title: Stabilizing effect of knots on proteins.
abstract: Molecular dynamics studies within a coarse-grained, structure-based model were used on two similar proteins belonging to the transcarbamylase family to probe the effects of the knot in the native structure of a protein. The first protein, N-acetylornithine transcarbamylase, contains no knot, whereas human ormithine transcarbamylase contains a trefoil knot located deep within the sequence. In addition, we also analyzed a modified transferase with the knot removed by the appropriate change of a knot-making crossing of the protein chain. The studies of thermally and mechanically induced unfolding processes suggest a larger intrinsic stability of the protein with the knot.
authors.affiliation: Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland.
authors.forename: Joanna I
authors.initials: JI
authors.lastname: Sułkowska
authors.forename: Piotr
authors.initials: P
authors.lastname: Sulkowski
authors.forename: P
authors.initials: P
authors.lastname: Szymczak
authors.forename: Marek
authors.initials: M
authors.lastname: Cieplak
mesh_terms: D003198:Computer Simulation; D004220:Disulfides / Q000737:chemistry; D006358:Hot Temperature; D006801:Humans; D008956:Models, Chemical; D009954:Ornithine Carbamoyltransferase / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013314:Stress, Mechanical
chemical_list: D004220:Disulfides; D009954:Ornithine Carbamoyltransferase