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.

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.