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Current Physical Chemistry

Volume 2 Issue 1
ISSN: 1877-9468
eISSN: 1877-9476

 

   All Titles

  Complexity in Protein Folding: Simulation Meets Experiment
  pp.4-11 (8) Authors: Amedeo Caflisch, Peter Hamm
doi: 10.2174/10004
   
      Abstract

We review our joint experimental-theoretical effort on the folding of photo-switchable α-helices. The folding kinetics of these peptides is profoundly non-exponential, which is attributed to a partitioning of the unfolded state into several misfolded traps. These traps are connected to the folded state in a hub-like fashion with folding barriers of different heights. Molecular dynamics simulations reveal a semi-quantitative agreement with the complex response observed in the experiment, allowing one to discuss the process in unprecedented detail. It is found that the nonexponential response is to a large extent introduced by the photo-linker used to initiate folding. Hence, folding of these cross-linked peptides emulates formation of a helical segment in the context of a globular protein rather than folding of an isolated peptide.

 
  Keywords: Molecular dynamics simulations, Time-resolved infrared spectroscopy, Protein folding, Cross-linked alpha-helix, Misfolded traps, Free energy surface of folding, Kinetic Partitioning, Steric Encumbrance, peptide, Backbone
  Affiliation: Department of Biochemistry, University of Zurich, Switzerland.
 
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