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.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Direct conversion of macrocyclic furans into macrocyclic isothiazoles

The first calixhetarenes with more than one heteroatom in the constituent rings are prepared in one step by treatment of calix[4]furan 1a and calix[6]furan 1b with ethyl carbamate, thionyl chloride and pyridine to give 2, 3, 4 and 5, 6, 7 respectively; these products have been characterised by X-ray crystallography which reveals that in 2 all eight heteroatoms lie on one face of the macrocyle.     

MIL-50, an open-framework GaPO with a periodic pattern of small water ponds and dry rubidium atoms: a combined XRD,NMR, and computational study

A new fluorinated gallium phosphate, MIL-50, has been synthesized under mild hydrothermal conditions using 1,6-diaminohexane. The chemical formula of MIL-50 is Rb(2)Ga(9)(PO(4))(8)(HPO(4))(OH)F(6).2N(2)C(6)H(18).7H(2)O. The structure is a network of hexameric units of Ga(3)(PO(4))(3)F(2) and Ga(3)(PO(4))(2)(HPO(4))F(3) via corner sharing. It creates a three-dimensional open-framework delimiting 6- and 18-ring channels running along the c axis. The diprotonated 1,6-diaminohexane and water molecules are trapped within the 18-ring pores, whereas the rubidium cations reside in the 6-ring ones. A double quantum (31)P NMR experiment and partial charge calculations indicate that water molecules are present under the form of periodic small clusters, lowering the multiplicity of one phosphorus site, P3. Though water hops within the clusters, the motion leaves the water pattern periodic. Rubidium is so tightly embedded into the framework that water moving in the large 18-ring channels does not reach it, leaving it therefore dry. The crystal framework may be ascribed to the orthorhombic space group Cmc2(1) (n degrees 36), a = 32.1510(2), b = 17.2290(3), c = 10.2120(1) A. The periodic water pattern has a different symmetry than that of the framework. A method has been devised to superpose the two sublattices that coexist in the same unit cell in order to have full occupancy of each site and to perform Madelung summations. This original method is of general interest for most zeolitic materials exhibiting a different symmetry for the framework and the template sublattices.     

13C-NMR studies on the cevanine alkaloids : the application of 13C-NMR spectrum for structure elucidation of new alkaloids,baimonidine and isoverticine

The ¹³C-NMR spectra of seven cavanine alkaloids isolated from Veratrum and Fritillaria plants were measured and their signals were assigned, and these results were applicated for structure elucidation of two new cevanine alkaloids, baimonidine and isoverticine, isolated from mature Fritillaria verticillata.     

Multipoint recognition of catecholamines by hydrindacene-based receptors accompanied by the complexation-induced conformational switching

The molecular recognition of catecholamines by hydrindacene-based receptors 1 and 2, as well as the durene-based receptor 3, and the guest-induced conformational changes are reported. These receptors selectively bind adrenaline and dopamine salts through the guests' ammonium group and 3-hydroxyl group on the aromatic ring. In the case of adrenaline, an additional hydrogen bond with a benzylic hydroxyl group is formed. In 2 % CD3CN/CDCl3, the association constants are of the order of 10(4) M(-1), which is much larger than with guests without the 3-hydroxyl groups (10(3) M(-1)). The two amide groups of receptor 1 can rotate freely around the C(aromatic)--C(amide) bond, whereas the tert-amide in 2 changes between two stable conformations at a slow enough rate to allow detection by (1)H NMR spectroscopy. In the absence of a guest molecule, the syn-conformer is less stable than the anti-conformer. On complex formation with adrenaline, the syn-conformer becomes dominant due to an intramolecular dipole-reversal effect in addition to multipoint hydrogen bonding.     

Pd-catalyzed selective addition of heteroaromatic C-H bonds to C-C triple bonds under mild conditions

Simple heteroarenes such as pyrroles and indoles undergo addition reactions to C-C triple bonds in the presence of a catalytic amount of Pd(OAc)(2) under very mild conditions, affording cis-heteroarylalkenes in most cases. The cleavage of aromatic C-H bonds is the possible rate-determining step in CH(2)Cl(2), and the addition of heteroaromatic C-H bonds to C-C triple bonds is in a trans-fashion.     

Extraction—spectrophotometric determination of trace amounts of iron in waters with pyrogallol red and zephiramine

The simple removal of excess of co-extracted reagent in the solvent extraction of metal complex anions with a quaternary ammonium salt greatly improves the determination of iron(II) with pyrogallol red and zephiramine. The method with pyrogallol red is suitable for the determination of trace amounts of iron in natural waters. The apparent molar absorptivities of the iron(II) complex in chloroform are 7.5×10⁴ and 10.3×10⁴ 1 mol^-1 cm^-1 at 560 and 298 nm, respectively. A large excess of reagent can be added, and the ternary complex can be completely extracted over the pH range 8.5–10. Masking agents allow most interferences to be suppressed. The method is suitable for the analysis of potable, river and sea waters.     

Convergence estimates for the wavelet-Galerkin method: superconvergence at the node points

In this paper we consider a regular 1-periodic initial value problem and Galerkin approximate solutions in subspaces ν _t spanned by scaled translates of a basic function?. Our goal is to estimate the error when? is in a class of functions which we name . Herer is a regularity parameter andm is related with a property (the Strang and Fix condition) which determines the best order of accuracy in theL ²-norm of approximations from ν _h . Whenm=r, includes all scaling functions corresponding tor-regular multiresolution analyses ofL ²(?). We get the exact node values of the given initial condition as coefficients for the approximate initial data. With this procedure, the coefficients of the resulting Galerkin solution can give a very accurate approximation of the exact solution at the node points, provided that? has many vanishing moments. Since this property is not satisfied in general, we work with another modified basic function?* constructed from the integer translates of?. GlobalL ²-estimates are also obtained.