How general is the nucleation–condensation mechanism?

Authors

  • Bengt Nölting,

    1. Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158-2517
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  • David A. Agard

    Corresponding author
    1. Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158-2517
    2. The Howard Hughes Medical Institute, University of California, San Francisco, California 94158-2517
    • Howard Hughes Medical Institute, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158-2517
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Abstract

We investigate the structures of the major folding transition states of nine proteins by correlation of published Φ-values with inter-residue contact maps. Combined with previous studies on six proteins, the analysis suggests that at least 10 of the 15 small globular proteins fold via a nucleation–condensation mechanism with a concurrent build-up of secondary and tertiary structure contacts, but a structural consolidation that is clearly nonuniformly distributed over the molecule and most intense in a single structural region suggesting the occurrence of a single folding nucleus. However, on average helix- and sheet-forming residues show somewhat larger Φ-values in the major transition state, suggesting that secondary structure formation is one important driving force in the nucleation–condensation in many proteins and that secondary-structure forming residues tend to be more prominent in folding nuclei. We synthesize the combined information on these 10 of 15 proteins into a unified nucleation–condensation mechanism which also accounts for effects described by the framework, hydrophobic collapse, zipper, and funnel models. Proteins 2008. © 2008 Wiley-Liss, Inc.

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