Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein |
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| Authors: | Zhu Yongjin Alonso Darwin O V Maki Kosuke Huang Cheng-Yen Lahr Steven J Daggett Valerie Roder Heinrich DeGrado William F Gai Feng |
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| Affiliation: | Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. |
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| Abstract: | 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. |
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