@article{bibcite_234,
  keywords = {Kinetics, Peptides, Protein Folding, Protein Structure, Secondary, Thermodynamics, Amino Acid Sequence, Molecular Sequence Data, Azo Compounds, Cross-Linking Reagents, Molecular Dynamics Simulation},
  author = {B. Paoli and R. Pellarin and A. Caflisch},
  title = {Slow folding of cross-linked alpha-helical peptides due to steric hindrance},
  abstract = {<p>The folding process of a 16-residue \&alpha;-helical peptide with an azobenzene cross-linker (covalently bound to residues Cys3 and Cys14) is investigated by 50 molecular dynamics simulations of 4 \&mu;s each. The folding kinetics at 281 K show a stretched exponential behavior but become simpler and much faster when a distance restraint is used to emulate a nonbulky cross-linker. The free-energy basin of the helical state is divided into two subbasins by a barrier that separates helical conformations with opposite orientations of the Arg10 side chain with respect to the azobenzene cross-linker. In contrast, such barrier is not present in the helical basin of the peptide with the nonbulky cross-linker, which folds with speed similar to the unrestrained peptide. These results indicate that the cross-linker slows down folding because of steric hindrance rather than its restraining effect on the two ends of the helical segment.</p>},
  year = {2010},
  journal = {The Journal of Physical Chemistry B},
  volume = {114},
  pages = {2023-2027},
  month = {2010 Feb 11},
  issn = {1520-5207},
  doi = {10.1021/jp910216j},
  language = {eng},
}