Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein.
Here, we describe the folding/unfolding kinetics of alpha3D, a small designed three-helix bundle. Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single-exponential process consistent with a minimal folding time of 3.2 +/- 1.2 micros (at approximately 50 degrees C), indicating that a protein can fold on the 1- to 5-micros time scale. Furthermore, the single-exponential nature of the relaxation indicates that the prefactor for transition state (TS)-folding models is probably >or=1 (micros)-1 for a protein of this size and topology. Molecular dynamics simulations and IR spectroscopy provide a molecular rationale for the rapid, single-exponential folding of this protein. alpha3D shows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways.
Zhu
Yongjin
Y
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
Alonso
Darwin O V
DO
Maki
Kosuke
K
Huang
Cheng-Yen
CY
Lahr
Steven J
SJ
Daggett
Valerie
V
Roder
Heinrich
H
DeGrado
William F
WF
Gai
Feng
F
D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics; D013997:Time Factors; D014508:Urea
D011506:Proteins; C119365:alpha3D protein, synthetic; D014508:Urea