title: Sequence determines degree of knottedness in a coarse-grained protein model.
abstract: Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.
authors: Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland.
authors: Thomas
authors: T
authors: Wüst
authors: Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128 Mainz, Germany.
authors: Daniel
authors: D
authors: Reith
authors: Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, 55128 Mainz, Germany.
authors: Peter
authors: P
authors: Virnau
mesh_terms: D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins