Computational mapping identifies the binding sites of organic solvents on proteins.

ABSTRACT: 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 c

SUBMITTER: Dennis S 

PROVIDER: S-EPMC123641 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature