Site-directed 13C solid-state NMR studies on membrane proteins: strategy and goals toward revealing conformation and dynamics as illustrated for bacteriorhodopsin labeled with [1-13C]amino acid residues

We have so far demonstrated that well-resolved and site-specifically assigned (13)C peaks as recorded by site-directed NMR study on (13)C-labeled membrane proteins can serve as a convenient probe to reveal their local conformation and dynamics. We attempted here to clarify the extent to which (13)C NMR spectra of (13)C-labeled fully hydrated bacteriorhodopsin (bR) as a typical membrane protein are visible or well resolved in the presence of inherent fluctuation motions with frequency of 10(2)-10(8) Hz, especially at the membrane surfaces. Accordingly, we estimated the relative proportion of (13)C NMR signals from the surface areas with and without peak suppression by the accelerated transverse relaxation effect by surface-bound Mn(2+) ions, which could be effective for residues within 8.7 angstroms of the membrane surface. It turned out that the experimental findings are consistent with the predicted amount of amino acid residues under consideration located within 8.7 angstroms of the surface for [1-(13)C]Val- and Ile-labeled bR and also [3-(13)C]Ala-bR. In contrast, (13)C NMR peaks from such surfaces area are almost completely or partially suppressed for [1-(13)C]Gly-, Ala-, Leu-, Phe- and Trp-labeled bR, as a result of plausible interference of the fluctuation frequency with frequency of magic angle spinning (10(4) Hz). We further assigned several (13)C NMR signals of [1-(13)C] Val-, Trp- and Ile-labeled bR on the basis of a variety of site-directed mutants with reference to those of the wild type. Further, we recorded the (13)C NMR of bR in lipid bilayers to search for the optimal conditions to be able to obtain signals with the highest peak intensities and spectral resolution. Backbone dynamics turn out to be essential for recording (13)C NMR spectra so as to escape from motional frequencies of the order of 10(4)-10(5) Hz, either in the direction of accelerated fluctuation or slowed motions in the direction of forming the 2D array.     

Synthetic alpha-mannosyl ceramide as a potent stimulant for an NKT cell repertoire bearing the invariant Valpha19-Jalpha26 TCR alpha chain

A NKT cell repertoire is characterized by the expression of the Valpha19-Jalpha26 invariant TCR alpha chain (Valpha19 NKT cell). This repertoire, as well as a well-established Valpha14-Jalpha281 invariant TCR alpha(+) NKT cell subset (Valpha14 NKT cell), has been suggested to have important roles in the regulation of the immune system and, thus, is a major therapeutic target. Here, we attempted to find specific antigens for Valpha19 NKT cells. Valpha19 as well as Valpha14 NKT cells exhibited reactivity to alpha-galactosyl ceramide (alpha-GalCer). Thus, a series of monoglycosyl ceramides with an axially oriented glycosidic linkage between the sugar and ceramide moiety were synthesized and their antigenicity to Valpha19 NKT cells was determined by measuring their immune responses in culture with glycolipids. Comprehensive examinations revealed substantial antigenic activity for Valpha19 NKT cells by alpha-mannosyl ceramide.     

Investigation of the detection limit for the determination,by pyrolysis-capillary GC,of the thickness of ultra thin PMMA layers coated on to PET film

The determination of nanometer thick layers of poly(methyl methacrylate) coated on to the surface of poly(ethylene terephthalate) film has been investigated by high resolution pyrolysis gas chromatography without sample pretreatment or modification of the instrumentation used. A good linear relationship was observed between the quantity of the characteristic pyrolysate and the thickness of the poly(methyl methacrylate) layer; the detection limit was sufficient to enable the quantitation of poly(methyl methacrylate)-to-poly(ethylene terephthalate) film thickness ratios of 1:20000 in composite materials.     

Chimeric (alpha/beta + alpha)-peptide ligands for the BH3-recognition cleft of Bcl-XL: critical role of the molecular scaffold in protein surface recognition

Molecules that bind to specific surface sites on proteins are of great interest from both fundamental and practical perspectives. We are exploring a ligand development strategy that is based on oligomers with discrete folding propensities ("foldamers"); we target a specific cleft on the cancer-associated protein Bcl-xL because this system is well characterized structurally. In vivo, this cleft binds to alpha-helical segments (BH3 domains) of other proteins. We evaluated several types of helical foldamer, built entirely from beta-amino acid residues or from mixtures of alpha- and beta-amino acid residues, and ultimately identified foldamers in the latter class that bind very tightly to Bcl-xL. Our results suggest that combining different types of foldamer backbones will be an effective and general strategy for creating high-affinity and specific ligands for protein surface sites.     

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction.

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.     

Photoinduced electron-transfer systems consisting of electron-donating pyrenes or anthracenes and benzimidazolines for reductive transformation of carbonyl compounds

Photoinduced electron-transfer reactions of several ketone substrates were studied to evaluate the utilities of 1,6-bis(dimethylamino)pyrene (BDMAP), 1,6-dimethoxypyrene (DMP), 9,10-bis(dimethylamino)anthracene (BDMAA), and 9,10-dimethoxyanthracene (DMA) as electron-donating sensitizers cooperating with 2-aryl-1,3-dimethylbenzimidazolines. BDMAP and DMP generally led higher conversion of ketones and better yield of reduction products compared to BDMAA and DMA.     

Synthesis of organosilicon polymers by using the Lewis-acid-catalyzed trans-allylsilylation of alkynes

The HfCl₄ catalyzed polymerization of allyl(4-ethynylphenyl)dimethylsilane (1a) proceeded smoothly to give poly[dimethyl-(1,4-pentadienyl)phenylsilane] (2a), and the HfCl₄ catalyzed reaction of 1-allyl-2-(4-ethynyphenyl)-1,1,2,2-tetramethyldisilane (1b) afforded poly[1,1,2,2-tetramethyl-1-(1,4-pentadienyl)-2-phenyldisilane] (2b). These polymerization reactions proceeded via the stereoselective trans-allylsilylation of the 4-ethynyl group attached to the aromatic ring.     

In situ monitoring of metal nanoparticle self-assembly on protein-functionalized glass by broadband optical waveguide spectroscopy

Broadband, time-resolved optical waveguide (OWG) spectroscopy has been used for in situ, real-time investigation into the self-assembly of metal nanoparticle monolayers. The OWG spectroscopy makes it possible to use the transverse electric (TE) and transverse magnetic (TM) modes to measure surface plasmon absorption of immobilized metal nanoparticles in two directions, parallel and normal to the waveguide surface. Therefore, this technique can provide direction-dependent information on the metal nanoparticles at the interface. In this paper, a 50-microm-thick glass plate was used as a slab waveguide and the kinetics of Au nanoparticle adsorption on a hemoglobin-functionalized glass substrate was examined in the early stage of self-assembly. The findings show that with the TE mode the surface plasmon resonance (SPR) behavior for immobilized Au nanoparticles is different from that with the TM mode.     

Oscillating frequency of piezoelectric quartz crystal in solutions

Oscillating frequencies of a piezoelectric crystal were measured in various solutions. One side of the crystal surface was coated with a silicon sealant. This coating was useful for measuring the oscillation of crystals in solutions for a wide range of products of density (?) and viscosity (η) and in electrolyte solutions. For measurement in solutions, the frequency change depended on the circuit used, whereas for measurements in air the circuit did not influence the frequency change. All experimental data showed that the frequency change from pure water, ΔF_w, followed ΔF_w = ? K(√?η ? √?_wη_w) except for electrolyte and polymer solutions, where K is a proportionality constant, η_w the density of pure water and η_w the viscosity of water.