The complete folding pathway of a protein from nanoseconds to microseconds

Abstract

Combining experimental and simulation data to describe all of the structures and the pathways involved in folding a protein is problematical. Transition states can be mapped experimentally by φ values1,2, but the denatured state3 is very difficult to analyse under conditions that favour folding. Also computer simulation at atomic resolution is currently limited to about a microsecond or less. Ultrafast-folding proteins fold and unfold on timescales accessible by both approaches4,5, so here we study the folding pathway of the three-helix bundle protein Engrailed homeodomain6. Experimentally, the protein collapses in a microsecond to give an intermediate with much native α-helical secondary structure, which is the major component of the denatured state under conditions that favour folding. A mutant protein shows this state to be compact and contain dynamic, native-like helices with unstructured side chains. In the transition state between this and the native state, the structure of the helices is nearly fully formed and their docking is in progress, approximating to a classical diffusion–collision model. Molecular dynamics simulations give rate constants and structural details highly consistent with experiment, thereby completing the description of folding at atomic resolution.

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Figure 1: Characterization of wild-type En-HD (WT) and the L16A mutant.
Figure 2: Protection factors for the amide groups of wild-type En-HD, calculated from the 1H/2H-exchange experiments at 5 °C.
Figure 3: Representative structures from the molecular dynamics simulations.
Figure 4: Kinetics of folding and unfolding.
Figure 5: The complete folding pathway of En-HD by experiment and simulation.

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Acknowledgements

This work was supported with an ‘Ikertzaileen prestakuntza’ grant (U.M.) from the Government of the Basque Country and with a Winston Churchill Scholarship (N.R.G). The computational studies were supported by the National Institutes of Health (to V.D.).

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Correspondence to Alan R. Fersht.

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Mayor, U., Guydosh, N., Johnson, C. et al. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421, 863–867 (2003). https://doi.org/10.1038/nature01428

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