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     

A polymeric photobase generator containing oxime–urethane groups: Crosslinking reaction and application to negative photoresist

A polymeric photobase generator containing oxime–urethane groups was prepared by copolymerization of methyl methacrylate and methacryloxyethyl benzophenoneoxime urethane, and its photo and thermal crosslinking reaction after irradiation was examined from the measurement of UV and IR absorption spectral changes, insoluble fraction, and molecular weight changes. The photo‐crosslinking reaction of the copolymer film was more efficient when irradiations were carried out with 310 nm UV light in the presence of benzophenone than with 254 nm UV light without the addition of benzophenone. The crosslinking reaction increased after postexposure baking (PEB), and this thermal crosslinking reaction mechanism was studied from the identification of the photolysis products of a model compound, benzophenoneoxime phenylurethane, by a high‐performance liquid chromatography. The results indicate that the thermal crosslinking reaction of the copolymer after PEB is due to the formation of urea‐type chemical bonds. Resist properties of the copolymer were examined from the measurement of normalized thickness and micropattern development. A negative tone image with a resolution of 2 μm was obtained with this copolymer, having a sensitivity (D) of 1200 mJ/cm² and contrast (γ_n) of 1.31, when irradiation was carried out with 310 nm UV light in the presence of benzophenone following chloroform development. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 975–984, 2004     

Metallic macrocycle with a 1,3-alternate calix[4]arene phosphorus ligand

The preparation of an 1,3-alternate calix[4]arene phosphorus ligand, 25,27-bis(2-(diphenylphosphino)ethoxy)-26,28-bis(1-propyloxy)calix[4]arene (3), is presented. Ligand 3 is obtained in three steps in 64% overall yield. Reaction of 3 with [Rh(cot)2]BF4 produced the encapsulated rhodium complex [Rh[(P,P)-diphen-calix[4]arene]]BF4 (4). As revealed by a single-crystal X-ray diffraction study, the rhodium center has a bent coordination environment with a P-Rh-P angle of 135.66(3) degrees. Palladation of 3 employing [Pd(MeCN)4](BF4)2 yielded the chelate palladium complex 7 in which the palladium center has a slightly bent configuration. Treatment of the ligand with Pd(cod)Cl2 and [Pd(eta3-C4H7)(THF)2]BF4 leads to the isolation of the monometallic complex. Full characterization includes X-ray structural studies of compounds 3, 4, and 6.     

Residual stress and deformation during rapid cooling process in an epoxy plate

Residual stress in the epoxy plate during a rapid cooling process was measured by the layer removal method and calculated by the linear thermoviscoelastic theory considering specific volume relaxation. The relaxations of the tensile modulus and specific volume were measured by an Instron thermomechanical analyzer. When the starting temperature of the cooling process was near the glass transition temperature of the cured epoxy, the residual stress in the epoxy plate was smaller than when the starting temperature was higher than the glass transition temperature. However, the transient stress in the cured epoxy plate was higher when the starting temperature was near the glass transition temperature than when the starting temperature was higher than the glass transition temperature. The quenched epoxy plate was compressed in the direction parallel to the surface and expanded in the thickness direction.     

Solid-phase microextraction coupled with high-performance liquid chromatography for the determination of phenylurea herbicides in aqueous samples

Solid-phase microextraction coupled with high-performance liquid chromatography was successfully applied to the analysis of nine phenylurea herbicides (metoxuron, monuron, chlorotoluron, isoproturon, monolinuron, metobromuron, buturon, linuron, and chlorbromuron). Polydimethylsiloxane-divinylbenzene (PDMS-DVB, 60 microm) and Carbowax-templated resin (CW-TPR, 50 microm) fibers were selected from four commercial fibers for further study because of their better extraction efficiencies. The parameters of the desorption procedure were studied and optimized. The effects of the properties of analytes and fiber coatings, carryover, duration and temperature of absorption, pH, organic solvent and ionic strength of samples were also investigated. External calibration with an aqueous standard can be used for the analysis of environmental samples (lake water) using either PDMS-DVB or CW-TPR fibers. Good precisions (1.0-5.9%) are achieved for this method, and the detection limits are at the level of 0.5-5.1 ng/ml.     

