title: Multiple folding pathways of proteins with shallow knots and co-translational folding.
abstract: We study the folding process in the shallowly knotted protein MJ0366 within two variants of a structure-based model. We observe that the resulting topological pathways are much richer than identified in previous studies. In addition to the single knot-loop events, we find novel, and dominant, two-loop mechanisms. We demonstrate that folding takes place in a range of temperatures and the conditions of most successful folding are at temperatures which are higher than those required for the fastest folding. We also demonstrate that nascent conditions are more favorable to knotting than off-ribosome folding.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Chwastyk
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
mesh_terms: D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D014176:Protein Biosynthesis; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics
chemical_list: D011506:Proteins