Protein Structure and Function. Application of Bioinformatics Methods - John Rigden 2014

Prediction of protein function based on its surface properties
Ligand-protein interaction
Properties of ligand-protein interactions

Perhaps the most critical Functions of a protein directly related to its surface are its interactions with other molecules. These interactions are fundamental to every aspect of life, ranging from METABOLISM to signal Transduction and beyond. This section examines Structure/156.html">Protein Interactions with small Ligand molecules. Other types of interactions will be discussed later in Chapter 9. Small ligand molecules are important not only as biological entities but also as drugs used to control aberrant protein functioning in diseases.

Protein-ligand interaction interfaces fall into two broad categories: the enzyme Active Site, which binds small molecules for subsequent chemical conversion, and binding pockets, which attach molecules without subsequent catalysis. Within active sites, amino acid residues are under evolutionary pressure to preserve both catalytic activity and The ability to specifically bind target molecules. Protein Families that transport or respond to small ligand molecules without further catalysis are not subject to the evolutionary pressures required to maintain catalytic activity; consequently, The properties of their binding sites often reflect The Diversity of small molecules capable of binding across different protein families. The complexity and costs associated with developing sufficiently selective drugs for this Class of interactions underscore this diversity.