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Title: Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon

Abstract

During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. This study utilizes a combination of arrest peptide experiments and coarse-grained molecular dynamics to measure and elucidate the molecular origins of forces that are exerted on NCs during cotranslational membrane insertion and translocation via the Sec translocon. The approach enables deconvolution of force contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. In particular, we show that forces due to NC-lipid interactions provide a readout of conformational changes in the Sec translocon, demonstrating that lateral gate opening only occurs when a sufficiently hydrophobic segment of NC residues reaches the translocon. The combination of experiment and theory introduced here provides a detailed picture of the molecular interactions and conformational changes during ribosomal translation that govern protein biogenesis.

Authors:
 [1];  [2];  [2];  [2];  [1]
+ Show Author Affiliations
  1. California Inst. of Technology (CalTech), Pasadena, CA (United States)
  2. Stockholm Univ. (Sweden)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1543513
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Biophysical Journal
Additional Journal Information:
Journal Volume: 115; Journal Issue: 10; Journal ID: ISSN 0006-3495
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biophysics

Citation Formats

Niesen, Michiel J. M., Müller-Lucks, Annika, Hedman, Rickard, von Heijne, Gunnar, and Miller, Thomas F. Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon. United States: N. p., 2018. Web. doi:10.1016/j.bpj.2018.10.002.
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Niesen, Michiel J. M., Müller-Lucks, Annika, Hedman, Rickard, von Heijne, Gunnar, & Miller, Thomas F. Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon. United States. https://doi.org/10.1016/j.bpj.2018.10.002
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Niesen, Michiel J. M., Müller-Lucks, Annika, Hedman, Rickard, von Heijne, Gunnar, and Miller, Thomas F. Wed . "Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon". United States. https://doi.org/10.1016/j.bpj.2018.10.002. https://www.osti.gov/servlets/purl/1543513.
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@article{osti_1543513,
title = {Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon},
author = {Niesen, Michiel J. M. and Müller-Lucks, Annika and Hedman, Rickard and von Heijne, Gunnar and Miller, Thomas F.},
abstractNote = {During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. This study utilizes a combination of arrest peptide experiments and coarse-grained molecular dynamics to measure and elucidate the molecular origins of forces that are exerted on NCs during cotranslational membrane insertion and translocation via the Sec translocon. The approach enables deconvolution of force contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. In particular, we show that forces due to NC-lipid interactions provide a readout of conformational changes in the Sec translocon, demonstrating that lateral gate opening only occurs when a sufficiently hydrophobic segment of NC residues reaches the translocon. The combination of experiment and theory introduced here provides a detailed picture of the molecular interactions and conformational changes during ribosomal translation that govern protein biogenesis.},
doi = {10.1016/j.bpj.2018.10.002},
journal = {Biophysical Journal},
number = 10,
volume = 115,
place = {United States},
year = {Wed Oct 10 00:00:00 EDT 2018},
month = {Wed Oct 10 00:00:00 EDT 2018}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.bpj.2018.10.002
Copyright Statement
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Citation Metrics:
Cited by: 23 works
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Figures / Tables:

Figure 1 Figure 1: Characterization of the physical processes that drive integration of a hydrophobic transmembrane domain. (a) CGMD simulation setup used to calculate pulling forces acting on an engineered hydrophobic H segment (orange) during co-translational integration. Shown is a CGMD snapshot at $L$= 28 ; the C-terminal bead is held fixedmore » and forces exerted by the nascent protein on that bead are calculated. (b) Experimental data reproduced from ref (26). Two peaks in the pulling-force profile are observed during the co-translational integration of the hydrophobic H segment. (c) CGMD data for H segments of varying Leucine content. Vertical dashed lines indicate the position of the corresponding peaks in the experimental results. (d-f) Representative CGMD configurations at $L$= 28 (d), $L$=39 (e), and $L$=57 (f). (g) CGMD pulling-force profiles for an H segment with nine leucine residues with default interactions (orange), non-specific lipid interactions (teal), and nonspecific channel interactions (purple). (h) The maximum value of $f$FL for the peak near $L$= 28 (teal) and the peak near $L$=39 (purple), obtained from CGMD (solid lines) and experiment (26) (dashed lines). Error bars indicate the standard error of the mean. Figure S2 provides an alternate version of this figure for which the simulated curves are scaled to enable easier comparison.« less
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    Works referencing / citing this record:

    Partially inserted nascent chain unzips the lateral gate of the Sec translocon
    journal, August 2019

    Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein
    journal, May 2020

    • Harrington, Haley R.; Zimmer, Matthew H.; Chamness, Laura M.
    • Journal of Biological Chemistry, Vol. 295, Issue 20
    • DOI: 10.1074/jbc.ra120.012706

    Domain topology, stability, and translation speed determine mechanical force generation on the ribosome
    journal, March 2019

    • Leininger, Sarah E.; Trovato, Fabio; Nissley, Daniel A.
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 12
    • DOI: 10.1073/pnas.1813003116

    A snapshot of membrane protein insertion
    journal, September 2019

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