Assessment of local friction in protein folding dynamics using a helix cross-linker

J Phys Chem B. 2013 Nov 27;117(47):14688-96. doi: 10.1021/jp409334h. Epub 2013 Nov 18.


Internal friction arising from local steric hindrance and/or the excluded volume effect plays an important role in controlling not only the dynamics of protein folding but also conformational transitions occurring within the native state potential well. However, experimental assessment of such local friction is difficult because it does not manifest itself as an independent experimental observable. Herein, we demonstrate, using the miniprotein trp-cage as a testbed, that it is possible to selectively increase the local mass density in a protein and hence the magnitude of local friction, thus making its effect directly measurable via folding kinetic studies. Specifically, we show that when a helix cross-linker, m-xylene, is placed near the most congested region of the trp-cage it leads to a significant decrease in both the folding rate (by a factor of 3.8) and unfolding rate (by a factor of 2.5 at 35 °C) but has little effect on protein stability. Thus, these results, in conjunction with those obtained with another cross-linked trp-cage and two uncross-linked variants, demonstrate the feasibility of using a nonperturbing cross-linker to help quantify the effect of internal friction. In addition, we estimate that a m-xylene cross-linker could lead to an increase in the roughness of the folding energy landscape by as much as 0.4-1.0k(B)T.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Cross-Linking Reagents / chemistry*
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Protein Folding*
  • Protein Stability
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Xylenes / chemistry*


  • Cross-Linking Reagents
  • Proteins
  • Xylenes
  • 3-xylene