Direct calculation of the binding free energies of FKBP ligands

Direct calculations of the absolute free energies of binding for eight ligands to FKBP protein were performed using the Fujitsu BioServer massively parallel computer. Using the latest version of the general assisted model building with energy refinement (AMBER) force field for ligand model parameters and the Bennett acceptance ratio for computing free-energy differences, we obtained an excellent linear fit between the calculated and experimental binding free energies. The rms error from a linear fit is 0.4 kcal/mol for eight ligand complexes. In comparison with a previous study of the binding energies of these same eight ligand complexes, these results suggest that the use of improved model parameters can lead to more predictive binding estimates, and that these estimates can be obtained with significantly less computer time than previously thought. These findings make such direct methods more attractive for use in rational drug design.     

Chirality Transfer in Propeller‐Shaped Cyclen?Calcium(II) Complexes: Metal‐Coordinating and Ion‐Pairing Anion Procedures

A series of quadruple‐stranded Na⁺ and Ca²⁺ complexes with octadentate cyclen ligands was synthesized to produce complexes that contained four different side‐arm combinations (one triazole? coumarin group and three pyridine groups ( 1 ), four pyridine groups ( 2 ), one triazole? coumarin group and three quinoline groups ( 3 ), and four quinoline groups ( 4 )). X‐ray crystallographic analysis revealed that no significant changes occurred in the stereostructure of these complexes upon replacing one pyridine group with a triazole? coumarin moiety, or by replacing Na⁺ ions with Ca²⁺ ions, although the coordination number of the complexes in the solid state decreased when pyridine groups were replaced by quinoline groups. In solution, all of the side arms were arranged in a propeller‐like pattern to yield an enantiomer pair of Δ and Λ forms in each metal complex. The addition of a tert‐butoxycarbonyl (Boc)‐protected amino acid anion, that is, a coordinative chiral carboxylate anion, to the cyclen? Ca²⁺ complex induced circular dichroism (CD) signals in the aromatic region by forming a 1:1 mixture of diastereomeric ternary complexes with opposite complex chirality, whilst the corresponding Na⁺ complexes rarely showed any response. In complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺, this chirality‐transfer process was efficiently followed by considering the induction of the CD signals at two different wavelengths, that is, the coumarin‐chromophore region and the aza‐aromatic region. The sign and intensity of the CD signal were significantly dependent on both the nature of the aza‐aromatic moiety and the enantiomeric purity of the external anion. These Ca²⁺ complexes worked as effective probes for the determination of the enantiomeric excess of the chiral anion. The cyclen? Ca²⁺ complexes also interacted with the non‐coordinative Δ‐TRISPHAT anion through an ion‐pairing mechanism to achieve chirality transfer from the anion to the metal complex; both complexes 1 ‐Ca²⁺ and 3 ‐Ca²⁺ clearly showed induced CD signals in the coumarin‐chromophore region, owing to ion‐paring interactions with the Δ‐TRISPHAT anion. Thus, the proper combination of an octadentate cyclen ligand and a metal center demonstrated effective chirality transfer.     

Stir-bar-sorptive extraction,with in-situ deconjugation,and thermal desorption with in-tube silylation,followed by gas chromatography-mass spectrometry for measurement of urinary 4-nonylphenol and 4-<Emphasis Type="Italic">tert</Emphasis>-octylphenol glucuronides

Bacterial quorum-sensing regulatory systems can be summarized in a simple model wherein an autoinducer molecule accumulates in cultures and stimulates regulatory changes in gene expression upon reaching a critical threshold concentration. Although quorum sensing was originally thought to be an isolated phenomenon governing the regulation of a handful of processes in only a few bacteria, it is now considered to be a widespread mechanism for coordinating bacterial gene expression. Over decades of research, investigations of autoinducer-mediated regulation have revealed that these systems are far more complicated than originally appreciated, and such discoveries have accelerated recently with the application of molecular and genomic tools. The focus of this review is to highlight recent advances describing complexities that go beyond the simple model of quorum sensing. These complexities include the regulation of autoinducer production and degradation, the presence of multiple quorum-sensing systems in individual bacteria that regulate diverse genes, often in coordination with other regulatory elements, and the influence of interorganismal interactions on quorum sensing.     

Effects of 2-hydroxypropyl α-cyclodextrin on the radioactive iodine sorption on activated carbon

Journal of Radioanalytical and Nuclear Chemistry - Effect of 2-hydroxypropyl α-cyclodextrin (α-HPCD) on the iodine adsorption onto activated carbon (AC) was investigated. The iodine...     

Liquid‐Crystalline Biomacromolecular Templates for the Formation of Oriented Thin‐Film Hybrids Composed of Ordered Chitin and Alkaline‐Earth Carbonate

Macroscopically ordered inorganic thin films have been formed on unidirectionally oriented, liquid‐crystalline chitin matrices. In the presence of poly(acrylic acid) (PAA), unidirectionally oriented chitin films act as templates for the formation of oriented thin‐film crystals of alkaline‐earth carbonates such as SrCO₃ and BaCO₃. The morphology and orientation of crystals are dependent on the metal ion concentration. For SrCO₃ crystallization, unidirectional thin films and hexagonal‐shaped thin films have been deposited from 200 and 25 mm concentration strontium solutions, respectively.     

