Analysis of transient membrane protein interactions by single-molecule diffusional mobility shift assay

Various repertoires of membrane protein interactions determine cellular responses to diverse environments around cells dynamically in space and time. Current assays, however, have limitations in unraveling these interactions in the physiological states in a living cell due to the lack of capability to probe the transient nature of these interactions on the crowded membrane. Here, we present a simple and robust assay that enables the investigation of transient protein interactions in living cells by using the single-molecule diffusional mobility shift assay (smDIMSA). Utilizing smDIMSA, we uncovered the interaction profile of EGFR with various membrane proteins and demonstrated the promiscuity of these interactions depending on the cancer cell line. The transient interaction profile obtained by smDIMSA will provide critical information to comprehend the crosstalk among various receptors on the plasma membrane.Subject terms: Fluorescence imaging, Super-resolution microscopy, Single-molecule biophysics     

Background-free,fast protein staining in sodium dodecyl sulfate polyacrylamide gel using counterion dyes,zincon and ethyl violet

A background-free, fast protein staining method in polyacrylamide gel electrophoresis using an acidic dye, zincon (ZC) and a basic dye, ethyl violet (EV) is described. It is based on the counterion dye staining technique that employs two oppositely charged dyes to form an ion-pair complex in staining solution. The selective binding of free dye molecules to proteins in acidic solution produces bluish violet-colored bands. It is a rapid and end-point staining procedure, involving only fixing and staining steps that are completed in 1-1.5 h. The detection limit of this method is 8-15 ng of protein that is comparable to the sensitivity of the colloidal Coomassie Brilliant Blue G (CBBG) stain. Due to its sensitivity and speed, this stain may be more practical than any other dye-based stains for routine laboratory purposes.     

Radiocatalytic H2 production with gamma-irradiation and TiO2 catalysts

The radioactive concentrations of radionuclides were measured in the soil and groundwater below the 12 GeV proton beam-line tunnel at KEK. Various long-lived radionuclides, (⁷Be, ²²Na, ⁴⁶Sc, ⁵⁴Mn, ⁶⁰Co, ¹³⁴Cs, ¹⁵²Eu and ¹⁵⁴Eu) were observed in the soil samples by -ray spectra measurements, and ³H was also detected by liquid scintillation counting. On the other hand, ³H, ²²Na and ⁵⁴Mn, which were leached from the soil were measured in the groundwater below the EP2 beam line. ³H and ²²Na were also found in slight amounts in groundwater collected in a well dug beside the East Counter Hall. From a comparison with the radioactive concentration in soil and groundwater, the order of the leaching percentages were ³H>²²Na>⁵⁴Mn. This tendency was in agreement with an experimental result of the RI laboratory.     

Oligoindole-based foldamers with a helical conformation induced by chloride

As a new type of foldamers, oligoindoles containing 4, 6, and 8 indole rings were synthesized, and their folding properties were characterized by a combination of 1H NMR techniques and UV/visible titration experiments. When chloride was added, the NH signals of the oligoindoles were downfield shifted as a result of hydrogen-bond formation, and the aromatic signals were upfield shifted by stacking between two indoles. Moreover, the ROESY experiment provided definitive NOE evidence for the helical stacking in the presence of chloride. Finally, the UV/visible titration experiments demonstrated that the oligoindoles formed 1:1 complexes with chloride, and the association constants greatly increased with increasing the number of the indole NHs. These observations are all consistent with the fact that oligoindoles adopt a helical conformation when complexed with chloride by hydrogen-bonding interactions.     

An efficient synthesis of novel carbocyclic nucleosides with use of ring-closing metathesis from D-lactose

This paper describes an efficient synthetic route for various types of novel carbocyclic nucleosides. The required stereochemistry of the targeted nucleosides was successfully obtained with use of Grubbs cyclization and Trost allylic alkylation from the carbohydrate chiral template "D-lactose".     

