but are quickly homogenized within a cell ("homoplasmy") during vegetative cell growth or through a few sexual generations.

The potential of protein disulfide isomerase as a therapeutic drug target.

Protein disulfide isomerase (PDI) is a multifunctional protein of the thioredoxin superfamily. PDI mediates proper protein folding by oxidation or isomerization and disrupts disulfide bonds by reduction; it also has chaperone and antichaperone activities. Although PDI localizes primarily to the endoplasmic reticulum (ER), it is secreted and expressed on the cell surface.

Screening for the Genes Involved in Bombykol Biosynthesis: Identification and Functional Characterization of Bombyx mori Acyl Carrier Protein.

Species-specific sex pheromones released by female moths to attract conspecific male moths are synthesized de novo in the pheromone gland (PG) via fatty acid synthesis (FAS). Biosynthesis of moth sex pheromones is usually regulated by a neurohormone termed pheromone biosynthesis activating neuropeptide (PBAN), a 33-aa peptide that originates in the subesophageal ganglion. In the silkmoth, Bombyx mori, cytoplasmic lipid droplets (LDs), which store the sex pheromone (bombykol) precursor fatty acid, accumulate in PG cells prior to eclosion.

Ultrafast photodynamics of furan.

Ultrafast photodynamics of furan has been studied by time-resolved photoelectron imaging (TRPEI) spectroscopy with an unprecedented time resolution of 22 fs. The simulation of the time-dependent photoelectron kinetic energy distribution (PKED) has been performed with ab initio nonadiabatic dynamics "on the fly" in the frame of time-dependent density functional theory. Based on the agreement between experimental and theoretical time-dependent photoelectron signal intensity as well as on PKED, precise time scales of ultrafast internal conversion from S(2) over S(1) to the ground state S(0) of furan have been revealed for the first time.

Synthesis and characterization of small circular double-stranded RNAs.

Small circular double-stranded RNAs (dsRNAs) were synthesized. The structural analysis by atomic force microscopy gave direct images for the interpretation of the structural strain present in circular dsRNAs. Finally, we demonstrated that circular dsRNA caused RNAi effect in cells.

Structural basis for oligosaccharide recognition of misfolded glycoproteins by OS-9 in ER-associated degradation.

Misfolded glycoproteins are translocated from endoplasmic reticulum (ER) into the cytosol for proteasome-mediated degradation. A mannose-6-phosphate receptor homology (MRH) domain is commonly identified in a variety of proteins and, in the case of OS-9 and XTP3-B, is involved in glycoprotein ER-associated degradation (ERAD). Trimming of outermost α1,2-linked mannose on C-arm of high-mannose-type glycan and binding of processed α1,6-linked mannosyl residues by the MRH domain are critical steps in guiding misfolded glycoproteins to enter ERAD.

A mechanism for single-stranded DNA-binding protein (SSB) displacement from single-stranded DNA upon SSB-RecO interaction.

Displacement of single-stranded DNA (ssDNA)-binding protein (SSB) from ssDNA is necessary for filament formation of RecA on ssDNA to initiate homologous recombination. The interaction between RecO and SSB is considered to be important for SSB displacement; however, the interaction has not been characterized at the atomic level. In this study, to clarify the mechanism underlying SSB displacement from ssDNA upon RecO binding, we examined the interaction between Thermus thermophilus RecO and cognate SSB by NMR analysis.

Frequency modulation of high-order harmonic fields with synthesis of two-color laser fields.

We report periodical frequency modulation of high-order harmonic fields observed by changing the delay between the driving two-color laser fields consisting of the fundamental and its second harmonic (SH) field. The amplitude of modulation has been up to ∼0.4 eV, which is larger than the bandwidth of the fundamental field.

Redox-responsive molecular helices with highly condensed π-clouds.

Helices have long attracted the attention of chemists, both for their inherent chiral structure and their potential for applications such as the separation of chiral compounds or the construction of molecular machines. As a result of steric forces, polymeric o-phenylenes adopt a tight helical conformation in which the densely packed phenylene units create a highly condensed π-cloud. Here, we show an oligomeric o-phenylene that undergoes a redox-responsive dynamic motion.

Novel polymerization catalysts and hydride clusters from rare-earth metal dialkyls.

This Review gives an overview on recent progress in the synthesis and chemistry of rare-earth metal dialkyl complexes bearing monoanionic ancillary ligands, with an emphasis on novel polymerization catalysts. These structurally well-defined and highly reactive compounds are prepared either by alkane elimination reactions between trialkyl rare-earth complexes and acidic neutral ligands, or by the metathetical reactions of rare-earth trihalides with the alkali metal salts of the corresponding ligands. On treatment with an appropriate borate compound, the dialkyl complexes are converted into the corresponding cationic monoalkyl species, which serve as excellent catalysts for the polymerization and copolymerization of a variety of olefins to yield a series of new polymer materials that exhibit novel properties.

Discovery of a small molecule PDI inhibitor that inhibits reduction of HIV-1 envelope glycoprotein gp120.

