Domains of a protein (Super secondary structure of proteins)

Domains of a protein (Super secondary structure of proteins)

Simple definition: Several motifs pack together to form compact, local, semi-independent units called domains.

Many proteins are composed of more than one subunit, where each subunit is a separate polypeptide chain and can form a stable folded structure by itself. Within a single subunit, contiguous portion of the polypeptide chain frequently folded into compact, local, semi independent units called domains.

Domains are larger associations of two or more secondary structures, two or more supersecondary elements, or mixtures of two or more secondary and supersecondary structures.

They can also be known as ‘folds’, and ‘modules’.

  • Domain is an independent unit, usually stable by itself.
  • It can comprise the whole protein or a part of the protein.
  • Domains are more complex and larger than motifs.
  • A domain can be made up of one or more well characterized motifs. Domain is also a super secondary structure (Made of multiple secondary structures).
  • Usually domains contains between 40 and 350 amino acids.
  • A polypeptide with 200 amino acids normally consists of two or more domains
  • Different domains of a protein are often associated with different functions. So domains can impart different functions to same protein.
  • Domain is the modular unit from which many larger proteins are constructed.
  • Domains are usually connected with relatively flexible areas of protein
  • Some ‘folds’ are built up from smaller motifs.
  • Other folds are not built up from smaller motifs.

Eg:  Sperm whale myoglobin (the first protein structure to be determined)

Important point: If a domain is cleaved off from its polypeptide chain, it will still be able to do its function.

Reason: The structure of domain does not depend on the interactions it has with the rest of the polypeptide chain. Therefore if it is cleaved off, it will retain its structure and thus the function too.

Each domain has a compact 3 – D structure. So they can be independently folded and stable.

Each domain has distinct function: Ca 2+ binding

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