Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Liquid crystalline properties of dissymmetric molecules IV. The substituent effect on thermal properties of nematic and smectic A phases in three aromatic ring systems with ester linkages

This paper describes the effect of substituent and ester linkage on smectic properties for some derivatives of 4-R -phenyl 4-(4-octyloxybenzoyloxy)benzoates (1), 4-octyloxyphenyl 4-(4-R-benzyloxy)benzoates (2), 4-(4-octyloxybenzoyloxy)phenyl 4- R -benzoates (3), and 4-R-phenyl 4-octyloxyphenyl terephthalates (4) where R = OCH₃, CH₃, OC₈H₁₇, C8H17, halogens, CF₃, OCF₃, CN, NO2, etc. The thermal properties are discussed in terms of the electrostatic nature of the substituents and the relative orientation of the ester groups with respect to both terminal substituents. The substituent effect on the layer structure of the smectic A phase is also examined by means of a small angle X-ray analysis.     

Design and synthesis of 2-(1,3-dialkoxy-2-methylpropan-2-yl)-1,3-diarylpropanes as tethering units for folded H-stacking polymers

1,3-Diarylpropenes 9 having a 1,3-dialkoxy-2-methylpropan-2-yl group were designed as tethering monomers for folded H-stacking polymers, and were readily synthesized from 2-ethoxymethylidene malonate in four- or five-steps, including a facile sequential addition–elimination–addition reaction of benzyl zinc reagents. The preference for the closed (stacked) conformation in the resulting 2-substituted 1,3-diarylpropanes 9 was evaluated using MM2 calculations, ¹H NMR analyses, and fluorescence measurements. Copolymerization of the resulting monomers 9 with compounds containing π-units provided polymers with blue-shifted UV-absorptions both in solution and as films, compared with that of a model compound containing a single π-unit. This optical property is unique to H-aggregated π-units.     

Clinical Perspectives of Theranostics

Theranostics is a precision medicine which integrates diagnostic nuclear medicine and radionuclide therapy for various cancers throughout body using suitable tracers and treatment that target specific biological pathways or receptors. This review covers traditional theranostics for thyroid cancer and pheochromocytoma with radioiodine compounds. In addition, recent theranostics of radioimmunotherapy for non-Hodgkin lymphoma, and treatment of bone metastasis using bone seeking radiopharmaceuticals are described. Furthermore, new radiopharmaceuticals for prostatic cancer and pancreatic cancer have been added. Of particular, F-18 Fluoro-2-Deoxyglucose (FDG) Positron Emission Tomography (PET) is often used for treatment monitoring and estimating patient outcome. A recent clinical study highlighted the ability of alpha-radiotherapy with high linear energy transfer (LET) to overcome treatment resistance to beta--particle therapy. Theranostics will become an ever-increasing part of clinical nuclear medicine.     

Effect of dopant structure on refractive index and glass transition temperature of polymeric fiber‐optic materials

Graded‐index plastic optical fibers, composed of doped polymers, have advantages over conventional glass optical fibers, but need to be developed further for practical application. Here, a variety of aromatic sulfide dopants were synthesized, and their effects on the refractive indexes and glass transition temperatures (T_g) of poly(methyl methacrylate) and methyl 2‐chloroacrylate/2,2,2‐trichloroethyl methacrylate copolymers were studied. While polymers containing large dopants exhibited relatively high refractive indices, their T_g values were low, making these materials unsuitable for graded‐index plastic optical fiber applications. Six dopants yielded polymers that exhibited higher T_g values than the conventionally used (diphenyl sulfide)‐doped polymer. The dopant dibenzothiophene, in particular, yielded polymers with the highest refractive indexes and T_g values, and polymers containing (phenylthio)benzene dopants also performed well. Copyright © 2013 John Wiley & Sons, Ltd.     

