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Tunnel Vision: Insights from Biochemical and Biophysical Studies

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Book cover Regulatory Nascent Polypeptides

Abstract

The ribosomal exit tunnel is a specialized microenvironment where peptide transit, folding, targeting, cofactor recruitment, and degradation of the nascent peptide occur in accordance with the chemistry of the nascent peptide and the needs of the cell. The physicochemical properties of the tunnel hosting a nascent chain underlie these functions. The dimensions of the tunnel dictate a tight squeeze for peptide, water, and dissolved ions, which has energetic consequences for elongation and folding of the nascent peptide. We consider here tunnel electrostatic potentials, confined water, peptide side chains, and the impact of these factors on tunnel–peptide interactions. We also discuss peptide folding in the tunnel, movement of the peptide along and through the tunnel, and regional discrimination along the tunnel. Whereas detailed processes at the peptidyl-transferase center and ribosome intersubunit motions have been the major focus for the past decade, the relatively unexplored biophysics and chemistry of the tunnel are likely to be the next coming-of-age story. This chapter is intended to help launch this exploration.

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Notes

  1. 1.

    In general, the frequency of action potential firing encodes the intensity of a signal, which can be detected by downstream respondents. Similarly, peptide pausing frequencies, amplitudes (dwell times), and patterns may encode information for anterograde and retrograde signaling along the tunnel.

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Authors and Affiliations

  1. Department of Physiology, University of Pennsylvania, 415 Curie Blvd., Philadelphia, PA, 19104, USA

    Carol Deutsch

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  1. Carol Deutsch
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Correspondence to Carol Deutsch .

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  1. Kyoto Sangyo University, Kita-ku, Kyoto, Japan

    Koreaki Ito

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Deutsch, C. (2014). Tunnel Vision: Insights from Biochemical and Biophysical Studies. In: Ito, K. (eds) Regulatory Nascent Polypeptides. Springer, Tokyo. https://doi.org/10.1007/978-4-431-55052-5_4

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