Question

Difference between module, domain and motifs in protein structure

Answer 1

Motifs are structural characteristics and domains are functional regions (not necessarily related to size). In a protein, a particular arrangement of amino acids or secondary structure that can be found in other proteins (not necessarily evolutionarily related) can be called a motif. If that particular arrangement is related to some function (DNA or protein binding, catalytic, etc.) then it is a domain. For example, the leucine zipper motif is usually found as part of a dimerization domain in many transcription factors.Apart from these two concepts (motifs, shorter sequences with resemblance among groups of proteins and domains, functional parts of a protein), it is interesting to consider the term protein module. A module is frequently used as synonimous to domain for protein structures, but relates more specifically to parts of a protein that have a defined fold. In princuiple a protein module could fold in its tertitary structure without the need of additional regions of the protein.Both are supersecondary structures, i.e. Made of multiple secondary structures. Domains are more complex and larger. They are compact structures of multiple secondary structures that are at a distance from each other. On the other hand, motifs can be structural or sequence. Sequence motifs share certain sequence of amino acids. Structural motifs are made of multiple secondary structures that are sequential to each other within the primary structure of a protein (e.g. Helix-loop-helix) and not separated by a random structure. Domains can contain a motif. Both domains and motifs can be functional or just mere structural.Domains are stable,folded, complexed and larger and emerge from the motif while motifs are stable speciall elements of  secondaray structure  and connection between them .

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