Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin

Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):612-7. doi: 10.1073/pnas.0408646102. Epub 2005 Jan 3.

Abstract

Steady-state and transient conformational changes upon the thermal unfolding of ubiquitin were investigated with nonlinear IR spectroscopy of the amide I vibrations. Equilibrium temperature-dependent 2D IR spectroscopy reveals the unfolding of the beta-sheet of ubiquitin through the loss of cross peaks formed between transitions arising from delocalized vibrations of the beta-sheet. Transient unfolding after a nanosecond temperature jump is monitored with dispersed vibrational echo spectroscopy, a projection of the 2D IR spectrum. Whereas the equilibrium study follows a simple two-state unfolding, the transient experiments observe complex relaxation behavior that differs for various spectral components and spans 6 decades in time. The transient behavior can be separated into fast and slow time scales. From 100 ns to 0.5 ms, the spectral features associated with beta-sheet unfolding relax in a sequential, nonexponential manner, with time constants of 3 micros and 80 micros. By modeling the amide I vibrations of ubiquitin, this observation is explained as unfolding of the less stable strands III-V of the beta-sheet before unfolding of the hairpin that forms part of the hydrophobic core. This downhill unfolding is followed by exponential barrier-crossing kinetics on a 3-ms time scale.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Kinetics
  • Protein Conformation
  • Protein Denaturation*
  • Protein Folding
  • Protein Structure, Secondary
  • Spectroscopy, Fourier Transform Infrared / methods
  • Temperature
  • Time
  • Ubiquitin / chemistry*

Substances

  • Ubiquitin