Cotranslational folding of deeply knotted proteins

J Phys Condens Matter. 2015 Sep 9;27(35):354105. doi: 10.1088/0953-8984/27/35/354105. Epub 2015 Aug 20.

Abstract

Proper folding of deeply knotted proteins has a very low success rate even in structure-based models which favor formation of the native contacts but have no topological bias. By employing a structure-based model, we demonstrate that cotranslational folding on a model ribosome may enhance the odds to form trefoil knots for protein YibK without any need to introduce any non-native contacts. The ribosome is represented by a repulsive wall that keeps elongating the protein. On-ribosome folding proceeds through a a slipknot conformation. We elucidate the mechanics and energetics of its formation. We show that the knotting probability in on-ribosome folding is a function of temperature and that there is an optimal temperature for the process. Our model often leads to the establishment of the native contacts without formation of the knot.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Haemophilus influenzae / enzymology*
  • Methyltransferases / chemistry*
  • Models, Molecular
  • Protein Biosynthesis*
  • Protein Conformation
  • Protein Folding*
  • Protein Stability
  • Ribosomes / chemistry*
  • Thermodynamics

Substances

  • Methyltransferases