8] Clefts and binding sites in protein receptors

Abstract

Publisher Summary This chapter discusses the methods for determining clefts and binding sites in protein receptors. Direct methods of cleft determination are aimed at the analysis of a receptor whose three-dimensional structure is known. The meaning of the term “protein surface” is discussed in the chapter so that all the methods can be related to a common set of definitions. The different classes of algorithms that have been used to define and display the surface, to look at mappings of topographic features, to quantify surface roughness and curvature, and to search for packing defects and sites are reviewed in the chapter. All these methods require a set of Cartesian coordinates and produce an essentially static picture of the receptor. Biomolecules are dynamic objects and undergo substantial conformational changes; each static picture should, therefore, be regarded as a snapshot. These stills should be combined into a moving trajectory or a partition function; this is implied whenever a new static method is introduced. Indirect methods of receptor mapping are applicable when the receptor structure is unknown, but the structures of a series of ligands that bind to the receptor at a common site are available. The binding site is deduced from the apparent common properties of the ligands—that is, the pharmacophore. The assumptions behind pharmacophore deduction are discussed in the chapter. The algorithms are illustrated in the chapter by case studies: the method of shape mapping is exemplified by a family of retinal isomers.