(Quasi‐)Racemic X‐ray Structures of Glycosylated and Non‐Glycosylated Forms of the Chemokine Ser‐CCL1 Prepared by Total Chemical Synthesis

Our goal was to obtain the X‐ray crystal structure of the glycosylated chemokine Ser‐CCL1. Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. We used glycosylated Ser‐CCL1 that had been prepared by total chemical synthesis as a homogeneous compound containing an N‐linked asialo biantennary nonasaccharide glycan moiety of defined covalent structure. Facile crystal formation occurred from a quasi‐racemic mixture consisting of glycosylated L ‐protein and non‐glycosylated‐D ‐protein, while no crystals were obtained from the glycosylated L ‐protein alone. The structure was solved at a resolution of 2.6–2.1 Å. However, the glycan moiety was disordered: only the N‐linked GlcNAc sugar was well‐defined in the electron density map. A racemic mixture of the protein enantiomers L ‐Ser‐CCL1 and D ‐Ser‐CCL1 was also crystallized, and the structure of the true racemate was solved at a resolution of 2.7–2.15 Å. Superimposition of the structures of the protein moieties of L ‐Ser‐CCL1 and glycosylated‐L ‐Ser‐CCL1 revealed there was no significant alteration of the protein structure by N‐glycosylation.     

Involvement of Proton Transfer for Carbon Dioxide Reduction Coupled with Extracellular Electron Uptake in Shewanella oneidensis MR‐1

Microbial biosynthesis of hydrocarbon from CO₂ reduction driven by electron uptake process from the cathodic electrode has gained intensive attention in terms of potential industrial application. However, a lack of a model system for detailed studies on the mechanism of the CO₂ reduction hinders the improvement in efficiency for microbial electrosynthesis. Here, we examined the mechanism of microbial CO₂ reduction at the cathode by a well‐described microbe for extracellular electron uptake, Shewanella oneidensis MR‐1, capable of reducing gaseous CO₂ to produce formic acid. Using whole‐cell electrochemical assay, we observed stable cathodic current production at ?0.65 V vs Ag/AgCl KCl sat. associated with the introduction of CO₂. The observed cathodic current was enhanced by the addition of 4 μM riboflavin, which specifically accelerates the electron uptake process of MR‐1 by the interaction to its outer‐membrane c‐type cytochromes. The significant impact of an uncoupler agent and a mutant strain of MR‐1 lacking sole F‐type ATPase suggested the importance of proton import to the cytoplasm for the cathodic CO₂ reduction. The present data suggest that MR‐1 potentially serves as a model system for microbial electrosynthesis from CO₂.     

Photolysis of triphenyl phosphate in aqueous methanol

Upon UV irradiation in methanol, triphenyl phosphate ( 1a ) gave biphenylyl phenyl phosphate ( 2a ) as the main product, whereas the addition of water to the solution caused an increase of the yield of biphenyl ( 3a ). These products were formed through a singlet excited state and an intramolecular excimer, respectively. © 1996 John Wiley & Sons, Inc.     

Free volumes in polystyrene probed by positron annihilation

Free volume characteristics in three samples of monodisperse polystyrene were investigated by positron annihilation technique over a temperature range from 300 to 380 K. The number-average molecular weight of the samples ranged from 5730 to 1,524,000. The observed lifetime spectra were resolved into three components, where the longest lifetime, τ₃ was associated with the pick-off annihilation of ortho-positronium (o-Ps) trapped by free volumes. The change of the temperature coefficient of τ₃ was observed at around 350 K, at which the value of τ₃ was a constant value of 2,3 ns for all specimens with different molecular weights. There was no discrete change of τ₃ in intensity, which is corresponding to the number of free volumes. The size of free volume at glass transition was evaluated to be 0.l nm³. © 1996 John Wiley & Sons, Inc.     

Electrochemical formation of cation-exchanging polypyrrole films within various hydrophilic–hydrophobic domains

The electrochemical polymerization technique has been successfully applied to produce conducting polymer film of controlled ion exchange properties. Polypyrrole films were prepared by electro-oxidative polymerization with doping some alkylsulfonates or Nafion. The ion exchange characteristics across polypyrrole films were examined by means of a novel electrochemical technique, namely, the in situ electrochemical quartz crystal microbalance (EQCM) method. According to EQCM measurements, exchanging ion species was found to be successfully controlled by changing the hydrophilic–hydrophobic balance of the incorporated sulfonated-based dopants. The film's characteristics became anion- to cation-exchanging as the dopants became more hydrophobic in nature. The polypyrrole–Nafion(poly(perfluoroethylene sulfonate)) composite film became to be a complete cation exchanger.