Mechanism of the hydrolysis of α-(<Emphasis Type="Italic">p</Emphasis>-nitrophenyl)cinnamonitrile derivatives

The rate constant hydrolysis of α-(p-nitrophenyl)cinnamonitrile(NCPN) and its derivatives have been determined at various pH, and the rate equation which can be applied over a wide pH range is obtained. On the basis of the rate equation, hydrolysis product, general base, and substituent effects, a plausible mechanism of hydrolysis has been proposed: At pH < 4.0, the hydrolysis was initiated by the addition of water to β-carbon of the carbon-carbon double bond. At pH > 8.5, the addition of hydroxide ion to the double bond was rate controlling. In the range of pH 4.0–8.5, these two reactions occurred competitively. Published in Russian in Kinetika i Kataliz, 2007, Vol. 48, No. 5, pp. 670–676. This article was submitted by the authors in English.     

Heat shock protein 27 interacts with vimentin and prevents insolubilization of vimentin subunits induced by cadmium

Vimentin is an intermediate filament that regulates cell attachment and subcellular organization. In this study, vimentin filaments were morphologically altered, and its soluble subunits were rapidly reduced via cadmium chloride treatment. Cadmium chloride stimulated three major mitogen-activated protein kinases (MAPKs): extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38, and led apoptotic pathway via caspase-9 and caspase-3 activations. In order to determine whether MAPKs were involved in this cadmium-induced soluble vimentin disappearance, we applied MAPK-specific inhibitors (PD98059, SP600125, SB203580). These inhibitors did not abolish the cadmium-induced soluble vimentin disappearance. Caspase and proteosome degradation pathway were also not involved in soluble vimentin disappearance. When we observed vimentin levels in soluble and insoluble fractions, soluble vimentin subunits shifted to an insoluble fraction. As we discovered that heat-shock protein 27 (HSP27) was colocalized and physically associated with vimentin in unstressed cells, the roles of HSP27 with regard to vimentin were assessed. HSP27-overexpressing cells prevented morphological alterations of the vimentin filaments, as well as reductions of soluble vimentin, in the cadmium-treated cells. Moreover, HSP27 antisense oligonucleotide augmented these cadmium-induced changes in vimentin. These findings indicate that HSP27 prevents disruption of the vimentin intermediate filament networks and soluble vimentin disappearance, by virtue of its physical interaction with vimentin in cadmium-treated SK-N-SH cells.     

Halogen-substituted thiophenol molecules on Cu(111)

Para-halosubstituted thiophenols (X-TPs, where X is Br, Cl, or F) form ordered islands and monolayers on Cu(111) at temperatures as low as 81 K. At incomplete coverages, all X-TPs adsorb with the dehydrogenated thiol group attached to the substrate and the substituted ring inclined toward the surface, as verified experimentally and theoretically. The structure of ordered islands has a pronounced dependence on the nature of the halogen substituent: while unsubstituted TP and pentafluoro-TP molecules do not self-assemble into extended ordered patterns at 81 K, X-TP molecules form a range of different structures which depend both on the size and electronegativity of the substituent, as well as on the coverage.     

Ruthenium‐catalyzed synthesis of quinolines via reductive heteroannulation of nitroarenes with 3‐amino‐1‐propanols

Nitroarenes are reductively cyclized with 3‐amino‐1‐propanols in dioxane/H₂O in the presence of a ruthenium catalyst and tin(II) chloride dihydrate together with isopropanol to afford the corresponding quinolines. A reaction pathway involving initial reduction of nitroarenes to anilines, propanol group transfer from 3‐amino‐1‐propanols to anilines, N‐alkylation of anilines by 3‐anilino‐1‐propanols and heteroannulation of 1,3‐dianilinopropanes is proposed.     

Modular fluorescence sensors for saccharides

Modular and modular polymer supported fluorescence photoinduced electron transfer (PET) sensors 2 and 3 with two boronic acid receptor units, a pyren-1-yl fluorophore, and hexamethylene linker show selective saccharide binding in aqueous methanolic solution at pH 8.21.