Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15486-91. doi: 10.1073/pnas.2136623100. Epub 2003 Dec 11.


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.

Publication types

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

MeSH terms

  • Kinetics
  • Models, Molecular
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Thermodynamics
  • Time Factors
  • Urea


  • Proteins
  • alpha3D protein, synthetic
  • Urea