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Computer-based redesign of a protein folding pathway

Abstract

A fundamental test of our current understanding of protein folding is to rationally redesign protein folding pathways. We use a computer-based design strategy to switch the folding pathway of protein G, which normally involves formation of the second, but not the first, β-turn at the rate limiting step in folding. Backbone conformations and amino acid sequences that maximize the interaction density in the first β-hairpin were identified, and two variants containing 11 amino acid replacements were found to be 4 kcal mol−1 more stable than wild type protein G. Kinetic studies show that the redesigned proteins fold 100× faster than wild type protein and that the first β-turn is formed and the second disrupted at the rate limiting step in folding.

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Figure 1: Protein G (ref. 10; top) and a model of the design variant NuG2.
Figure 2: CD spectra and stabilities of protein G and design variants.
Figure 3: The redesigned proteins fold faster than wild type protein G.
Figure 4: The folding mechanism of NuG1/D46A is switched.

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Acknowledgements

We thank V. Grantcharova, T. Kortemme, C. Rohl, M. Scalley-Kim and J. Tsai for helpful comments on the manuscript. We would like to thank S. Purvine for help with sequencing NuG2 using the ion-source decay method with a MALDI mass spectrometer. B.K. was supported by the Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation fellowship. S.N. was supported by the Hall-Ammerer-Washington Research Foundation fellowship.

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Correspondence to David Baker.

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Nauli, S., Kuhlman, B. & Baker, D. Computer-based redesign of a protein folding pathway. Nat Struct Mol Biol 8, 602–605 (2001). https://doi.org/10.1038/89638

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