The first basic level is the amino acid sequence. The 20 most common amino acids
found in proteins are joined together into a polypeptide chain during the process of protein synthesis, catalyzed by the ribosome. To a large extent, the amino acid sequence defines the secondary structure
(α-helices and β-sheets) and of course the tertiary structure (domains
) of proteins. However, in many cases, we also need to consider the effect of the local environment on structure stabilization. The most obvious example is that of membrane proteins, a considerable part of which is embedded into the hydrophobic environment of membranes. As a result, they lose their native structure outside the membrane and form large aggregates. For this reason, during purification, we need detergent to keep these proteins in a soluble state.
The tertiary structure is defined by the arrangement of the secondary structure elements in space, a fold. The fold is a characteristic feature of the tertiary structure. The currently known three-dimensional protein structures have been classified into around 1300 unique folds. In a later chapter, we will discuss some examples of these folds and the CATH databases
where folds and domains are classified, and the relationships between the fold and protein evolutionary origin are revealed.