gramicidin-a and tetramethylammonium

The accurate description of protein-ligand binding energies and configurations is an important problem in molecular biology with many applications in medicine and pharmacology. Molecular dynamics (MD) simulations provide the required accuracy but they are too slow for searching binding positions. Conversely, docking methods are much faster but have limited accuracy. An appropriate combination of the two methods could avoid the shortcomings associated with each, thus offering a better approach to the protein-ligand binding problem. Here we investigate the feasibility of such a combined docking-MD approach in a well-defined system: binding of organic cations to the gramicidin A channel. We use the AutoDock program to generate a set of protein-ligand binding configurations, which are then refined in MD simulations. For each system, we examine the binding configuration in detail and calculate the binding free energy by constructing the potential of mean force for the ligand. Our results show that AutoDock provides suitable initial configurations, which can be used profitably in MD simulations to obtain an accurate description of protein-ligand binding with a reasonable computational effort.

Topics: Cations; Computer Simulation; Gramicidin; Hydrogen Bonding; Methylamines; Models, Molecular; Molecular Conformation; Organic Chemicals; Quaternary Ammonium Compounds; Software; Tetraethylammonium

The effect of nigericin on aggregation of bovine platelets was investigated in media containing the chloride salts of various alkali metal cations of quaternary ammonium cations. In medium with K+, which has the highest permeability with the ionophore among the cations tested, nigericin slightly enhanced both ADP- and thrombin-induced aggregation. In medium with Na+, nigericin scarcely affected ADP-induced aggregation, and slightly inhibited thrombin-induced aggregation. In media with Cs+, choline and tetramethylammonium, it inhibited the aggregations induced by both ADP and thrombin. Measurement of the cytoplasmic pH with the fluorescent probe 2',7'-bis(carboxyethyl)5,6-carboxyfluorescein showed that nigericin increased the intracellular pH in K+ medium and caused its stable decrease (of about 0.6) in Cs+, choline and tetramethylammonium media, but caused only a small transient decrease in medium with Na+. These results suggest that the effects of nigericin on platelet aggregation are mainly due to its effects on the cytoplasmic pH. This conclusion is supported by the findings that the effects on platelet aggregation of other types of ionophore tested were also proportional to their effects on the cytoplasmic pH.

Topics: Adenosine Diphosphate; Animals; Anti-Bacterial Agents; Blood Platelets; Cations; Cattle; Cesium; Choline; Cytoplasm; Gramicidin; Hydrogen-Ion Concentration; Nigericin; Platelet Aggregation; Potassium; Quaternary Ammonium Compounds; Sodium; Thrombin; Valinomycin