Single-molecule electrophoresis of beta-hairpin peptides by electrical recordings and Langevin dynamics simulations

We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various beta-hairpin peptides across the staphylococcal alpha-hemolysin (alphaHL) protein pore at single-molecule resolution. The beta-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the beta-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded beta-hairpin peptides occurred more slowly. In this case, the beta-hairpin peptides traversed the alphaHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a beta-barrel protein pore is dependent on the folding features of the polypeptide.     

Langevin dynamics simulations of the diffusion of molecular knots in tensioned polymer chains

Motivated by recent experiments, in which knots have been tied in individual biopolymer molecules, we use Langevin dynamics simulations to study the diffusion of a knot along a tensioned polymer chain. We find that the dependence of the knot diffusion coefficient on the tension can be non-monotonic. This behavior can be explained by the model, in which the motion of the knot involves cooperative displacement of a local knot region. At low tension, the overall viscous drag force that acts on the knot region is proportional to the number N of monomers that participate in the knot, which decreases as the tension is increased, leading to faster diffusion. At high tension the knot becomes tight and its dynamics are dominated by the chain's internal friction, which increases with the increasing tension, thereby slowing down the knot diffusion. This model is further supported by the observation that the knot diffusion coefficient measured across a set of different knot types is inversely proportional to N. We propose that the lack of tension dependence of the knot diffusion coefficients measured in recent experiments is due to the fact that the experimental values of the tension are close to the turnover between the high- and low-force regimes.     

Modification of methylaluminoxane-activated ansa-zirconocene catalysts with triisobutylaluminum-transformations of reactive cations studied by NMR spectroscopy

When triisobutylaluminum (AliBu(3)) is added to solutions containing methylaluminoxane (MAO) and rac-[Me(2)Si(ind)(2)ZrCl(2)] (ind: indenyl) in C(6)D(6), NMR spectra show that methyl-bridged mixed-alkylaluminum dimers Al(mu-Me)(2)Me(4-x)iBu(x) predominate. These dimers react with MAO under partial transfer of isobutyl groups and induce a conversion of the initially prevailing cationic trimethylaluminum adduct rac-[Me(2)Si(ind)(2)Zr(mu-Me)(2)AlMe(2) (+)] to rac-[Me(2)Si(ind)(2)Zr(mu-Me)(2)AlMeiBu(+)] and rac-[Me(2)Si(ind)(2)Zr(mu-Me)(2)AliBu(2) (+)]. These species are unstable and release isobutene under formation of zirconocene hydrides.     

Complexes of titanium and zirconium based on [C5Me4CH2-(2-C5H4N)] ligand

Half-sandwich [η⁵:η¹-κN-C₅Me₄CH₂-(2-C₅H₄N)]MCl₃ (M = Ti (4), Zr (5)) and sandwich [η⁵-C₅Me₄CH₂-(2-C₅H₄N)][η⁵-C₅Me₅]ZrCl₂ (6) ring-peralkylated complexes have been prepared and characterized. Evidence of the intramolecular coordination of the side-chain pyridyl group both in 4 and 5 in solutions is provided by NMR spectroscopy data. Crystal structure of an adduct 5-py with one molecule of pyridine has been established by X-ray diffraction analysis.     

Novel antimitotic agents related to tubuloclustin: synthesis and biological evaluation

Tubuloclustin [N-(7-adamant-2-yloxy-7-oxoheptanoyl)-N-deacetylcolchicine], a highly cytotoxic anti-tubulin compound is known for its ability to promote microtubule disassembly followed by the formation of tubulin clusters of unique morphology. Three series of antimitotic agents related to tubuloclustin were designed and synthesized in order to enhance the molecular diversity of “tubuloclustin-like” family of compounds. The series of compounds with modified adamantane moiety was highly potent in cytotoxic effect on human lung carcinoma A549 cells (EC50 = 6–400 nM) and was active in affecting the microtubule arrays and induction of strong tubulin clusterization. In two other sets of compounds, the colchicine moiety of tubuloclustin was replaced by podophyllotoxin or combretastatin A-4. All combretastatin A-4 derivatives displayed noticeable cytotoxic activity (\(\hbox {EC}50=0.8{-}1.6\,\upmu \hbox {M}\)) but their effect on microtubules depended on the position of the linker attachment. Podophyllotoxin derivatives were also toxic to A549 cells (\(\hbox {EC}50=0.38{-}0.50\,\upmu \hbox {M}\)) and caused both microtubule depolymerization and some tubulin clustering. The data obtained gave additional evidence that the whole panel of C7-colchicine, podophyllotoxin and combretastatin derivatives could manifest clustering effect, and the strength of this effect correlated with cytotoxic activity of the compounds.     

