A one-dimensional free energy surface does not account for two-probe folding kinetics of protein α3 D

Feng Liu, Charles Dumont, Yongjin Zhu, William F. Degrado, Feng Gai, Martin Gruebele

Research output: Contribution to journalArticlepeer-review

Abstract

We present fluorescence-detected measurements of the temperature-jump relaxation kinetics of the designed three-helix bundle protein α3 D taken under solvent conditions identical to previous infrared-detected kinetics. The fluorescence-detected rate is similar to the IR-detected rate only at the lowest temperature where we could measure it (326 K). The fluorescence-detected rate decreases by a factor of 3 over the 326-344 K temperature range, whereas the IR-detected rate remains nearly constant over the same range. To investigate this probe dependence, we tested an extensive set of physically reasonable one-dimensional (1D) free energy surfaces by Langevin dynamics simulation. The simulations included coordinate- and temperature-dependent roughness, diffusion coefficients, and IR/fluorescence spectroscopic signatures. None of these can reproduce the IR and fluorescence data simultaneously, forcing us to the conclusion that a 1D free energy surface cannot accurately describe the folding of α3 D. This supports the hypothesis that α3 D has a multidimensional free energy surface conducive to downhill folding at 326 K, and that it is already an incipient downhill folder with probe-dependent kinetics near its melting point.

Original languageEnglish (US)
Article number061101
JournalJournal of Chemical Physics
Volume130
Issue number6
DOIs
StatePublished - 2009

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

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