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Single-molecule detection reveals knot sliding in TrmD denaturation
Peng Wang1, Lijiang Yang, Pengcheng Liu
1Department of Chemical Biology, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, PR China.
Chemistry (Weinheim an Der Bergstrasse, Germany)
|March 21, 2013
Summary
Knotted proteins retain their knots even in the unfolded state. During unfolding, the knot in TrmD protein slides towards the C-terminal, driven by interactions within the polypeptide chain.
Area of Science:
- Protein topology
- Biophysics
- Molecular dynamics
Background:
- A growing number of proteins are identified with knots in their polypeptide chains.
- The formation mechanisms and reasons behind these complex protein topologies remain largely unknown.
- Experimental data on knot dynamics during protein folding is scarce.
Purpose of the Study:
- To investigate the knot's behavior in the denatured state of TrmD, a knotted protein.
- To understand the knot's movement during the protein unfolding process.
- To characterize the structural properties of the knot in its unfolded state.
Main Methods:
- Utilized single-molecule fluorescence resonance energy transfer (smFRET) experiments.
- Employed molecular dynamics (MD) simulations.
- Studied TrmD, a tRNA methyltransferase from Escherichia coli, as a model system.
Main Results:
- The knot persists in the unfolded state of TrmD, similar to YibK and YbeA proteins.
- Both smFRET and MD simulations showed the knot sliding towards the C-terminal during unfolding.
- This sliding is attributed to interactions between the N-terminal β-sheet core and the native knot region.
- The knot's size in the unfolded state does not exceed its native state size.
- The knot exhibited "downhill" sliding accompanied by chain collapse in the denatured state.
Conclusions:
- Knots are stable topological features present even in the unfolded states of proteins.
- Knot movement during unfolding is a directed process, influenced by intramolecular interactions.
- The findings provide insights into the folding pathways of knotted proteins and their unique structural properties.
