Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins

The importance and utility of Ala(β) methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins is explored. Using (2)H and (13)C relaxation measurements in {U-(2)H; Ala(β)-[(13)CHD(2)]}-labeled Malate Synthase G (MSG)--an 82-kDa monomeric enzyme that contains 73 Ala(β) methyl groups--we show that the vast majority of selectively labeled Ala(β) methyls are highly ordered. A number of NMR applications used for solution studies of structure and dynamics of large protein molecules can benefit from proximity of Ala(β) methyls to the protein backbone and their high degree of ordering. In the case of MSG, these applications include the measurement of (1)H-(13)C residual dipolar couplings in Ala(β) methyls, characterization of slow (μs-to-ms) dynamics at the substrates' binding sites, and methyl-TROSY-based NOE spectroscopy performed on {U-(2)H; Ala(β)-[(13)CH(3)]; Ile(δ1)-[(13)CH(3)]; Leu,Val-[(13)CH(3)/(12)CD(3)]}-labeled samples where the number of methyl probes for derivation of distance restraints is maximized compared to the state-of-the-art ILV labeling methodology.     

Clearance of host cell impurities from plasmid-containing lysates by boronate adsorption

The ability of boronate adsorption to clear Escherichia coli impurities directly from plasmid-containing lysates (∼pH 5.2) was evaluated. Results show that 3-aminophenyl boronate (PB) controlled pore glass (CPG) is able to adsorb not only those species that bear cis-diol groups (RNA, lipopolysaccharides-LPS), and are thus able to form covalent bonds with boronate, but also cis-diol-free proteins and genomic DNA (gDNA) fragments, while leaving most plasmid DNA in solution. Control runs performed with phenyl Sepharose and with PB-free CPG beads ruled out hydrophobic interactions with the phenyl ring and non-specific interactions with the glass matrix, respectively, as being responsible for RNA and gDNA adsorption. In batch mode, up to 97.6 ± 3.1% of RNA, 94.6 ± 0.8% of proteins and 96.7 ± 11.7% of gDNA were cleared after 30 min, with a plasmid yield of 64%. In fixed-bed mode, most of the plasmid was recovered in the flowthrough (96.2 ± 4.0%), even though the RNA (65.5 ± 2.8%), protein (84.4 ± 1.3%) and gDNA clearance (44.7 ± 14.1%) were not as effective. In both cases, the LPS content was removed to a residual value of less than 0.005 EU/ml. The method is fast and straightforward, circumvents the need for pre-treatment of the feed and may contribute to shorten plasmid purification processes, as the treated streams can proceed directly to the final polishing steps.     

An improved procedure for the diastereoselective addition of triorganozincates to N-(tert-butanesulfinyl)imines: use of catalytic dialkylzinc

The addition of triorganozincates to (R)-N-(tert-butanesulfinyl)benzaldimine has been performed with very good results by using a catalytic amount of Me₂Zn (0.15 equiv) to generate the organozincate. Yields and/or diastereoselectivities of the formed α-branched sulfinamides improve in comparison with the values obtained in the same reactions carried out with an excess of a previously formed triorganozincate. On the other hand, the transfer of the two alkyl groups of a dialkylzinc reagent to the imine has been achieved by using 0.5 equiv of dialkylzinc and 1.5 equiv of MeMgBr to generate the trialkylzincate. In both methods, good to excellent yields and diastereomeric ratios (up to 98:2) have been obtained.     

Solution NMR evidence for symmetry in functionally or crystallographically asymmetric homodimers

A recurrent theme of many structural studies of homo-oligomeric protein systems is concerned with verification that the conformation observed in a crystal represents the functionally relevant structure. An asymmetric conformation adopted by two chemically identical subunits in homo-oligomers can represent an intrinsic property of a protein or be an artifact induced by crystal packing forces. Solution NMR studies can distinguish between these two possibilities. Using methyl-based NMR spectroscopy, we provide evidence for symmetry in the absence of ligands in several homodimeric proteins that are either asymmetric functionally and/or adopt different conformations of the two subunits in available X-ray structures.     

Influence of Excitation Wavelength (UV or Visible Light) on the Photocatalytic Activity of Titania Containing Gold Nanoparticles for the Generation of Hydrogen or Oxygen from Water

Gold nanoparticles supported on P25 titania (Au/TiO(2)) exhibit photocatalytic activity for UV and visible light (532 nm laser or polychromatic light λ > 400 nm) water splitting. The efficiency and operating mechanism are different depending on whether excitation occurs on the titania semiconductor (gold acting as electron buffer and site for gas generation) or on the surface plasmon band of gold (photoinjection of electrons from gold onto the titania conduction band and less oxidizing electron hole potential of about -1.14 V). For the novel visible light photoactivity of Au/TiO(2), it has been determined that gold loading, particle size and calcination temperature play a role in the photocatalytic activity, the most active material (Φ(H2) = 7.5% and Φ(O2) = 5.0% at 560 nm) being the catalyst containing 0.2 wt % gold with 1.87 nm average particle size and calcined at 200 °C.     

Development of a flow method for the determination of phosphate in estuarine and freshwaters—Comparison of flow cells in spectrophotometric sequential injection analysis

A sequential injection system with dual analytical line was developed and applied in the comparison of two different detection systems viz; a conventional spectrophotometer with a commercial flow cell, and a multi-reflective flow cell coupled with a photometric detector under the same experimental conditions. The study was based on the spectrophotometric determination of phosphate using the molybdenum-blue chemistry. The two alternative flow cells were compared in terms of their response to variation of sample salinity, susceptibility to interferences and to refractive index changes. The developed method was applied to the determination of phosphate in natural waters (estuarine, river, well and ground waters). The achieved detection limit (0.007 μM PO₄³⁻) is consistent with the requirement of the target water samples, and a wide quantification range (0.024–9.5 μM) was achieved using both detection systems.     

DNA microarraying on compact disc surfaces. Application to the analysis of single nucleotide polymorphisms in Plum pox virus

The potential of using compact discs as high throughput screening platforms for DNA microarraying is discussed and applied to discriminate genetic variations of Plum pox virus.     

Direct access to enantiomerically enriched alpha-amino phosphonic acid derivatives by organocatalytic asymmetric hydrophosphonylation of imines

A simple and efficient organocatalytic enantioselective hydrophosphonylation of imines to enantiomerically enriched alpha-amino phosphonates is reported. By using 10 mol % of quinine as the catalyst in the enantioselective addition of diethyl phosphite to N-Boc protected imines, alpha-amino phosphonates are obtained in moderate to good yields and with up to 94% ee.     

Compression of silver sulfide: X-ray diffraction measurements and total-energy calculations

Angle-dispersive X-ray diffraction measurements have been performed in acanthite, Ag(2)S, up to 18 GPa in order to investigate its high-pressure structural behavior. They have been complemented by ab initio electronic structure calculations. From our experimental data, we have determined that two different high-pressure phase transitions take place at 5 and 10.5 GPa. The first pressure-induced transition is from the initial anti-PbCl(2)-like monoclinic structure (space group P2(1)/n) to an orthorhombic Ag(2)Se-type structure (space group P2(1)2(1)2(1)). The compressibility of the lattice parameters and the equation of state of both phases have been determined. A second phase transition to a P2(1)/n phase has been found, which is a slight modification of the low-pressure structure (Co(2)Si-related structure). The initial monoclinic phase was fully recovered after decompression. Density functional and, in particular, GGA+U calculations present an overall good agreement with the experimental results in terms of the high-pressure sequence, cell parameters, and their evolution with pressure.