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Folding zones inside the ribosomal exit tunnel

Nature Structural & Molecular Biology volume 12, pages 11231129 (2005) | Download Citation

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Abstract

Helicity of membrane proteins can be manifested inside the ribosome tunnel, but the determinants of compact structure formation inside the tunnel are largely unexplored. Using an extended nascent peptide as a molecular tape measure of the ribosomal tunnel, we have previously demonstrated helix formation inside the tunnel. Here, we introduce a series of consecutive polyalanines into different regions of the tape measure to monitor the formation of compact structure in the nascent peptide. We find that the formation of compact structure of the polyalanine sequence depends on its location. Calculation of free energies for the equilibria between folded and unfolded nascent peptides in different regions of the tunnel shows that there are zones of secondary structure formation inside the ribosomal exit tunnel. These zones may have an active role in nascent-chain compaction.

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Acknowledgements

We thank S.W. Englander, L. Mayne and R. Horn for helpful discussions and insights. We thank S. White, R. Horn, A. Kosolapov and J. Lear for critical reading of the manuscript. This work was supported by US National Institutes of Health Grant GM 52302.

Author information

Affiliations

  1. Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6085, USA.

    • Jianli Lu
    •  & Carol Deutsch

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Carol Deutsch.

Supplementary information

PDF files

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    Supplementary Fig. 1

    Pegylated Cys64 tape measure is ribosome-attached

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    Supplementary Table 1

    Final extents and rate constants of alanine-containing peptides.

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DOI

https://doi.org/10.1038/nsmb1021

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