@article {415, title = {Stabilizing effect of knots on proteins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 16}, pages = {19714-9}, 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.}, keywords = {Computer Simulation, Disulfides, Hot Temperature, Humans, Models, Chemical, Ornithine Carbamoyltransferase, Protein Folding, Protein Structure, Secondary, Stress, Mechanical}, issn = {1091-6490}, doi = {10.1073/pnas.0805468105}, author = {Joanna I. Sulkowska and Sulkowski, Piotr and Szymczak, P and Cieplak, Marek} }