Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach

We outline a joint academic/industrial (CNRS/AVENTIS) functional genomics project aiming at the discovery of new anti-bacterial gene targets. Starting from all publicly available bacterial genomes, a subset of the most evolutionary conserved protein-coding genes has been identified. We retained genes with clear homolog in E. coli and at least one gram-positive bacterium among B.subtilis, M. tuberculosis, L. lactis or S. pyogenes. This subset was further reduced to genes encoding non-membrane proteins of unknown or hypothetical functions. The 221 E. coli Open Reading Frames (ORFs) identified through this comprehensive bioinformatic analysis are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallisation and X-ray diffraction. Our strategy was designed to focus on promising wide-spectrum targets as well as original biochemical pathways. Bioinformatics is used throughout all phases of project, including the initial large-scale comparative genomics analyses, the purification/expression and crystallisation stages for the detection of helpful sequence-specific features (e.g. cofactor binding motifs, non-structured N- or C- term extremities, etc ), and finally for the interpretation of the structures in conjunction with multiple sequence alignments for the identification of key residues, interaction areas on molecular surfaces, and overall function predictions.     

Synthesis of some heterocyclic skeletons via organoiron complexes. Crystal and molecular structure of (5a,6,7,8,9,9a-η6-1,4-benzoxathiino[3,2-b]pyridine)(η5-cyclopentadienyl)iron hexafluorophosphate

Synthesis of the heterocyclic skeletons of some biologically active compounds from (η⁶-o-dichlorobenzene)(η⁵-cyclopentadienyrl)iron hexafluorophosphate in a two step procedure is described. Cyclopentadienyliron hexafluorophosphate complexes of 1,4-benzodioxino[2,3-b]pyridine, 1,4-benzoxathiino[3,2-b]pyridine, 10H-pyrido[3,2-b]benzoxazine, benzo[b]naphtho[2,3-e][1,4]dioxin, 4-methylbenzo[b]benzopyran-2-one[7,6-e][1,4]dioxin and benzo[b]anthracen-9,10-diono[1,2-e][1,4]dioxin were isolated and characterized. Upon pyrolytic sublimation of these complexes the free heterocycles were obtained and characterized. (η⁶-1,4-Benzoxathiino[3,2-b]pyridine)(η⁵-cyclopentadienyl)iron hexafluorophosphate crystalizes in the orthothombic system, space group Pbca; the dihedral angle between the planes of outer rings was found to be 176.8 (1).     

Synthesis and characterization of mannosyl mimetic derivatives based on a beta-cyclodextrin core

The synthesis of branched beta-cyclodextrins substituted with mannosyl mimetic derivatives at one primary hydroxy group is described. It was shown that the self-inclusion phenomenon observed for the target compounds in water did not preclude the inclusion properties of the cyclodextrin moiety.     

Structural aspects of the metal-insulator transitions in V0.985Al0.015O2

The crystal structure of V_0.985Al_0.015O₂ has been refined from single-crystal X-ray data at four temperatures. At 373°K it has the tetragonal rutile structure. At 323°K, which is below the first metal-insulator transition, it has the monoclinic M₂ structure, where half of the vanadium atoms are paired with alternating short (2.540 Å) and long (3.261 Å) V-V separations. The other half of the vanadium atoms form equally spaced (2.935 Å) zigzag V chains. At 298°K, which is below the second electric and magnetic transition, V_0.985Al_0.015O₂ has the triclinic T structure where both vanadium chains contain V-V bonds, V(1)-V(1) = 2.547 Å and V(2)-V(2) = 2.819 Å. At 173°K the pairing of the V(1) chain remains constant: V(1)-V(1) = 2.545 Å, whereas that of the V(2) chain decreases: V(2)-V(2) = 2.747 Å. From the variation of the lattice parameters as a function of temperature it seems that these two short V-V distances will not become equal at lower temperatures. The effective charges as calculated from the bond strengths at 298 and 173°K show that a cation disproportionation has taken place between these two temperatures. About 20% of the V⁴⁺ cations of the V(1) chains have become V³⁺ and correspondingly 20% of the V⁴⁺ cations of the V(2) chains have become V⁵⁺. This disproportionation process would explain the difference between the two short V-V distances. Also it would explain why the T → M₁ transition does not take at lower temperatures.     

Comprehensive two-dimensional liquid chromatography for the characterization of functional acrylate polymers

Comprehensive two-dimensional liquid chromatography-size-exclusion chromatography (LC x SEC) was investigated as a tool for the characterization of functional poly(methyl methacrylate) (PMMA) polymers. Ultraviolet-absorbance and evaporative light-scattering detection (ELSD) were used. A simple method to quantify ELSD data is presented. Each data point from the ELSD chromatogram can be converted into a mass concentration using experimental calibration curves. The qualitative and quantitative information obtained on two representative samples is used to demonstrate the applicability of LC x SEC for determining the mutually dependent molar-mass distributions (MMD) and functionality-type distributions (FTD) of functional polymers. The influence of the molar mass on the retention behavior in LC was investigated using LC x SEC for hydroxyl-functional PMMA polymers. The critical conditions, at which retention is--by definition--independent of molar mass, were not exactly the same for PMMA series with different end-groups. Our observations are in close agreement with theoretical curves reported in the literature. However, for practical applications of LC x SEC it is not strictly necessary to work at the exact critical solvent composition. Near-critical conditions are often sufficient to determine the mutually dependent distributions (MMD and FTD) of functional polymers.     

Interaction of nonionic surfactants with copolymer microgel particles of NIPAM and acrylic acid

Binding of the nonionic surfactants Triton X-100 and Triton X-405 onto linear copolymers of N-isopropylacrylamide (NIPAM) and acrylic acid and to cross-linked microgel particles of similar composition but differing in their cross-link densities has been studied. The binding capacities vary for each of these polymeric systems, being smallest for the linear copolymer. The binding is also significantly less in all cases for the more hydrophilic surfactant, namely, Triton X-405. By comparing estimates of the pore or "cage" size within the microgel particles with the dimensions of the free micelles in solution, it is concluded that micelles of Triton X-100 form within the microgel particles more readily for the lower cross-linked microgel particles. However, micelles do not form as easily inside either microgel for Triton X-405. The swelling/deswelling behavior of each of the two microgels, in the presence of the surfactants, has been explained in terms of their relative binding behavior and how this contributes to the osmotic pressure difference inside and outside the microgel particles and also in terms of micelle "bridging" of the polymer network, causing shrinkage.     

Self-assembled monolayers on Au microelectrodes

Long chain alkanethiols self-assembled monolayers (SAMs) formed on Au microelectrodes showed higher sensitivity towards defects than the same monolayers on macroelectrodes. The analysis of cyclic voltammetry and electrochemical impedance spectroscopy (EIS) experiments performed on covered microelectrodes were consistent with the formation of pinholes of about 10 nm in diameter. Moreover, the EIS data exhibited a specific behavior that was interpreted invoking the short circuiting of the pinholes impedance by the surrounding surface of the microelectrode in the high frequency domain, whereas in the low frequencies, the surface covered by the SAM was assume to act as an insulator.