= Protein motif
A \b[protein motif] is a recognizable recurring pattern in a <protein>'s sequence or three-dimensional arrangement. A <protein sequence motif> describes characteristic residues and allowed variation; a <protein structural motif> describes a recurring spatial combination of structural elements. A motif can be part of a <protein domain>, without by itself being an independently folding domain or specifying the whole protein's function.
Sequence-pattern notation makes a useful distinction explicit. PROSITE uses defined residues, alternatives and wildcard positions to describe signatures found in <protein sequences>.<PROSITE user manual>[Patterns, profiles and pattern syntax]{ref} For an original illustration, take the invented four-position pattern `A-x-G-x`, with each `x` allowed any of 20 standard <amino acids>. It matches $20^2=400$ different residue strings. Finding a match therefore does not uniquely identify a sequence, much less prove a particular biochemical activity. This teaching pattern is not asserted to be a real biological signature.
The <EF hand> supplies a structural example: two <alpha helices> flank a loop associated with <calcium ion> binding in canonical members. Recognizing the arrangement, measuring binding and determining its physiological role are different kinds of evidence.<EF-hand calcium-binding domain signature and profile in PROSITE>[Description, helix-loop-helix organization and atypical/nonbinding regions]{ref}
Motifs are useful because local arrangements can recur in proteins with different overall architectures. A sequence signature can guide comparison or experimentation; a structure can test whether the relevant residues approach one another in space. Neither the word “motif” nor a pattern hit alone supplies an affinity measurement or a complete functional annotation.
Back to article page
