We can define Supersecondary structures as combinations of alpha-helices and beta-structures connected through loops, that form patterns that are present in many different protein structures. These folding patterns are stabilized through the same kind of linkages than the tertiary level. Sometimes the term “motif” is used to describe these supersecondary structures.
These structures can be relatively simples, as alpha-alpha (two alpha helixes linked by a loop), Beta-Beta (two beta-strands linked by a loop), Beta-alpha-Beta (Beta-strand linked to an alpha helix that is also linked to other beta strand, by loops) or more complexes structures, like the Greek key motiv or the beta-barrel.
It is very interesting in these motifs that these repetitive structures can be very different in their primary structure and they can be present in very different proteins. Some proteins have no supersecondary structures.
They are stable, independently folding, compact structural units within a protein, formed by segments of the polypeptide chain, with relative independent structure and function distinguishable from other regions and stabilized through the same kind of linkages than the tertiary level.
Following this definition, in this representation of Pyruvate kinase, it is possible to distinguish three domains:
Protein domains may be considered as elementary units of protein structure and evolution, capable, to some extent, of folding and functioning autonomously. A domain sometimes contain motifs, sometimes don’t.
The tertiary structure of many proteins is built from several domains
Often each domain has a separate function to perform for the protein, such as:
– Bind a small ligand
– Spanning the plasma membrane (transmembrane proteins)
– Contain the catalytic site (enzymes)
– DNA-binding (in transcription factors)
– Providing a surface to bind specifically to another protein
In some (but not all) cases, each domain in a protein is encoded by a separate exon in the gene encoding that protein.