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Title: Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding

Abstract

Protein folding can begin co-translationally. Due to the difference in timescale between folding and synthesis, co-translational folding is thought to occur at equilibrium for fastfolding domains. In this scenario, the folding kinetics of stalled ribosome-bound nascent chains should match the folding of nascent chains in real time. To test if this assumption is true, we compare the folding of a ribosome-bound, multi-domain calcium-binding protein stalled at different points in translation with the nascent chain as is it being synthesized in real-time, via optical tweezers. On stalled ribosomes, a misfolded state forms rapidly (1.5 s). However, during translation, this state is only attained after a long delay (63 s), indicating that, unexpectedly, the growing polypeptide is not equilibrated with its ensemble of accessible conformations. Slow equilibration on the ribosome can delay premature folding until adequate sequence is available and/or allow time for chaperone binding, thus promoting productive folding.

Authors:
 [1];  [1];  [2];  [3]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
  2. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); Johns Hopkins Univ., Baltimore, MD (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1559262
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Alexander, Lisa M., Goldman, Daniel H., Wee, Liang M., and Bustamante, Carlos. Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding. United States: N. p., 2019. Web. doi:10.1038/s41467-019-10647-6.
Alexander, Lisa M., Goldman, Daniel H., Wee, Liang M., & Bustamante, Carlos. Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding. United States. doi:10.1038/s41467-019-10647-6.
Alexander, Lisa M., Goldman, Daniel H., Wee, Liang M., and Bustamante, Carlos. Thu . "Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding". United States. doi:10.1038/s41467-019-10647-6. https://www.osti.gov/servlets/purl/1559262.
@article{osti_1559262,
title = {Non-equilibrium dynamics of a nascent polypeptide during translation suppress its misfolding},
author = {Alexander, Lisa M. and Goldman, Daniel H. and Wee, Liang M. and Bustamante, Carlos},
abstractNote = {Protein folding can begin co-translationally. Due to the difference in timescale between folding and synthesis, co-translational folding is thought to occur at equilibrium for fastfolding domains. In this scenario, the folding kinetics of stalled ribosome-bound nascent chains should match the folding of nascent chains in real time. To test if this assumption is true, we compare the folding of a ribosome-bound, multi-domain calcium-binding protein stalled at different points in translation with the nascent chain as is it being synthesized in real-time, via optical tweezers. On stalled ribosomes, a misfolded state forms rapidly (1.5 s). However, during translation, this state is only attained after a long delay (63 s), indicating that, unexpectedly, the growing polypeptide is not equilibrated with its ensemble of accessible conformations. Slow equilibration on the ribosome can delay premature folding until adequate sequence is available and/or allow time for chaperone binding, thus promoting productive folding.},
doi = {10.1038/s41467-019-10647-6},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {6}
}

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Works referenced in this record:

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    Works referencing / citing this record:

    Small protein domains fold inside the ribosome exit tunnel
    journal, February 2016

    • Marino, Jacopo; von Heijne, Gunnar; Beckmann, Roland
    • FEBS Letters, Vol. 590, Issue 5
    • DOI: 10.1002/1873-3468.12098

    Hidden Markov Analysis of Trajectories in Single-Molecule Experiments and the Effects of Missed Events
    journal, March 2012


    The ribosome destabilizes native and non-native structures in a nascent multidomain protein: EF-G Folding on the Ribosome
    journal, May 2017

    • Liu, Kaixian; Rehfus, Joseph E.; Mattson, Elliot
    • Protein Science, Vol. 26, Issue 7
    • DOI: 10.1002/pro.3189

    Protein folding within the cell is influenced by controlled rates of polypeptide elongation
    journal, November 1992

    • Crombie, Tanya; Swaffield, Jonathan C.; Brown, Alistair J. P.
    • Journal of Molecular Biology, Vol. 228, Issue 1
    • DOI: 10.1016/0022-2836(92)90486-4

