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Published online before print August 1, 2006
Protein Science, DOI: 10.1110/ps.062297006
 Copyright © 2006 The Protein Society
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Fundamental processes of protein folding: Measuring the energetic balance between helix formation and hydrophobic interactions

Wujing Xian1, Peter J. Connolly2, Marcela Oslin3, Andrew C. Hausrath4 and John J. Osterhout4

1 Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
2 Vertex Pharmaceuticals, Cambridge, Massachusetts 02139, USA
3 The Rowland Institute for Science, Cambridge, Massachusetts 02142, USA
4 Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA

(RECEIVED April 19, 2006; FINAL REVISION April 19, 2006; ACCEPTED May 1, 2006)

Theories of protein folding often consider contributions from three fundamental elements: loops, hydrophobic interactions, and secondary structures. The pathway of protein folding, the rate of folding, and the final folded structure should be predictable if the energetic contributions to folding of these fundamental factors were properly understood. {alpha}t{alpha} is a helix-turn-helix peptide that was developed by de novo design to provide a model system for the study of these important elements of protein folding. Hydrogen exchange experiments were performed on selectively 15N-labeled {alpha}t{alpha} and used to calculate the stability of hydrogen bonds within the peptide. The resulting pattern of hydrogen bond stability was analyzed using a version of Lifson-Roig model that was extended to include a statistical parameter for tertiary interactions. This parameter, x, represents the additional statistical weight conferred upon a helical state by a tertiary contact. The hydrogen exchange data is most closely fit by the XHC model with an x parameter of 9.25. Thus the statistical weight of a hydrophobic tertiary contact is ~5.8x the statistical weight for helix formation by alanine. The value for the x parameter derived from this study should provide a basis for the understanding of the relationship between hydrophobic cluster formation and secondary structure formation during the early stages of protein folding.

Keywords: hydrogen exchange; Lifson-Roig; hydrophobicity; protein folding; peptide model; helix

Reprint requests to: John J. Osterhout, Department of Biochemistry and Molecular Biophysics, BSW 352, P.O. Box 210088, University of Arizona, Tucson, AZ 85721; e-mail: johno{at}email.arizona.edu; fax: (520) 626-9204.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062297006.


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