Biaryl-based anion receptors bearing thiourea groups: fluoride anion receptor

The synthesis, characterization and binding studies with anions for biaryl-based anion receptors bearing thiourea groups have been described. The results revealed that receptors (1 and 2) showed good selectivity and binding affinity for F^?, and among them binaphthyl-based receptor (1a) showed the best binding affinity for F^? in comparison to other tested anions (Cl^?, Br^?, I^?, $ {\text{NO}}_{3}^{ - } ,\;{\text{HSO}}_{4}^{ - } , $ AcO^? and $ {\text{H}}_{2} {\text{PO}}_{4}^{ - } $ ). This is probably due to the fact that the moderate rigidity of binaphthyl skeleton in 1a is able to provide the better geometry of two thiourea groups for incorporating F^? into the binding pocket. The higher basicity of F^? also participated in this selectivity.     

Regioselective Dichlorination of a Non‐Activated Aliphatic Carbon Atom and Phenolic Bismethylation by a Multifunctional Fungal Flavoenzyme

The regioselective functionalization of non‐activated carbon atoms such as aliphatic halogenation is a major synthetic challenge. A novel multifunctional enzyme catalyzing the geminal dichlorination of a methyl group was discovered in Aspergillus oryzae (Koji mold), an important fungus that is widely used for Asian food fermentation. A biosynthetic pathway encoded on two different chromosomes yields mono‐ and dichlorinated polyketides (diaporthin derivatives), including the cytotoxic dichlorodiaporthin as the main product. Bioinformatic analyses and functional genetics revealed an unprecedented hybrid enzyme (AoiQ) with two functional domains, one for halogenation and one for O‐methylation. AoiQ was successfully reconstituted in vivo and in vitro, unequivocally showing that this FADH₂‐dependent enzyme is uniquely capable of the stepwise gem‐dichlorination of a non‐activated carbon atom on a freestanding substrate. Genome mining indicated that related hybrid enzymes are encoded in cryptic gene clusters in numerous ecologically relevant fungi.     

Photosensitizing Electron Transfer Processes of Fullerenes,Carbon Nanotubes,and Carbon Nanohorns

In this account, studies on the photosensitizing electron transfer of nanocarbons, such as fullerenes, single‐walled carbon nanotubes (SWCNTs), and carbon nanohorns (CNH), performed in our laboratory for about 15 years in the early 21st century have been briefly reviewed. These novel nanocarbons act as excellent electron acceptors, when they are linked to light‐absorbing electron donors, such as porphyrins or phthalocyanines. For such molecule–nanocarbon hybrids, the direct confirmation of fast, transient, electron‐transfer phenomena must be performed with time‐resolved spectroscopic methods, such as transient absorption spectral measurements, in addition to fluorescence time‐profile measurements in the wide‐wavelength regions. Careful use of these methods affords useful information to understand photoinduced electron‐transfer mechanisms. In addition, kinetic data obtained by these methods can assist in the construction of light‐active devices, such as photovoltaic cells and solar H₂‐generation systems.     

Inhibition of translation by small RNA-stabilized mRNA structures in human cells

RNA-mediated gene regulation and expression are critically dependent on both nucleic acid architecture and recognition. We present a novel mechanism for the regulation of gene expression through direct RNA-RNA interactions between small RNA and mRNA in human cells. Using mRNA reporters containing G-rich sequences in the 5'-untranslated region (5'-UTR), in the coding region, or both, we showed that G-rich small RNAs bind to the reporter mRNAs and form an intermolecular RNA G-quadruplex that can inhibit gene translation in living cells. Using a combination of circular dichroism (CD) and RNase footprinting in vitro, we found that the intermolecular G-quadruplexes show a parallel G-quadruplex structure. We next investigated whether the intermolecular G-quadruplex is present in living cells. Employing the fluorophore-labeled probes, we found that two G-rich RNA molecules form an intermolecular G-quadruplex structure in living cells. These results extend the concept of small RNA-mediated expression and suggest an important role for such RNA structures in the inhibition of mRNA translation.     

Neutrino mass constraints on beta decay

Using the general connection between the upper limit on the neutrino mass and the upper limits on certain types of non-standard-model interactions that can generate loop corrections to the neutrino mass, we derive constraints on some non-standard-model d --> ue- nu interactions. When cast into limits on n --> pe- nu coupling constants, our results yield constraints on scalar and tensor weak interactions improved by more than an order of magnitude over the current experimental limits. When combined with the existing limits, our results yield absolute value(C(S)/C(V)) approximately < 5 x 10(-3), absolute value(C'(S)/C(V)) approximately < 5 x 10(-3), absolute value(C(T)/C(A)) approximately < 1.2 x 10(-2), and absolute value(C'(T)/C(A)) approximately < 1.2 x 10(-2).