    Limitations of Constant-Force-Feedback Experiments
    journal, October 2012

    • Elms, Phillip J.; Chodera, John D.; Bustamante, Carlos J.
    • Biophysical Journal, Vol. 103, Issue 7
    • DOI: 10.1016/j.bpj.2012.06.051

    Cotranslational Protein Folding inside the Ribosome Exit Tunnel
    journal, September 2015


    tRNA concentration fine tunes protein solubility
    journal, July 2012


    The Geometry of the Ribosomal Polypeptide Exit Tunnel
    journal, July 2006


    Quality over quantity: optimizing co-translational protein folding with non-‘optimal’ synonymous codons
    journal, June 2016


    Protein synthesis by pure translation systems
    journal, July 2005


    In vitro assays for the determination of aminoacyl-tRNA synthetase editing activity
    journal, February 2008


    Co-Translational Folding Trajectory of the HemK Helical Domain
    journal, May 2018


    Secondary Structure Formation of a Transmembrane Segment in Kv Channels
    journal, June 2005


    A bacterial calcium-binding protein homologous to calmodulin
    journal, September 1987

    • Swan, David G.; Hale, Richard S.; Dhillon, Namrita
    • Nature, Vol. 329, Issue 6134
    • DOI: 10.1038/329084a0

    Ultrahigh-resolution optical trap with single-fluorophore sensitivity
    journal, February 2011

    • Comstock, Matthew J.; Ha, Taekjip; Chemla, Yann R.
    • Nature Methods, Vol. 8, Issue 4
    • DOI: 10.1038/nmeth.1574

    Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
    journal, February 2009

    • Zhang, Gong; Hubalewska, Magdalena; Ignatova, Zoya
    • Nature Structural & Molecular Biology, Vol. 16, Issue 3
    • DOI: 10.1038/nsmb.1554

    α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel
    journal, February 2010

    • Bhushan, Shashi; Gartmann, Marco; Halic, Mario
    • Nature Structural & Molecular Biology, Vol. 17, Issue 3
    • DOI: 10.1038/nsmb.1756

    NMR solution structure of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea
    journal, June 2003


    The accuracy of codon recognition by polypeptide release factors
    journal, February 2000

    • Freistroffer, D. V.; Kwiatkowski, M.; Buckingham, R. H.
    • Proceedings of the National Academy of Sciences, Vol. 97, Issue 5
    • DOI: 10.1073/pnas.030541097

    Ribosome exit tunnel can entropically stabilize  -helices
    journal, December 2005

    • Ziv, G.; Haran, G.; Thirumalai, D.
    • Proceedings of the National Academy of Sciences, Vol. 102, Issue 52
    • DOI: 10.1073/pnas.0508234102

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    journal, June 2006

    • Moffitt, J. R.; Chemla, Y. R.; Izhaky, D.
    • Proceedings of the National Academy of Sciences, Vol. 103, Issue 24
    • DOI: 10.1073/pnas.0603342103

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    journal, March 2012

    • Yu, H.; Liu, X.; Neupane, K.
    • Proceedings of the National Academy of Sciences, Vol. 109, Issue 14
    • DOI: 10.1073/pnas.1107736109

    The molten globule state is unusually deformable under mechanical force
    journal, February 2012

    • Elms, P. J.; Chodera, J. D.; Bustamante, C.
    • Proceedings of the National Academy of Sciences, Vol. 109, Issue 10
    • DOI: 10.1073/pnas.1115519109

    Calcium-dependent folding of single calmodulin molecules
    journal, July 2012

    • Stigler, J.; Rief, M.
    • Proceedings of the National Academy of Sciences, Vol. 109, Issue 44
    • DOI: 10.1073/pnas.1201801109

    In vivo translation rates can substantially delay the cotranslational folding of the Escherichia coli cytosolic proteome
    journal, December 2012

