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Hydrophobic core packing in the SH3 domain folding transition state

Nature Structural Biology volume 9, pages 126–130 (2002)Cite this article

Abstract

How tightly packed is the hydrophobic core of a folding transition state structure? We have addressed this question by characterizing the effects on folding kinetics of >40 substitutions of both large and small amino acids in the hydrophobic core of the Fyn SH3 domain. Our results show that residues at three positions, which we designate as the 'core folding nucleus', are tightly packed in the transition state, and substitutions at these positions cause the largest changes in the folding rate. The other six positions examined appear to be loosely packed; thus, substitutions at these positions with larger hydrophobic residues generally accelerate folding, presumably by increasing the rate of nonspecific hydrophobic collapse. Surprisingly, the folding rate can be greatly accelerated by residues that also significantly destabilize the native state structure. Furthermore, mutants with identical thermodynamic stability can differ by up to 55-fold in their folding rates. These results highlight the importance of hydrophobic core composition, as opposed to only topology, in determining the folding rate of a protein. They also provide a new explanation for the 'abnormal' Φ-values observed in many protein folding kinetics studies.

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Figure 1: Structure of the Fyn SH3 domain (1FYN).
Figure 2: Dependence of the observed folding rates of mutants on the concentration of GuHCl.
Figure 3: Plot of the ΔΔGu of each mutant versus its Tm.
Figure 4: Correlation between the effects of hydrophobic core mutations on folding kinetics and the change in residue side chain volume.

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Acknowledgements

We thank H.S. Chan and K. Maxwell for critical reading of the manuscript. This work was supported by a grant from the Canadian Institutes of Health Research.

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Authors and Affiliations

  1. Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

    Julian G.B. Northey, Ariel A. Di Nardo & Alan R. Davidson

  2. Department of Molecular and Medical Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

    Alan R. Davidson

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  1. Julian G.B. Northey
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  2. Ariel A. Di Nardo
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  3. Alan R. Davidson
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Correspondence to Alan R. Davidson.

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Northey, J., Di Nardo, A. & Davidson, A. Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Mol Biol 9, 126–130 (2002). https://doi.org/10.1038/nsb748

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