NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

Comment: 2004's fastest organic and biomolecular chemistry!

In January 2004, the Royal Society of Chemistry launched Organic & Biomolecular Chemistry (OBC) - a journal promising to provide high quality research from all aspects of synthetic, physical and biomolecular organic chemistry. The journal was set to build upon the foundations laid down by its predecessor publications (J. Chem. Soc., Perkin Trans. 1 and J. Chem. Soc., Perkin Trans. 2) as well as complement the subject coverage already published in prestigious general chemistry journals such as Chemical Communications and Chemical Society Reviews. Nearly two years on, just how is the programme developing and what can the community expect to see from the Royal Society of Chemistry (RSC)?     

Synthesis and characterization of carbohydrate-based phospholipids

Novel carbohydrate-based phospholipids containing two saturated C(12) (dilauroyl ribo-phosphocholine) (DLRPC), C(14) (dimyristoyl ribo-phosphocholine) (DMRPC), and C(20) (diarachadonyl ribo-phosphocholine) (DARPC) carboxylic acid chains were synthesized. The physical properties of the supramolecular structures formed by these compounds were compared to those formed by their direct glycerol analogues dilauroyl phosphocholine (DLPC), dimyristoyl phosphocholine (DMPC), and diarachadonyl phosphocholine (DAPC). Modulated differential scanning calorimetry (MDSC) and X-ray diffraction data indicated that with chain lengths < or =14 carbons, the carbohydrate backbone increased the thermal stability of the bilayer below the phase-transition temperature (T(m)) as compared to the glycerol-based lipids. With longer chains (C(20)), the bilayer structure was destabilized as compared to glycerol-based lipids. NMR studies of a DMRPC vesicle dispersion reveal split choline headgroup signals and distinct magnetization transfer effects arising from the "inner" and "outer" surfaces of the bilayer vesicle. Modulated differential scanning calorimetry also demonstrated that glycerol- and carbohydrate-based lipids mix, as evidenced by a single intermediate T(m). In addition, carbohydrate-based lipid/cholesterol mixtures exhibited a decrease in enthalpy with an increase in cholesterol concentration. Unlike glycerol phospholipids, carbohydrate lipids were resistant to enzymatic degradation by phospholipase A(2) (PLA(2)).     

Synthesis and solid-state organization of coil-ring-coil block copolymers

Shape-persistent macrocycles based on the phenyl-ethynyl-butadienyl backbone containing two extraannular hydroxyl groups were prepared by the oxidative coupling of the appropriate phenylethynyl oligomers. Carbodiimide-directed coupling with independently synthesized polystyrene carboxylic acid oligomers led to ABA coil-ring-coil block copolymers in which the central macrocycle serves as rigid and the polystyrene oligomers as flexible elements. Depending on the size of the coil blocks, these structures aggregate in cyclohexane into supramolecular hollow cylindrical brushes in which the rigid core is surrounded by the flexible matrix. However, in the solid state it is not possible to identify a morphology in which isolated channels based on aggregated macrocycles are embedded in a matrix of polystyrene. Detailed X-ray and electron diffraction studies on samples prepared from a solution in cyclohexane under equilibrium conditions show that the material adopts a lamellar morphology in the solid state in which columns of macrocycles are aggregated into layers which are separated by polystyrene.     

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.     

Short and stereoselective synthesis of C-glycosylated glycine derivatives from glycals by radical addition and reduction

Only three steps are required for the convenient synthesis of 2-C-branched glyco-amino acids from glycals with good yields and stereoselectivities.     

Thermal degradation studies of alkyl-imidazolium salts and their application in nanocomposites

Increasing the thermal stability of organically-modified layered silicates is one of the key points in the successful technical application of polymer-layered silicate nanocomposites on the industrial scale. To circumvent the detrimental effect of the lower thermal stability of alkyl ammonium-treated montmorillonite, a series of alkyl-imidazolium molten salts were prepared and characterized by elemental analysis, thermogravimetry (TGA) and thermal desorption mass spectroscopy (TDMS). The effect of counter ion, alkyl chain length and structural isomerism on the thermal stability of the imidazolium salts was investigated. Alkyl-imidazolium-treated montmorillonite clays were prepared by ion exchange of the imidazolium salts with Na-montmorillonite. These organically-modified clays were characterized by X-ray diffraction (XRD), TDMS and thermogravimetry coupled with Fourier transform infrared spectroscopy (TGA-FTIR), and compared to the conventional quaternary alkyl ammonium montmorillonite. Results indicate that the counter ion has an effect on the thermal stability of the imidazolium salts, and that imidazolium salts with PF₆⁻, N(SO₂CF₃)₂⁻ and BF₄⁻ anions are thermally more stable than the halide salts. A relationship was observed between the chain length of the alkyl group and the thermo-oxidative stability; as the chain length increased from propyl, butyl, decyl, hexadecyl, octadecyl to eicosyl, the stability decreased. The results also show that the imidazolium-treated montmorillonite has greater thermal stability compared to the imidazolium halide. Analysis of the decomposition products by FTIR provides an insight about the decomposition products which are water, carbon dioxide and hydrocarbons.     

From model compounds to extended pi-conjugated systems: synthesis and properties of dithieno[3,2-b:2',3'-d]phospholes

To explore their suitability for applications in molecular optoelectronics and as sensory materials, novel dithieno[3,2-b:2',3'-d]phospholes have been synthesized and their reactivity and properties investigated. An efficient two-step synthesis allowed for a modular assembly of differently functionalized compounds. The dithieno[3,2-b:2',3'-d]phosphole system exhibits extraordinary optoelectronic properties with respect to wavelength, intensity, and tunability. Owing to the nucleophilic nature of the central phosphorus atom, its significant electronic influence on the conjugated pi system can be altered selectively by chemically facile modifications such as oxidation or complexation with Lewis acids or transition metals. All the dithienophosphole species presented show very strong blue photoluminescence with excellent quantum yield efficiencies supporting their potential utility as blue-light emitting components in organic light emitting diodes (OLEDs). Furthermore, depending on the electronic nature of the phosphorus center, the materials exhibit distinctive optoelectronic properties suggesting that the dithieno[3,2-b:2',3'-d]phosphole system may be useful as sensory material. Theoretical calculations, including time-dependent DFT methods, revealed the excellent predictability of the structures and optoelectronic properties of the functionalized dithienophospholes allowing the design of future dithieno[3,2-b:2',3'-d]phosphole-based materials to be "stream-lined". By using tin-functionalized dithienophosphole monomers, a strategy, which involves Stille coupling, towards extended pi-conjugated materials with significantly redshifted optoelectronic properties is also presented.     

Metal/oxide interfacial reactions: Oxidation of metals on SrTiO3 (100) and TiO2 (110)

We studied chemical reactions between ultrathin metal films (Al, Cr, Fe, Mo) and single-crystal oxides (SrTiO3 (100), TiO2 (110)) with X-ray photoelectron spectroscopy (XPS). The work function of the metal and the electron density in the oxide strongly influence the reaction onset temperature (T(RO)), where metal oxidation is first observed, and the rate of metal oxidation at the metal/oxide interfaces. The Fermi levels of the two contacting phases affect both the space charges formed at the interfaces and the diffusion of ionic defects across the interfaces. These processes, which determine metal oxidation kinetics at relatively low temperatures, can be understood in the framework of the Cabrera-Mott theory. The results suggest that the interfacial reactivity is tunable by modifying the Fermi level (E(F)) of both contacting phases. This effect is of great technological importance for a variety of devices with heterophase boundaries.