Structural, electronic properties and stability of tungsten mono- and semi-carbides: A first principles investigation

First principles calculations have been performed with the purpose to understand the comparative peculiarities of the structural, electronic properties and stability for all phases formed in the tungsten-carbon system: hexagonal and cubic mono-carbides WC and four polymorphs (α, β, γ and ε) of semi-carbide W₂C. All calculations were performed by means of the full-potential linearized augmented plane wave method (FLAPW). The generalized gradient approximation (GGA) in the Perdew-Burke-Ernzerhof (PBE) formalism was used for the exchange and correlation energy functional. The geometries of all WC and W₂C phases were optimized and their structural parameters and theoretical density were established. Besides, we have evaluated the formation energies (E_form) of all the tungsten carbides. Based on our estimations we can arrange all investigated W-C phases depending on their stability in the following sequence: h-WC>ε-W₂C>β-W₂C>γ-W₂C>α-W₂C>c-WC. Here three carbides (h-WC, ε-W₂C and β-W₂C) are stable (E_form<0), γ-W₂C belongs to metastable systems (E_form∼0), whereas α-W₂C and c-WC appear to be unstable (E_form>0). Moreover, band structures, total and partial densities of states were obtained and analyzed systematically for all W-C phases in comparison with other available theoretical and experimental data.     

Electrodeposition polymers as immobilization matrices in amperometric biosensors: improved polymer synthesis and biosensor fabrication

Electrodeposition polymers can be precipitated on electrode surfaces upon electrochemical-induced modulations of the pH value in the diffusion zone in front of the electrode. The formed polymer films can be used as immobilization matrices in amperometric biosensors. In order to rationally control the thus obtained biosensor properties, it is indispensable to develop strategies for the reproducible synthesis of electrodeposition polymers as well as methods for the non-manual and reproducible sensor fabrication. Based on instrumental developments such as a specifically designed parallel synthesizer with improved stirring and temperature control, an automatic pipetting robot for the preparation of the monomer mixtures and controlled removal of polymerization inhibitors, the reproducible synthesis of libraries of electrodeposition polymers was achieved. Moreover, the polymerization process could be monitored using in-line thermocouples, and it could be shown that the chosen strategies led to reproducible polymerization reactions. By adaptation of an electrochemical robotic system integrating a Au microtiter plate and automatic electrode cleaning by means of a polishing wheel reproducible biosensor fabrication using glucose oxidase as a model enzyme could be demonstrated. These results open the route for the rational development of biosensors and control of the sensor properties by choosing specifically designed electrodeposition polymers.      

The interplay of inverted redox potentials and aromaticity in the oxidized states of new pi-electron donors: 9-(1,3-dithiol-2-ylidene)fluorene and 9-(1,3-dithiol-2-ylidene)thioxanthene derivatives

Derivatives of 9-(1,3-dithiol-2-ylidene)fluorene (9) and 9-(1,3-dithiol-2-ylidene)thioxanthene (10) have been synthesised using Horner-Wadsworth-Emmons reactions of (1,3-dithiol-2-yl)phosphonate reagents with fluorenone and thioxanthen-9-one. X-ray crystallography, solution electrochemistry, optical spectroscopy, spectroelectrochemistry and simultaneous electrochemistry and electron paramagnetic resonance (SEEPR), combined with theoretical calculations performed at the B3P86/6-31G** level, elucidate the interplay of the electronic and structural properties in these molecules. These compounds are strong two-electron donors, and the oxidation potentials depend on the electronic structure of the oxidised state. Two, single-electron oxidations (E(1)ox < E(1)ox) were observed for 9-(1,3-dithiol-2-ylidene)fluorene systems (9). In contrast, derivatives of 9-(1,3-dithiol-2-ylidene)thioxanthene (10) display the unusual phenomenon of inverted potentials (E(1)ox > E(1)ox) resulting in a single, two-electron oxidation process. The latter is due to the aromatic structure of the thioxanthenium cation (formed on the loss of a second electron), which stabilises the dication state (10(2+)) compared with the radical cation. This contrasts with the nonaromatic structure of the fluorenium cation of system 9. The two-electron oxidation wave in the thioxanthene derivatives is split into two separate one-electron waves in the corresponding sulfoxide and sulfone derivatives 27-29 owing to destabilisation of the dication state.     

On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data

We propose a method for calculating absolute free energies from Monte Carlo or molecular-dynamics data. The method is based on the identity that expresses the partition function Q as a Boltzmann average: 1Q=w(p,x)exp[betaH(p,x)], where w(p,x) is an arbitrary weight function such that its integral over the phase space is equal to 1. In practice, to minimize statistical errors the weight function is chosen such that the regions of the phase space where sampling statistics are poor are excluded from the average. The "ideal" weight function would be the equilibrium phase-space density exp[-betaH(p,x)]Q itself. We consider two methods for constructing the weight function based on different estimates of the equilibrium phase-space density from simulation data. In the first method, it is chosen to be a Gaussian function, whose parameters are obtained from the covariance matrix of the atomic coordinates. In the second, a clustering algorithm is used to attempt partitioning the data into clusters corresponding to different basins of attraction visited by the system. The weight function is then constructed as a superposition of Gaussians calculated for each cluster separately. We show that these strategies can be used to improve upon previous methods of estimating absolute entropies from covariance matrices.