A knot or not a knot? SETting the record 'straight' on proteins.
A novel knot found in the SET domain is examined in the light of five recent crystal structures and their descriptions in the literature. Using the algorithm of Taylor it was established that the backbone chain does not form a true knot. However, only two crosslinks corresponding to hydrogen-bonds were needed to form a knotted structure. Such loosely knotted structures formed by hydrogen-bonded crosslinks were assessed as lying between covalent crosslinks (such as disulphide bonds) and threaded-loops which are formed by close (unbonded) contacts between different parts of the chain. The term pseudo-knot was introduced (from the RNA field) to distinguish hydrogen-bonded 'knots'.
Taylor
William R
WR
Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK. wtaylor@nimr.mrc.ac.uk
Xiao
Bing
B
Gamblin
Steven J
SJ
Lin
Kuang
K
D000465:Algorithms; D020134:Catalytic Domain; D003198:Computer Simulation; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase / Q000737:chemistry; D006860:Hydrogen Bonding; D008780:Methyltransferases / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011496:Protein Methyltransferases; D011506:Proteins / Q000737:chemistry*
D004220:Disulfides; D011506:Proteins; D000076983:Histone Methyltransferases; D008780:Methyltransferases; D011496:Protein Methyltransferases; D011495:Histone-Lysine N-Methyltransferase