Circular permutation in proteins
arrangement of amino acid sequence
A circular permutation is a relationship between proteins whereby the proteins have a changed order of amino acids in their peptide sequence. The result is a protein structure with different connectivity, but overall similar three-dimensional (3D) shape. In 1979, the first pair of circularly permuted proteins – concanavalin A and favin (both lectins) – were discovered; over 2000 such proteins are now known.
Circular permutation can occur as the result of evolutionary events, posttranslational modifications, or artificially engineered mutations. The two main models proposed to explain the evolution of circularly permuted proteins are permutation by duplication and fission and fusion. Permutation by duplication occurs when a gene undergoes duplication to form a tandem repeat, before redundant sections of the protein are removed; this relationship is found between saposin and swaposin. Fission and fusion occurs when partial proteins fuse to form a single polypeptide, such as in nicotinamide nucleotide transhydrogenases.
Circular permutations are routinely engineered in the laboratory to improve their catalytic activity or thermostability, or to investigate properties of the original protein.
Traditional algorithms for sequence alignment and structure alignment are not able to detect circular permutations between proteins. New non-linear approaches have been developed that overcome this and are able to detect topology-independent similarities.
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