Structural motif

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a supersecondary structure, which also appears in a variety of other molecules. Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions.

Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not have to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" structure.

In proteins

In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. Note that, while the spatial sequence of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying gene. In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. Structural motifs may also appear as tandem repeats.

Beta hairpin: Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids between them.
Greek key: Four beta strands, three connected by hairpins, the fourth folded over the top.
Omega loop: A loop in which the residues that make up the beginning and end of the loop are very close together.
Helix-loop-helix: Consists of alpha helices bound by a looping stretch of amino acids. This motif is seen in transcription factors.
Zinc finger: Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins.
Helix-turn-helix: Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression.
Nest: Extremely common. Three consecutive amino acid residues form an anion-binding concavity.
Niche: Extremely common. Three or four consecutive amino acid residues form a cation-binding feature.

gollark: The other other one... reads numbers, maybe.

gollark: I think one of these is meant as a self-replicator, and the other writes numbers.

gollark: ```x86asmLOOP2:inc INCBUFadd TEMP !-50 INCBUFmnz TEMP I !LOOP2LOOP:re 8 BEE#wr 1 BEE#! 01 BEEmov I !LOOPTEMP: ! 0BEE: ! 0INCBUF: ! 4```And the other other one.

gollark: Here is the other program I wrote.

gollark: ```x86asmLOOP:inc INCBUFadd TEMP !-50 INCBUF# debug print#! 01 INCBUF#wr 0 INCBUF#re 0 INCBUFmnz TEMP I !LOOPhaltINCBUF: ! 1TEMP: ! 0OUT: ! 44```

Structural motif

In proteins

See also

References

Further reading