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J Mol Biol. 2017 Jun 16;429(12):1873-1888. doi: 10.1016/j.jmb.2017.04.019. Epub 2017 May 5.

Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel.

Author information

1
Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA.
2
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA.
3
Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
4
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
5
Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: cjd@mail.med.upenn.edu.

Abstract

All proteins are synthesized by the ribosome, a macromolecular complex that accomplishes the life-sustaining tasks of faithfully decoding mRNA and catalyzing peptide bond formation at the peptidyl transferase center (PTC). The ribosome has evolved an exit tunnel to host the elongating new peptide, protect it from proteolytic digestion, and guide its emergence. It is here that the nascent chain begins to fold. This folding process depends on the rate of translation at the PTC. We report here that besides PTC events, translation kinetics depend on steric constraints on nascent peptide side chains and that confined movements of cramped side chains within and through the tunnel fine-tune elongation rates.

KEYWORDS:

nascent peptide elongation; ribosome; side-chain dependent elongation rates; translation; unnatural amino acid incorporation

PMID:
28483649
PMCID:
PMC5511029
DOI:
10.1016/j.jmb.2017.04.019
[Indexed for MEDLINE]
Free PMC Article

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