PMID: 11933058Apr 5, 2002Paper

Classification of proteins based on the properties of the ligand-binding site: the case of adenine-binding proteins

Proteins
Valentina CappelloUwe Koch

Abstract

Comparative analysis of protein binding sites for similar ligands yields information about conserved interactions, relevant for ligand affinity, and variable interactions, which are important for specificity. The pattern of variability can indicate new targets for a pharmacologically validated class of compounds binding to a similar site. A particularly vast group of therapeutically interesting proteins using the same or similar substrates are those that bind adenine-containing ligands. Drug development is focusing on compounds occupying the adenine-binding site and their specificity is an issue of paramount importance. We use a simple scheme to characterize and classify the adenine-binding sites in terms of their intermolecular interactions, and show that this classification does not necessarily correspond to protein classifications based on either sequence or structural similarity. We find that only a limited number of the different hydrogen bond patterns possible for adenine-binding is used, which can be utilized as an effective classification scheme. Closely related protein families usually share similar hydrogen patterns, whereas non-polar interactions are less well conserved. Our classification scheme can be used to selec...Continue Reading

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Citations

Nov 19, 2003·Journal of Molecular Biology·Stephen A CammerJacquelyn S Fetrow
Jul 2, 2003·Current Opinion in Structural Biology·Kengo Kinoshita, Haruki Nakamura
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Nov 20, 2003·Journal of the American Chemical Society·Lisong MaoXiche Hu

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