Residues responsible for distinct biological functions are characterized by different statistical features of sequential and spatial neighborhoods: A thermolysin example

Abstract

An investigation of the functional topography of thermolysin was carried out using frequency analysis of its primary and tertiary structures. The statistical validity of this approach was estimated for the enzyme active site, the substrate-binding pocket, the inter-domain interface and calcium-binding sites' predictions. We showed that frequency analysis of primary structure could be employed to predict the localization of contiguous parts of the inter-domain interface. The same approach appears to be unsuitable to a search for conformation-dependent enzyme active sites and substrate-binding pockets. In contrast, frequency analysis of the spatial neighborhood is not effective for predicting the inter-domain interface as distinct from the active site, substrate-binding pocket and calcium-binding sites. These differences should be taken into account when investigating and understanding protein structure—function relationships.