title: Cotranslational folding of deeply knotted proteins.
abstract: Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.
authors: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
authors: Mateusz
authors: M
authors: Chwastyk
authors: Marek
authors: M
authors: Cieplak
mesh_terms: D006193:Haemophilus influenzae / Q000201:enzymology*; D008780:Methyltransferases / Q000737:chemistry*; D008958:Models, Molecular; D014176:Protein Biosynthesis; D011487:Protein Conformation; D017510:Protein Folding; D055550:Protein Stability; D012270:Ribosomes / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D008780:Methyltransferases