Research Projects

Proteins can fold by forming non-trivial topologies, such as knots and slip knots, which have fascinated biophysicists, chemists, and mathematicians. The main goal is to understand the mechanism by which a linear polypeptide chain spontaneously and reversibly folds to a knotted structure without external physical force, why they form a knot, and the biological function of the knotted protein. Computer simulations have shown the possibility of an intermediate configuration with a slip knot during the early folding process, and kinetic folding experiments have demonstrated the detection of knotted conformation in denatured proteins. However, direct experimental observation of the signature of the knot formation in a given protein is yet to be demonstrated. One possible way to understand this is to directly observe the reversible folding/unfolding transitions of knotted proteins, which are known to have slip knot configurations in their denatured states. A single-molecule experiment is an ideal candidate to directly observe rare molecular events. Previous work has demonstrated that an externally controlled electric field at the solid-state nanopore can bias the folding-unfolding equilibrium of a protein to denatured states, and single-molecule trajectories of transition between folded, intermediate, and unfolded protein states can be directly resolved at sub-microseconds time resolution by measuring ionic-current through the nanopore. This research aims to combine nanopore ionic-current measurements and barrier crossing dynamics to directly observe the knot-forming single-molecule trajectories in YibK and YbeA proteins, and to determine if the structural fluctuation of knotted proteins is coupled to the translocation.