Computational mapping places molecular probes-small molecules or functional groups-on a protein surface to identify the most favorable binding positions. Although x-ray crystallography and NMR show that organic solvents bind to a limited number of sites on a protein, current mapping methods result in hundreds of energy minima and do not reveal why some sites bind molecules with different sizes and polarities. We describe a mapping algorithm that explains the origin of this phenomenon. The algorithm has been applied to hen egg-white lysozyme and to thermolysin, interacting with eight and four different ligands, respectively. In both cases the search finds the consensus site to which all molecules bind, whereas other positions that bind only certain ligands are not necessarily found. The consensus sites are pockets of the active site, lined with partially exposed hydrophobic residues and with a number of polar residues toward the edge. These sites can accommodate each ligand in a number of rotational states, some with a hydrogen bond to one of the nearby donor͞acceptor groups. Specific substrates and͞or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations.T he mapping of a protein by experimental or computational tools involves placing molecular probes-small organic molecules or functional groups-around the protein surface to determine the most favorable binding positions. Larger molecules that are candidates for high affinity ligands can be constructed by combining the probes at (or near) their optimal binding sites. This site-mapping and fragment-assembly strategy provides an important approach to drug design (1-6). Experimental approaches to mapping include x-ray crystallography (7-10) and NMR techniques (11, l2). In the multiple solvent crystal structure method (7-10), the x-ray structure of a protein is repeatedly solved in a variety of organic solvents, each representing a different functional group. In NMR methods, the binding of small molecules in aqueous solution is detected by chemical shifts of the protein and by the observation of intermolecular nuclear Overhauser effects (NOEs) between protons of the protein and the ligand (11).Because the probes are generally unrelated to any natural substrate of the protein, one would expect largely nonspecific binding. However, both x-ray crystallography (7-10) and NMR (11) reveal only a limited number of bound ligand positions, and a pocket of the active site tends to form a consensus site that binds many ligands, irrespective of their sizes and polarities. An NMR study by Liepinsh and Otting (11) shows that methanol, methylene chloride, acetonitrile (CCN), acetone (ACN), DMSO, isopropanol (IPA), t-butanol, and urea all bind to the specificity-determining site (site C) of the hen egg-white lysozyme (HEWL). Recent multiple solvent crystal structure studies of thermolysin (TLN) (9, 10) show that IPA, ACN, CCN, and phenol (IPH) bind preferenti...

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Ab initio calculations were performed on prototypical intramolecular H atom transfer reactions in alkyl radicals, namely, the identity reactions of 1,2-, 1,3-, 1,4-, and 1,5 intramolecular isomerizations in the ethyl, 1-propyl, 1-butyl, and 1-pentyl radicals, respectively. The equilibrium geometries and the transition structures have been optimized at the UHF/6-31G* and/or UMP2/6-311G** levels. The activation energies at 0 K were calculated with the MP-SAC2 and BAC-MP4 methods. The computed barrier heights (41.1, 41.6, 24.6, 17.2 kcal mol-1 at the MP-SAC2 and 43.1, 41.0, 25.1, and 18.8 kcal mol-1 at the BAC-MP4 level of theory) follow the trend expected and are in reasonable agreement with experimental data on related reactions. The differences between the ab initio barrier heights of alkyl isomerizations and that of the corresponding bimolecular reaction are in good agreement with the strain energies of the corresponding cycloalkanes.