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Circular permutation in proteins
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<p>A circular permutation is a relationship between <a href="/facts/Protein/Jxmagu3E">proteins</a> whereby the proteins have a changed order of <a href="/facts/Amino_acid/WDxYwBny">amino acids</a> in their <a href="/facts/Peptide_sequence/QNBoERdu">peptide sequence</a>. The result is a <a href="/facts/Protein_structure/BptnTs9X">protein structure</a> with different connectivity, but overall similar three-dimensional (3D) shape. In 1979, the first pair of circularly permuted proteins – <a href="/facts/Concanavalin_A/36fcWIg8">concanavalin A</a> and <a href="/facts/Lectin/I7Clqx4X">lectin</a> – were discovered; over 2000 such proteins are now known. </p><p>Circular permutation can occur as the result of <a href="/facts/Evolution/Hj0qAaBk">evolutionary</a> events, <a href="/facts/Posttranslational_modification/KMUayTIc">posttranslational modifications</a>, or <a href="/facts/Protein_engineering/veRAR1SF">artificially engineered</a> mutations. The two main models proposed to explain the evolution of circularly permuted proteins are <i>permutation by duplication</i> and <i>fission and fusion</i>. Permutation by duplication occurs when a <a href="/facts/Gene/e1swwPY6">gene</a> undergoes <a href="/facts/Gene_duplication/CcfJYsDF">duplication</a> to form a <a href="/facts/Tandem_repeat/V40yCKFJ">tandem repeat</a>, before redundant sections of the protein are removed; this relationship is found between <a href="/facts/Prosaposin/jvFvUEMT">saposin</a> and swaposin. Fission and fusion occurs when partial proteins fuse to form a single polypeptide, such as in <a href="/facts/NAD(P)%252B_transhydrogenase_(Si-specific)/K5FmkKYe">nicotinamide nucleotide transhydrogenases</a>. </p><p>Circular permutations are routinely engineered in the laboratory to improve their <a href="/facts/Catalysis/LPBS7TQC">catalytic activity</a> or <a href="/facts/Thermostability/PnqTAwae">thermostability</a>, or to investigate properties of the original protein. </p><p>Traditional <a href="/facts/Algorithm/fnl5NmRt">algorithms</a> for <a href="/facts/List_of_sequence_alignment_software/6AJKAI0p">sequence alignment</a> and <a href="/facts/Structural_alignment_software/n00b8g2l">structure alignment</a> are not able to detect circular permutations between proteins. New <a href="/facts/Nonlinear_system/4aYItALC">non-linear</a> approaches have been developed that overcome this and are able to detect <a href="/facts/Protein_topology/pNXTH8nv">topology</a>-independent similarities. </p>