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Assessing the effect of dynamics on the closed-loop protein-folding hypothesis.

Sree V Chintapalli1, Christopher J R Illingworth, Graham J G Upton

  • 1School of Biological Sciences, University of Essex, , Wivenhoe Park, Colchester CO4 3SQ, UK.

Journal of the Royal Society, Interface
|November 22, 2013
PubMed
Summary

The closed-loop hypothesis suggests ~25-residue loops are key to protein folding. Our study shows while these loops are important, a larger residue set is crucial for efficient protein folding.

Keywords:
closed loopsclosed-loop hypothesisconnectivityhydrophobicityprotein foldingtotal contact distance

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • The closed-loop (loop-n-lock) hypothesis posits that ~25-residue loops, stabilized by interactions at their ends (locks), are critical for protein structure.
  • Previous research linked total contact distance (TCD) to protein folding rates.

Purpose of the Study:

  • To investigate the role of loop-n-lock structures in protein folding.
  • To refine the correlation between TCD and folding rates by focusing on lock-interacting residues.

Main Methods:

  • Coarse-grain elastic network simulations were performed.
  • Loop lengths in diverse proteins were analyzed.
  • Total contact distance (TCD) calculations were conducted, with and without considering all residues.
  • Molecular dynamics simulations were used to analyze the protein core/nucleus.

Main Results:

  • A bias towards loops of approximately 25 residues was observed.
  • An improved correlation (r² = 0.76) between TCD and folding rate was found when considering only residues contacting the loop locks, compared to all residues (r² = 0.65).
  • Evidence suggested a protein core/nucleus of similar size to the lock-interacting residues.

Conclusions:

  • The closed-loop hypothesis is partially supported, highlighting the importance of loop-n-lock structures.
  • Efficient protein folding depends on a larger set of residues than just those forming the locks.
  • The original hypothesis may be too simplistic, with a broader set of residues being critical.