title: Mechanically tightening a protein slipknot into a trefoil knot.
abstract: The knotted/slipknotted polypeptide chain is one of the most surprising topological features found in certain proteins. Understanding how knotted/slipknotted proteins overcome the topological difficulty during the folding process has become a challenging problem. By stretching a knotted/slipknotted protein, it is possible to untie or tighten a knotted polypeptide and even convert a slipknot to a true knot. Here, we use single molecule force spectroscopy as well as steered molecular dynamics (SMD) simulations to investigate how the slipknotted protein AFV3-109 is transformed into a tightened trefoil knot by applied pulling force. Our results show that by pulling the N-terminus and the threaded loop of AFV3-109, the protein can be unfolded via multiple pathways and the slipknot can be transformed into a tightened trefoil knot involving ∼13 amino acid residues as the polypeptide chain is apparently shortened by ∼4.7 nm. The SMD simulation results are largely consistent with our experimental findings, providing a plausible and detailed molecular mechanism of mechanical unfolding and knot tightening of AFV3-109. These simulations reveal that interactions between shearing β-strands on the threaded and knotting loops provide high mechanical resistance during mechanical unfolding.
authors.affiliation: Department of Chemistry, University of British Columbia , Vancouver, BC V6T 1Z1, Canada.
authors.forename: Chengzhi
authors.initials: C
authors.lastname: He
authors.forename: Guillaume
authors.initials: G
authors.lastname: Lamour
authors.forename: Adam
authors.initials: A
authors.lastname: Xiao
authors.forename: Joerg
authors.initials: J
authors.lastname: Gsponer
authors.forename: Hongbin
authors.initials: H
authors.lastname: Li
mesh_terms: D000595:Amino Acid Sequence; D018625:Microscopy, Atomic Force; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics
chemical_list: D011506:Proteins