Kinetics of exchange processes in the adsorption of proteins on solid surfaces

The homogeneous exchange process whereby IgG molecules adsorbed onto latex particles are replaced by IgG molecules from the bulk solution was studied by means of 125I radiolabeling. The exchange mechanism was investigated on surfaces saturated with either labeled or unlabeled proteins in the presence of a solution of the opposite species in two sets of independent experiments. After rinsing of the surface by pure buffer followed by supplementary IgG adsorption, the exchange process followed a kinetic law of first order with respect to the IgG molecules from the bulk solution, and the apparent exchange rate constant was (2.3 +/- 0.4) x 10(-5) cm.hr-1.

Reaction between Ellagic Acid and an Ultimate Carcinogen

The reaction coordinate between a typical ultimate carcinogen benzo[a]pyrene-7,8-diol-9,10-epoxide (BPDE) and ellagic acid, a proven chemopreventive agent active against cancers caused by polycyclic aromatic hydrocarbons (PAHs), was examined by density functional theory (DFT) and semiempirical MO calculations, and activation energy was calculated. The effect of a polar environment was included using Tomasi and the Langevin dipoles methods. The calculated BPDE/ellagic acid reaction free energy of activation is found to be in decent agreement with experimental data [Sayer, J. M. et al. J. Am. Chem. Soc. 1982, 104, 5562-5564]. This work sheds light on the mechanism of action of ellagic acid. Quantum chemical calculations of this kind are valuable for the design of ellagic acid derivatives with even lower activation energy and increased reactivity toward ultimate carcinogens as well as controlled reactivity toward DNA.

Incidence of partial charges on ion selectivity in potassium channels

Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K(+) ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K(+) and Na(+) can play a role as for ionic selectivity and conductance.

Role of water molecules in the KcsA protein channel by molecular dynamics calculations

Molecular dynamics simulations supported by electrostatic calculations have been conducted on the KcsA channel to determine the role of water molecules in the pore. Starting from the X-ray structure of the KcsA channel in its closed state at 2.0 angstroms resolution, the opening of the pore towards a conformation built on the basis of EPR results is studied. We show that water molecules act as a structural element for the K+ ions inside the filter and the hydrophobic cavity of the channel. In the filter, water tends to enhance the depth of the wells occupied by the K+ ions, while in the cavity there is a strong correlation between the water molecules and the cavity ion. As a consequence, the protein remains very stable in the presence of three K+ ions in the selectivity filter and one in the cavity. The analysis of the dynamics of water molecules in the cavity reveals preferred orientations of the dipoles along the pore axis, and a correlated behavior between this dipole orientation and the displacement of the K+ ion during the gating process.

A Bregman-proximal point algorithm for robust non-negative matrix factorization with possible missing values and outliers - application to gene expression analysis

Background

Non-Negative Matrix factorization has become an essential tool for feature extraction in a wide spectrum of applications. In the present work, our objective is to extend the applicability of the method to the case of missing and/or corrupted data due to outliers.

Results

An essential property for missing data imputation and detection of outliers is that the uncorrupted data matrix is low rank, i.e. has only a small number of degrees of freedom. We devise a new version of the Bregman proximal idea which preserves nonnegativity and mix it with the Augmented Lagrangian approach for simultaneous reconstruction of the features of interest and detection of the outliers using a sparsity promoting ℓ₁ penality.

Conclusions

An application to the analysis of gene expression data of patients with bladder cancer is finally proposed.