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A protein sequence that can encode native structure by disfavoring alternate conformations

Nature Structural Biology volume 9, pages 381–388 (2002)Cite this article

Abstract

The linear sequence of amino acids contains all the necessary information for a protein to fold into its unique three-dimensional structure. Native protein sequences are known to accomplish this by promoting the formation of stable, kinetically accessible structures. Here we describe a Pro residue in the center of the third transmembrane helix of the cystic fibrosis transmembrane conductance regulator that promotes folding by a distinct mechanism: disfavoring the formation of a misfolded structure. The generality of this mechanism is supported by genome-wide transmembrane sequence analyses. Furthermore, the results provide an explanation for the increased frequency of Pro residues in transmembrane α-helices. Incorporation by nature of such 'negative folding determinants', aimed at preventing the formation of off-pathway structures, represents an additional mechanism by which folding information is encoded within the evolved sequences of proteins.

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Figure 1: P205S mutant CFTR misfolds and aggregates in vivo.
Figure 2: Structure and integration of wild type and mutant CFTR m3.
Figure 3: Translocon-mediated integration of wild type and mutant CFTR m3.
Figure 4: Characterization of misfolded CFTR-m3.
Figure 5: Contextual importance of proline for integral membrane protein folding.
Figure 6: Mechanism by which Pro residues promote α-helical integral membrane protein folding.
Figure 7: Energetics of CFTR m3 folding and misfolding.

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Acknowledgements

We thank members of the Thomas and Rizo laboratories for valuable discussions, S. Madden and B. Riek for expert technical assistance, B. Rost for prediction of TM α-helices, and L. Gierasch, D. Hilgemann, E. Ross, B. Goldsmith, R. Ranganathan, S. Muallem and S. Sprang for helpful comments. This work was supported by research grants from the Cystic Fibrosis Foundation and the National Institutes of Health-NIDDK to P.J.T. P.H.T is supported by an NIH predoctoral training grant. M.J.C. is the recipient of a CF Foundation fellowship. P.J.T. is an Established Investigator of the American Heart Association.

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Authors and Affiliations

  1. Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, 75390-9040, Texas, USA

    W. Christian Wigley, Michael J. Corboy, Todd D. Cutler, Patrick H. Thibodeau & Philip J. Thomas

  2. Department of Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, 75390-9040, Texas, USA

    Patrick H. Thibodeau

  3. Department of Biological Sciences, Columbia University, New York, 10027, New York, USA

    Jorge Oldan & John F. Hunt

  4. Department of Pharmacology and BK21 Project for Medical Sciences, Yonsei University College of Medicine, 120-752, 134 Sinchon-dong, Seodaemun-gu, Seoul, Korea

    Min Goo Lee

  5. Departments of Biochemistry and Pharmacology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, 75390-9041, Texas, USA

    Josep Rizo

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Wigley, W., Corboy, M., Cutler, T. et al. A protein sequence that can encode native structure by disfavoring alternate conformations. Nat Struct Mol Biol 9, 381–388 (2002). https://doi.org/10.1038/nsb784

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