    • Ciryam, P.; Morimoto, R. I.; Vendruscolo, M.
    • Proceedings of the National Academy of Sciences, Vol. 110, Issue 2
    • DOI: 10.1073/pnas.1213624110

    Direct single-molecule observation of calcium-dependent misfolding in human neuronal calcium sensor-1
    journal, August 2014

    • Heidarsson, P. O.; Naqvi, M. M.; Otazo, M. R.
    • Proceedings of the National Academy of Sciences, Vol. 111, Issue 36
    • DOI: 10.1073/pnas.1401065111

    Quantitative determination of ribosome nascent chain stability
    journal, November 2016

    • Samelson, Avi J.; Jensen, Madeleine K.; Soto, Randy A.
    • Proceedings of the National Academy of Sciences, Vol. 113, Issue 47
    • DOI: 10.1073/pnas.1610272113

    Translation and folding of single proteins in real time
    journal, May 2017

    • Wruck, Florian; Katranidis, Alexandros; Nierhaus, Knud H.
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 22
    • DOI: 10.1073/pnas.1617873114

    Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome
    journal, September 2018

    • Farías-Rico, José Arcadio; Ruud Selin, Frida; Myronidi, Ioanna
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 40
    • DOI: 10.1073/pnas.1812756115

    Ionic effects on the elasticity of single DNA molecules
    journal, June 1997

    • Baumann, C. G.; Smith, S. B.; Bloomfield, V. A.
    • Proceedings of the National Academy of Sciences, Vol. 94, Issue 12
    • DOI: 10.1073/pnas.94.12.6185

    Solid-state synthesis and mechanical unfolding of polymers of T4 lysozyme
    journal, January 2000

    • Yang, G.; Cecconi, C.; Baase, W. A.
    • Proceedings of the National Academy of Sciences, Vol. 97, Issue 1
    • DOI: 10.1073/pnas.97.1.139

    Precision methylome characterization of Mycobacterium tuberculosis complex (MTBC) using PacBio single-molecule real-time (SMRT) technology
    journal, December 2015

    • Zhu, Lingxiang; Zhong, Jun; Jia, Xinmiao
    • Nucleic Acids Research, Vol. 44, Issue 2
    • DOI: 10.1093/nar/gkv1498

    A tutorial on hidden Markov models and selected applications in speech recognition
    journal, January 1989

    • Rabiner, L. R.
    • Proceedings of the IEEE, Vol. 77, Issue 2
    • DOI: 10.1109/5.18626

    Calcium-induced folding of a fragment of calmodulin composed of EF-hands 2 and 3
    journal, June 2007

    • Lakowski, Ted M.; Lee, Gregory M.; Okon, Mark
    • Protein Science, Vol. 16, Issue 6
    • DOI: 10.1110/ps.072777107

    NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea
    journal, January 1999

    • Aitio, Helena; Heikkinen, Sami; Äinen, Ilkka Kilpel
    • Protein Science, Vol. 8, Issue 12
    • DOI: 10.1110/ps.8.12.2580

    Kinetic and structural comparison of a protein’s cotranslational folding and refolding pathways
    journal, May 2018

    • Samelson, Avi J.; Bolin, Eric; Costello, Shawn M.
    • Science Advances, Vol. 4, Issue 5
    • DOI: 10.1126/sciadv.aas9098

    The Complex Folding Network of Single Calmodulin Molecules
    journal, October 2011


    The Ribosome Modulates Nascent Protein Folding
    journal, December 2011


    Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo
    journal, April 2015


    Entropic elasticity of lambda-phage DNA
    journal, September 1994


    Translational tuning optimizes nascent protein folding in cells
    journal, April 2015


    Cotranslational protein folding on the ribosome monitored in real time
    journal, November 2015


    A simple real-time assay for in vitro translation
    journal, December 2014


    On Some Criteria for Estimating the Order of a Markov Chain
    journal, August 1981