Paper Citing NAMD - Abstract
He, Chengzhi; Lamour, Guillaume; Xiao, Adam; Gsponer, Joerg; Li, Hongbin
Mechanically Tightening a Protein Slipknot into a Trefoil Knot
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:11946-11955, AUG 27 2014
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 similar to 13 amino acid residues as the polypeptide chain is apparently shortened by similar to 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 beta-strands on the threaded and knotting loops provide high mechanical resistance during mechanical unfolding.
