title: Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin.
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.
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Hoi Sung
authors.initials: HS
authors.lastname: Chung
authors.forename: Munira
authors.initials: M
authors.lastname: Khalil
authors.forename: Adam W
authors.initials: AW
authors.lastname: Smith
authors.forename: Ziad
authors.initials: Z
authors.lastname: Ganim
authors.forename: Andrei
authors.initials: A
authors.lastname: Tokmakoff
mesh_terms: D007700:Kinetics; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods; D013696:Temperature; D013995:Time; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: D025801:Ubiquitin