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Molecular origins of internal friction effects on protein-folding rates

Author

Listed:
  • David de Sancho

    (University of Cambridge)

  • Anshul Sirur

    (University of Cambridge)

  • Robert B. Best

    (Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health)

Abstract

Recent experiments on protein-folding dynamics have revealed strong evidence for internal friction effects. That is, observed relaxation times are not simply proportional to the solvent viscosity as might be expected if the solvent were the only source of friction. However, a molecular interpretation of this remarkable phenomenon is currently lacking. Here, we use all-atom simulations of peptide and protein folding in explicit solvent, to probe the origin of the unusual viscosity dependence. We find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction. The influence of this landscape roughness can, in turn, be quantitatively explained by a rate theory including memory friction. This insensitivity of local barrier crossing to solvent friction is expected to contribute to the viscosity dependence of folding rates in larger proteins.

Suggested Citation

  • David de Sancho & Anshul Sirur & Robert B. Best, 2014. "Molecular origins of internal friction effects on protein-folding rates," Nature Communications, Nature, vol. 5(1), pages 1-10, September.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5307
    DOI: 10.1038/ncomms5307
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    Cited by:

    1. Kirill Zinovjev & Paul Guénon & Carlos A. Ramos-Guzmán & J. Javier Ruiz-Pernía & Damien Laage & Iñaki Tuñón, 2024. "Activation and friction in enzymatic loop opening and closing dynamics," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Benjamin A. Dalton & Henrik Kiefer & Roland R. Netz, 2024. "The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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