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.     

Novel alignment method of small molecules using the Hopfield Neural Network

Molecular alignment is an important step in three-dimensional quantitative structure-activity relationship (3D-QSAR) such as comparative molecular field analysis (CoMFA). A reasonable molecular alignment is necessary for building a 3D-QSAR model. In this paper, a novel method for molecular alignment using the Hopfield Neural Network (HNN) is introduced. Four kinds of chemical properties are assigned to each atom of a molecule. Then, those properties between two molecules correspond to each other using HNN. To validate our method, HNN was applied to 12 pairs of enzyme inhibitors cited from the Protein Data Bank (PDB). As a result, our method could successfully reproduce the real molecular alignments obtained from X-ray crystallography.     

Significant differences in site of protonation and extent of fragmentations in chemical ionization and fast atom bombardment mass spectrometry of simple bifunctional compounds. A mechanistic implication for formation of protonated molecules

Chemical ionization (CI) and fast atom bombardment (FAB) mass spectra of simple bifunctional aromatic compounds were compared. Some significant differences were revealed with respect to the site of protonation and extent of fragmentations. Unlike conventional CI ionization, the protonated molecule formation by FAB could not be accounted for by ordinary proton transfer reactions in the gas phase. The observed ions under FAB conditions appear to be regulated by proton exchange reactions through frequent collisions in some particular region between the matrix and the gas phase.     

Fischer-Tropsch synthesis over cobalt catalysts supported on modified SiO2 with mesoporous silica

SiO₂ was modified by hexagonal mesoporous silica to form a mixture with meso-/macroporous sizes and used as support of Co catalysts for Fischer-Tropsch synthesis in a slurry phase. A synergistic effect on the activity of Co catalyst was found. The catalytic properties are related to the state of surface Co and the character of support.     

Flow injection analysis of potassium using an all-solid-state potassium-selective electrode as a detector

The concentration of potassium was determined by a combination of flow injection analysis (FIA) with an all-solid-state potassium sensor detection. The all-solid-state potassium-selective electrode possessing long-term potential stability was fabricated by coating an electroactive polypyrrole/poly(4-styrenesulfonate) film electrode with a plasticized poly(vinyl chloride) membrane containing valinomycin. The simple FIA system developed in this laboratory demonstrated sensitivity identical to that in the batch system and achieved considerably rapid assay (150 samples h⁻¹). Analyses of soy sauce and control serum samples by this FIA system yielded results in good agreement with those obtained by conventional measurements.     

Hydrodynamic limit for a spin system on a multidimensional lattice

Summary The hydrodynamic limit for a Markov process of [0, )-valued spin fields on a periodic multidimensional lattice is studied. In the process a positive real number, called energy, is attached to each site of the lattice and each couple of adjacent sites exchange thier energy by random amounts at random times. The law of the exchange is such that the sum of the total energy is conserved, and that the process is reversible and of gradient type for the energy distribution. We show that under diffusion type scaling of space and time, the macroscopic energy distribution converges to a deterministic limit which is characterized by a non-linear diffusion equation /t=2^–1P(), whereP is an increasing function which in a typical case equals const·².     

Anionic polymerization and copolymerization of S-methyl thiomethacrylate

S-Methyl thiomethacrylate (methyl thiolmethacrylate, MTMA) was polymerized with a variety of anionic initiators such as n-BuLi, octylpotassium, PhMgBr, and Et₂AlNPh₂ in toluene and THF. Stereoregularity of the polymer (PMTMA) was determined from the ¹H-NMR spectrum of poly(methyl methacrylate), which had been derived from PMTMA, because the α-methyl resonance in the ¹H-NMR spectrum of PMTMA was not satisfactorily solved owing to the overlap of pentad signals. The ¹³C-NMR spectrum of PMTMA also showed the splitting due to pentad sequences. Stereoregularity of PMTMA was always low compared with that of poly(methyl methacrylate), which was prepared under the same reaction conditions. MTMA was much more reactive than methyl methacrylate and methacrylonitrile in the copolymerization with n-BuLi in toluene and in THF at ?78°C. The lower stereoregulation of the polymerization of MTMA and the higher reactivity of MTMA were mainly ascribed to the higher resonance effect of MTMA.