Introduction. William R. Taylor developed an algorithm for detecting knots in protein backbones ( Taylor, "A deeply knotted protein structure and how it might fold", Nature 406:916-919, 2000). He scanned 3,440 sequence-different published protein structures from the Protein Data Bank. Only eight genuine knots were found, most of which were simple trefoil knots and had been previously described. However several knots were detected in proteins not previously recognized as knotted. One was in acetohydroxy acid isomeroreductase ("AAIR", 1yve, 1qmg) , and was particularly interesting because of how deeply it sits in the folded protein backbone (far away from the ends) and because it is a more complicated figure-of-eight knot.
In his paper cited above, Taylor states "Pulling the ends of a given piece of string will usually decide whether it is knotted or not. Because we hold the ends, the string and our body form a closed circle and there is no danger of untying the knot as it is pulled." "The ends of protein chains (being charged) tend to lie on the surface ...." "An alternative approach is to invert the problem: rather than extending the termini outwards, these can be left fixed and the rest of the protein made to shrink around them. This was done [mathematically] by contracting the protein as if it were a rubber band."
Thanks to William R. Taylor (Division of Mathematical Biology, National Institute for Medical Research, the Ridgeway, Mill Hill, London UK) who kindly provided results of his calculations for the displays at this site.
1YVE: V. Biou, R. Dumas, C. Cohen-Addad, R. Douce, D. Job, E. Pebay-Peyroula, EMBO J 16:3405 (1997).
1QMG: K. Thomazeau, R. Dumas, F. Halgand, R. Douce, V. Biou, Acta Crystallogr., Sect.D 56:389 (2000).
* 1TPH: Z. Zhang, S. Sugio, E. A. Komives, K. D. Liu, J. R. Knowles, G. A. Petsko, D. Ringe, Biochemistry 33:2830 (1994).
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