Quantitative determination of ribosome nascent chain stability.
Accurate protein folding is essential for proper cellular and organismal function. In the cell, protein folding is carefully regulated; changes in folding homeostasis (proteostasis) can disrupt many cellular processes and have been implicated in various neurodegenerative diseases and other pathologies. For many proteins, the initial folding process begins during translation while the protein is still tethered to the ribosome; however, most biophysical studies of a protein's energy landscape are carried out in isolation under idealized, dilute conditions and may not accurately report on the energy landscape in vivo. Thus, the energy landscape of ribosome nascent chains and the effect of the tethered ribosome on nascent chain folding remain unclear. Here we have developed a general assay for quantitatively measuring the folding stability of ribosome nascent chains, and find that the ribosome exerts a destabilizing effect on the polypeptide chain. This destabilization decreases as a function of the distance away from the peptidyl transferase center. Thus, the ribosome may add an additional layer of robustness to the protein-folding process by avoiding the formation of stable partially folded states before the protein has completely emerged from the ribosome.
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.|California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.
Avi J
AJ
Samelson
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.|California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.
Madeleine K
MK
Jensen
California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.
Randy A
RA
Soto
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.|California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.|Department of Chemistry, University of California, Berkeley, CA 94720.
Jamie H D
JH
Cate
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; marqusee@berkeley.edu.|California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.
Susan
S
Marqusee
D004926:Escherichia coli / Q000378:metabolism; D008727:Methotrexate / Q000494:pharmacology; D010447:Peptide Hydrolases / Q000378:metabolism; D014176:Protein Biosynthesis / Q000187:drug effects; D017510:Protein Folding / Q000187:drug effects; D055550:Protein Stability / Q000187:drug effects; D059748:Proteolysis / Q000187:drug effects; D011994:Recombinant Proteins / Q000378:metabolism; D012270:Ribosomes / Q000187:drug effects / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D014508:Urea / Q000494:pharmacology
D011994:Recombinant Proteins; D014508:Urea; D010447:Peptide Hydrolases; D008727:Methotrexate
cotranslational folding; protein folding; protein stability; pulse proteolysis