Speeding up biomolecular interactions by molecular sledding

Numerous biological processes involve association of a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Similarly, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.     

IPG with electrodic plateaus (and other unusual procedures for 2-DE)

We describe some simple changes to the geometry of the IPG strips that make them suitable to the loading of very large sample volumes and of high-salt solutions. Of special relevance is the possibility of using strips with immobilized plateau(s) to either side of the gradient, or to both, also in connection with in-gel rehydration protocols and focusing in stock trays. The only requirement to achieve this is to leave the all-ready-made attitude and go back to custom polymerization of the IPGs in one's laboratory.     

Enantioselective hydrogenation with self-assembling rhodium phosphane catalysts: influence of ligand structure and solvent

Three sets of new and related chiral phospholane and phosphepine ligands have been prepared for Rh-catalyzed enantioselective hydrogenation. The size and substitution pattern of the cyclic monophosphanes were varied. More importantly, the ligands differ in the nature of the heterocyclic group linked to the trivalent phosphorus atom: 2-pyridone or 2-alkoxypyridine. In the corresponding Rh complexes, the pyridone units of two monodentate P ligands can assemble by hydrogen bonding and form chelates. In contrast, synthetic precursors bearing alkoxypyridine appendages are not able to aggregate via intramolecular hydrogen bonds. The nature of self-assembly is dependent on the nature of the P ligand and the solvent used for the hydrogenation (CH2Cl2 vs. MeOH). These features affect the rate of the reaction as well as the enantioselectivity, which varied in the range of 0-99 % ee Complexation studies and DFT calculations were performed to explain these differences.     

Theoretical elastic moduli for disordered packings of interconnected spheres

A theoretical model has been developed which provides analytical expressions for the elastic moduli of disordered isotropic ensembles of spheres interconnected by physical bonds. Young's and shear moduli have been derived assuming an ideal random isotropic network and the radial distribution function for disordered packings of spheres. The interparticle interactions are accounted for in terms of surface forces for the two distinct cases of perfectly rigid spheres and spheres deformable at contact. A theoretical expression is also derived in a similar way for the bulk or compressibility modulus. In this case, an atomistic approach has been followed based on the analogy with noble gas solids and colloidal crystals. Also in this case, disordered spatial distribution of the spheres is described statistically. For the case of colloidal aggregates, a total two-body mean-field interaction potential is used which includes the Born repulsion energy. This latter contribution plays an essential role in determining the compression behavior of systems of particles aggregated in the primary minimum of the potential well and, therefore, must not be neglected. Both the expression of the Young's modulus and that of the compressibility modulus derived in this work are found to be consistent with two distinct sets of experimental data which recently appeared in the literature.     

Interaction of lipophilic gemcitabine prodrugs with biomembrane models studied by Langmuir-Blodgett technique

The stability and bioavailability of anticancer agents, such as gemcitabine, can be increased by forming prodrugs. Gemcitabine is rapidly deaminated to the inactive metabolite (2('),2(')-difluorodeoxyuridine), thus to improve its stability a series of increasingly lipophilic gemcitabine prodrugs linked through the 4-amino group to valeroyl, lauroyl, and stearoyl acyl chains were synthesized. Studies of monolayer properties are important to improve understanding of biological phenomena involving lipid/gemcitabine or lipid/gemcitabine derivative interactions. The interfacial behavior of monolayers constituted by DMPC plus gemcitabine or lipophilic gemcitabine prodrugs at increasing molar fractions was studied at the air/water interface at temperatures below (10 degrees C) and above (37 degrees C) the lipid phase transition. The effect of the hydrophobic chain length of gemcitabine derivatives on the isotherm of pure DMPC was investigated by surface tension measurement, and the results are reported as molar fractions as a function of mean molecular area per molecule. The results show that the compounds interact with DMPC producing mixed monolayers that are subject to an expansion effect, depending on the prodrug chain length. The results give useful hints of the interaction of these prodrugs with biological membranes and increase knowledge on the incorporation site of such compounds, as a function of their lipophilicity, in a lipid carrier; they may lead to improved liposomal formulation design.     

Generation of k-jets on toric varieties

The notion of a k-convex -support function for a toric variety is introduced. A criterion for a line bundle L to generate k-jets on X is given in terms of the k-convexity of the -support function . Equivalently L is proved to be k-jet ample if and only if the restriction to each invariant curve has degree at least k. Received October 22, 1997; in final form January 12, 1998     

Effects in B–doped KDP crystals irradiated with neutrons of large spectra energy

The results obtained for the r₆₃ electro‐optic coefficient of B‐doped and undoped KDP (KH₂PO₄) crystals irradiated with neutrons (including thermalized neutrons) produced by scattering of 30 Mev cyclotron protons on a target of Ta²⁰¹, are presented and compared to those obtained for non‐irradiated doped and undoped crystals. The B‐doped (H₃BO₃, Na₂B₄O₇ and Li₂B₄O₇) crystals were obtained by the conventional growth method by temperature decrease with 1 wt % dopant concentration in solution. The thermal neutron flux was around ϕ = 1. 10¹⁰ n/cm² s. Pulses of ∼15 μs long, in damped oscillatory mode (V= 8 kV, τ=1.95 μs) were used for the electro‐optic measurements. A Pockels cell, a photomultiplier, a He‐Ne laser (λ=632.8 nm, 5 mW, linearly polarized) and a Tk 720 A oscilloscope complete the experimental setup. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Lifetimes and transition probabilities of Xe II: Experimental measurements and theoretical calculations

In this work we make an experimental and theoretical investigation of transition probabilities (A) and lifetimes of Xe II. Eighteen A_ij's corresponding to the 6p-6d array were measured using a Laser Produced Plasma (LPP) as the spectroscopic source. The ab initio (AI) and Least Square Fitting (LSF) approaches were used to calculate the atomic parameters. Relativistic corrections and Configuration Interaction (CI) effects have been taken into account using the HFR approach described by Cowan. Whereas the AI parameters corresponding to 6p levels are not very affected by CI effects, several of the 6d levels with J=1/2, 3/2and 5/2 making transitions to the fundamental levels 5p⁵ are affected by CI effects due to both, discrete nd and continuum states, modifying their lifetimes values. An extensive comparison with other measurements and calculations are made. In particular, concerned with branching ratio and forbidden transitions. Received 15 July 1999