Protein disulfide isomerase (PDI) is a promiscuous protein with multifunctional properties. PDI mediates proper protein folding by oxidation or isomerization and disrupts disulfide bonds by reduction. The entry of HIV-1 into cells is facilitated by the PDI-catalyzed reductive cleavage of disulfide bonds in gp120.

Proteomics accelerating the identification of the target molecule of bioactive small molecules.

Failures in many drug development programs in the past decades were related to unspecified mechanism of action and poor pharmacokinetic (PK) properties. Recent developments are focused on well defined targets, improved PK profiles, however, not much is known about off-target effects, especially those responsible for diminishing drug activity. Steadily increasing application of proteomics in drug development should expose clinically relevant proteins for the analysis of drug effects, to show what group of patients will respond and who should not be treated with an agent.

Crystal structures of human secretory proteins ZG16p and ZG16b reveal a Jacalin-related β-prism fold.

ZG16p is a secretory protein that mediates condensation-sorting of pancreatic enzymes to the zymogen granule membrane in pancreatic acinar cells. ZG16p interacts with glycosaminoglycans and the binding is considered to be important for condensation-sorting of pancreatic enzymes. ZG16b/PAUF, a paralog of ZG16p, has recently been found to play a role in gene regulation and cancer metastasis.

Relationship between Ca2+-affinity and shielding of bulk water in the Ca2+-pump from molecular dynamics simulations.

The sarcoplasmic reticulum Ca(2+)-ATPase transports two Ca(2+) per ATP hydrolyzed from the cytoplasm to the lumen against a large concentration gradient. During transport, the pump alters the affinity and accessibility for Ca(2+) by rearrangements of transmembrane helices. In this study, all-atom molecular dynamics simulations were performed for wild-type Ca(2+)-ATPase in the Ca(2+)-bound form and the Gln mutants of Glu771 and Glu908.

Symbiotic bacterium modifies aphid body color.

Color variation within populations of the pea aphid influences relative susceptibility to predators and parasites. We have discovered that infection with a facultative endosymbiont of the genus Rickettsiella changes the insects' body color from red to green in natural populations. Approximately 8% of pea aphids collected in Western Europe carried the Rickettsiella infection.

ECHO-LNA conjugates: hybridization-sensitive fluorescence and its application to fluorescent detection of various RNA strands.

Hybridization-sensitive fluorescent DNA probes containing the nucleotide units of locked nucleic acid (LNA) have been developed. Exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes that incorporated LNA nucleotides achieved high thermostability of the hybrid with target RNA strands. The appropriately designed ECHO-LNA chimeric probes exhibited an effective on-off switching property of fluorescence depending on hybridization with RNA and facilitated fluorescent detection of the TAR RNA strand forming a hairpin structure and distinction of one base difference in PLAC4 RNA sequence.

Promiscuous activity of ER glucosidase II discovered through donor specificity analysis of UGGT.

In glycoprotein quality control system in the endoplasmic reticulum (ER), UGGT (UDP-glucose:glycoprotein glucosyltransferase) and glucosidase II (G-II) play key roles. UGGT serves as a glycoprotein folding sensor by virtue of its unique specificity to glucosylate glycoproteins at incompletely folded stage. By using various UDP-Glc analogues, we first analyzed donor specificity of UGGT, which was proven to be rather narrow.

High-resolution soft X-ray photoelectron spectroscopy of liquid water.

High-resolution soft X-ray photoelectron spectra of liquid water (H(2)O and D(2)O) were measured using a liquid beam photoelectron spectrometer. The 1a(1) (O1s) band and the lowest valence 1b(1) band had single peaks, which is not consistent with the split 1b(1)→ 1a(1) of the X-ray emission band of liquid water if the splitting is assumed to originate from level shifts in two different hydrogen bonding structures. The second valence 3a(1) band of liquid water exhibited a flat top implying that two bands exist underneath a broad feature, which is similar to the case of the 3a(1) band of amorphous ice.

Steroid degradation in Comamonas testosteroni.

Steroid degradation by Comamonas testosteroni and Nocardia restrictus have been intensively studied for the purpose of obtaining materials for steroid drug synthesis. C. testosteroni degrades side chains and converts single/double bonds of certain steroid compounds to produce androsta-1,4-diene 3,17-dione or the derivative.

Up-and-down movement of a sliding actin filament in the in vitro motility assay.

We observed a three-dimensional up-and-down movement of an actin filament sliding on heavy mero-myosin (HMM) molecules in an in vitro motility assay. The up-and-down movement occurred along the direction perpendicular to the planar glass plane on which the filament demonstrated a sliding movement. The height length of the up-and-down movement was measured by monitoring the extent of diminishing fluorescent emission from the marker attached to the filament in the evanescent field of attenuation.

Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases.

Enzymatic synthesis of poly(α-ethyl β-aspartate) by poly(ethylene glycol) modified poly(aspartate) hydrolase-1.

We recently discovered that poly(aspartate) (PAA) hydrolase-1 from Pedobacter sp. KP-2 has a unique property of specifically cleaving the amide bond between β-aspartate units in thermally synthesized PAA (tPAA). In the present study, the enzymatic synthesis of poly(α-ethyl β-aspartate) (β-PAA) was performed by taking advantage of the substrate specificity of PAA hydrolase-1.