ASEDock is a novel docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. We have introduced two novel concepts into ASEDock. One is an ASE model, which is defined by the combination of alpha spheres generated at a concavity in a protein and the excluded volumes around the concavity. The other is an ASE score, which evaluates the shape similarity between the ligand and the ASE model. The ASE score selects and refines the initial pose by maximizing the overlap between the alpha spheres and the ligand, and minimizing the overlap between the excluded volume and the ligand. Because the ASE score makes good use of the Gaussian-type function for evaluating and optimizing the overlap between the ligand and the site model, it can pose a ligand onto the docking site relatively faster and more effectively than using potential energy functions. The posing stage through the use of the ASE score is followed by full atomistic energy minimization. Because the posing algorithm of ASEDock is free from any bias except for shape, it is a very robust docking method. A validation study using 59 high-quality X-ray structures of the complexes between drug-like molecules and the target proteins has demonstrated that ASEDock can faithfully reproduce experimentally determined docking modes of various druglike molecules in their target proteins. Almost 80% of the structures were reconstructed within the estimated experimental error. The success rate of approximately 98% was attained based on the docking criterion of the root-mean-square deviation (RMSD) of non-hydrogen atoms (< or = 2.0 A). The markedly high success of ASEDock in redocking experiments clearly indicates that the most important factor governing the docking process is shape complementarity.

The development and validation of the program Ph4Dock is presented. Ph4Dock is a novel automated ligand docking program that makes best use of pharmacophoric features both in a ligand and at concave portions of a protein. By mapping of pharmacophores of the ligand to the pharmacophoric features that represent the concaves of the target protein, Ph4Dock realizes an efficient and accurate prediction of the binding modes between the ligand and the protein. To validate the potential of this unique docking algorithm, we have selected 43 reliable crystal structures of protein-ligand complexes. All of the ligands are druglike, and they are varied in nature. The diffraction-component precision index (DPI) originally used in crystallography was applied in this study in order to evaluate the docking results quantitatively. The root-mean-square deviation (rmsd) between non-hydrogen atoms of the ligand in the prediction and experimental results were analyzed using DPI. The rmsd values for 25 structures, consisting of almost 60% of the dataset, are less than three times of the corresponding DPI values. It means that the precision of docking results obtained by Ph4Dock is mostly equivalent to the experimental error in these cases. The present study has demonstrated that Ph4Dock can accurately reproduce the experimentally determined docking modes if the reliable crystal structures are used. Normally the success rate of the docking is judged using rmsd < or = 2.0 A as the criterion. The Ph4Dock marked an appreciably good success rate of 86% based on this criterion.

A fluorescent probe, 1,6-diphenyl-1,3,5-hexatriene, was incorporated in four different biological membranes, the purple membrane of Halobacterium halobium, human erythrocyte membrane, rabbit sarcoplasmic reticulum membrane, and rat liver mitochondrial membrane. Time-resolved fluorescence depolarization of the probe suggested that the rotational Brownian motion of the probe in the membranes was restricted in the angular range. The motion of the rod-shaped, lipophilic probe molecule, expected to reflect closely the motion of neighboring lipid hydrocarbon chains, was analyzed in terms of the wobbling-in-cone model in which the major axis of the probe was assumed to wobble freely in a cone of semiangle theta c with a wobbling diffusion constant Dw. At 35 degrees C, Dw in the four membranes, in the above order, ranged between 0.048 and 0.15 ns-1 and theta c between 31 and 53 degrees. From the rotational rate Dw, the viscosity against the wobbling motion was calculated to be 0.9-0.3 P. When the temperature was raised from 10 to 35 degrees C, Dw in all membranes increased approximately 3-fold, corresponding to activation energies of 7-8 kcal/mol, and theta c increased by about 10 degrees, except for the purple membrane in which the angular range remained narrow. The same characteristic temperature dependence has been found in many model membrane systems that contain unsaturated lecithins, suggesting an important role of unsaturated phospholipids in the dynamic structure of the lipid hydrocarbon chain region of biological membranes at physiological temperatures. Comparison with model systems suggests that proteins and cholesterol act mainly as barriers that narrow the angular range.

Ultrasonic relaxation of multilamellar liposomes formed from dipalmitoylphosphatidylcholine was measured near the gel-to-liquid crystal transition by a differential ultrasonic resonator. The relaxation time and strength increased remarkably near the transition temperature, indicating a pseudocritical phenomenon. A quantitative analysis of the relaxation in terms of thermodynamic relationships between specific heat, thermal-expansion coefficient, and compressibility showed that more than 90% of the total endothermic heat of the transition arises from the latent heat. The temperature dependence of the ultrasonic relaxation parameters was also analyzed by the Landau theory; we obtain a small but finite difference, 0.6 degree C, between the pseudocritical temperature and the transition temperature. These results provide a quantitative description of both the first-order and second-order characters of the gel-to-liquid crystal transition.