Starting from this chapter and continuing through the next three chapters, we introduce the basics of protein structural bioinformatics. Proteins perform most essential biological and chemical functions in a cell. They play important roles in structural, enzymatic, transport, and regulatory functions. The protein functions are strictly determined by their structures. Therefore, protein structural bioinformatics is an essential element of bioinformatics. This chapter covers some basics of protein structures and associated databases, preparing the reader for discussions of more advanced topics of protein structural bioinformatics.

AMINO ACIDS

The building blocks of proteins are twenty naturally occurring amino acids, small molecules that contain a free amino group (NH2) and a free carboxyl group (COOH). Both of these groups are linked to a central carbon (Cα), which is attached to a hydrogen and a side chain group (R) (Fig. 12.1). Amino acids differ only by the side chain R group. The chemical reactivities of the R groups determine the specific properties of the amino acids.

Amino acids can be grouped into several categories based on the chemical and physical properties of the side chains, such as size and affinity for water. According to these properties, the side chain groups can be divided into small, large, hydrophobic, and hydrophilic categories. Within the hydrophobic set of amino acids, they can be further divided into aliphatic and aromatic. Aliphatic side chains are linear hydrocarbon chains and aromatic side chains are cyclic rings. Within the hydrophilic set, amino acids can be subdivided into polar and charged.