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Three key residues form a critical contact network in a protein folding transition state

Nature volume 409, pages 641–645 (2001)Cite this article

Abstract

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements—which determine the role of individual residues in stabilizing the transition state1,2—as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase3, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6 Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.

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Figure 1: Native structure of acylphosphatase, AcP.
Figure 2: Comparison of φcalci with φexpi.
Figure 3: Properties of the transition-state ensemble, TSE, of AcP.
Figure 4: Representation of the TSE of AcP calculated with the improved model (see Methods).

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Acknowledgements

We thank F. Chiti and A. Fersht for discussions and comments on this work. We also thank G. Ramponi and N. Taddei for continuing collaborations involving AcP. The Oxford Centre for Molecular Science is supported by BBSRC, EPSRC and MRC. M.V. is supported by an EMBP long-term fellowship. E.P. is supported in Oxford by an EC fellowship. C.M.D. is supported in part by a programme grant from the Wellcome Trust. M.K. Thanks Oxford University for inviting him to spend a year as Eastman Visiting Professor. Much of this work was done while he was in Oxford; the part done at Harvard was supported in part by the National Institutes of Health.

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Authors and Affiliations

  1. Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QT, UK

    Michele Vendruscolo, Emanuele Paci, Christopher M. Dobson & Martin Karplus

  2. Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 4 rue Blaise Pascal, Strasbourg, 67000, France

    Emanuele Paci & Martin Karplus

  3. Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, 02138, Massachusetts, USA

    Martin Karplus

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  1. Michele Vendruscolo
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  4. Martin Karplus
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Correspondence to Christopher M. Dobson or Martin Karplus.

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Vendruscolo, M., Paci, E., Dobson, C. et al. Three key residues form a critical contact network in a protein folding transition state. Nature 409, 641–645 (2001). https://doi.org/10.1038/35054591

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