Synthesis, structure and heterogeneous catalytic activities of Cu-containing polymeric compounds: anion effect and comparison of homogeneous vs. heterogeneous catalytic activity

The structures of new polymeric compounds containing Cu(II) ions and btp (2,6-bis(N'-1,2,4-triazolyl)pyridine) ligands have been determined. The btp ligands bridge Cu(II) ions to form double zigzag chains, [Cu(ClO4)2(btp)2] 3 with perchlorate anions, and form single zigzag chains, [Cu(btp)(H2O)4](SO4).2H2O 4 with sulfate anions. The polymeric compound 3 was found to effectively catalyze the epoxide ring-opening reaction with methanol, while polymeric compound 4 was almost inactive with epoxides under the same conditions. The polymeric compound 3 showed an efficient catalytic activity and regioselective reactivity in the ring opening of epoxides and allowed reuse without a significant loss of activity through three runs with epoxides.     

Cyclometallated Pd(II) azido complexes containing 6-phenyl-2,2'-bipyridyl or 2-phenylpyridyl derivatives: synthesis and reactivity toward organic isocyanides and isothiocyanates

Cyclometallated palladium(II) azido complexes containing C,N,N- or C,N-donor ligands, [Pd(N(3))L](HL = 6-phenyl-2,2'-bipyridine or 2-phenylpyridyl derivatives), showed different reactivities toward organic isocyanides and isothiocyanates. In particular, aryl isocyanides (CN-Ar) underwent insertion into the orthometallated Pd-C bond on the phenyl moiety of the supporting ligand (L) in [Pd(N(3))L] or [Pd(N(3))(PR(3))L] to selectively give carbodiimido [[Pd(N=C=N-Ar)L]], imidoyl [[Pd(N(3))(-C=N-Ar)(PR(3))L]], or imidoyl carbodiimido complexes [[Pd(N=C=N-Ar)(-C=N-Ar)L] or [Pd(N=C=N-Ar)(-C=N-Ar)(PR(3))L]], depending on reaction conditions. Interestingly, reactions of [Pd(N(3))(PR(3))L] with organic isothiocyanates gave unusual dinuclear complexes [(micro-SCN(4)-R)PdL](2), exhibiting the concurrent S- and N-coordinating thio-tetrazole bridge.     

Fluoride-facilitated deuterium exchange from DMSO-d6 to polyamide-based cryptands

Multiple deuterium exchange between DMSO-d6 and amide hydrogens in two hexaamido cryptand fluoride receptors has been verified by 19F and 2H NMR and FAB mass spectral studies. Structural results for one of the complexes indicate a tricapped trigonal prism hydrogen bond coordination geometry around an encapsulated fluoride, with hydrogen bonds from fluoride to six amide and three phenyl hydrogens.     

Nanophase segregation and water dynamics in the dendrion diblock copolymer formed from the Fréchet polyaryl ethereal dendrimer and linear PTFE

We propose a new material consisting of a dendrion copolymer formed from (a) a water-soluble dendritic polymer and (b) a hydrophobic backbone. Using molecular dynamics simulations techniques, we determine the structure and dynamics of the dendrion formed by second-generation Fréchet polyaryl ethereal dendrimer as the hydrophilic component and linear polytetrafluoroethylene (PTFE) as the hydrophobic polymer, with 5 and 10 wt % of water. We find that this material produces a well-developed nanoscale structure in which water forms a continuous nanophase, making this new family of compounds promising candidates for applications in fuel cell membranes. We find that the water molecules are incorporated into the dendrimer block of the copolymer to form a nanophase-segregated structure. The well-developed nanophase-segregated structures rendered by this material have characteristic dimensions of segregation ( approximately 30 Angstrom) and dendrimer conformational properties that are independent of water content. Calculations of water dynamics and proton transport in these nanophase-segregated structures indicate that the dendrion copolymer membrane with 10 wt % of water content has a water structure and transport properties equivalent to that of the hydrated Nafion membrane with 20 wt % of water content.     

An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material

We have developed an improved method for constructing a full-length cDNA library using small quantity of material by modifying the original oligo-capping method. In our devised method, total RNAs are used in sequential oligo-capping steps directly without preliminary mRNA purification. Using this method, we constructed full- length cDNA libraries from 100 mg of total RNA. These libraries contained 8x10(5) to 8x10(6) independent clones with average insert sizes of 2.0 kb. Moreover, the number of full-length cDNAs containing the translation initiation codon ATG in the constructed libraries was estimated to 60-70%. In addition, 54% of the known cDNAs had a longer 5' end than the corresponding genes in the public database. Our results show that the method can be effectively used to construct full-length enriched cDNA libraries, especially, if starting material is limited.