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

Niesen, Michiel J. M.; Müller-Lucks, Annika; Hedman, Rickard; von Heijne, Gunnar; Miller, Thomas F.

doi:10.1016/j.bpj.2018.10.002

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

Journal Article · Wed Oct 10 00:00:00 EDT 2018 · Biophysical Journal

DOI:https://doi.org/10.1016/j.bpj.2018.10.002· OSTI ID:1543513

Niesen, Michiel J. M. ^[1]; Müller-Lucks, Annika ^[2]; Hedman, Rickard ^[2]; von Heijne, Gunnar ^[2]; Miller, Thomas F. ^[1]

California Inst. of Technology (CalTech), Pasadena, CA (United States)
Stockholm Univ. (Sweden)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1543513

Journal Information:: Biophysical Journal, Journal Name: Biophysical Journal Journal Issue: 10 Vol. 115; ISSN 0006-3495

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (48)

Cryo-EM structure of the ribosome–SecYE complex in the membrane environment Frauenfeld, Jens; Gumbart, James; Sluis, Eli O. van der Nature Structural & Molecular Biology, Vol. 18, Issue 5 https://doi.org/10.1038/nsmb.2026	journal	April 2011
Charge-driven dynamics of nascent-chain movement through the SecYEG translocon Ismail, Nurzian; Hedman, Rickard; Lindén, Martin Nature Structural & Molecular Biology, Vol. 22, Issue 2 https://doi.org/10.1038/nsmb.2940	journal	January 2015
The Sec61p Complex Mediates the Integration of a Membrane Protein by Allowing Lipid Partitioning of the Transmembrane Domain Heinrich, Sven U.; Mothes, Walther; Brunner, Josef Cell, Vol. 102, Issue 2 https://doi.org/10.1016/S0092-8674(00)00028-3	journal	July 2000
Decrypting protein insertion through the translocon with free-energy calculations Gumbart, James C.; Chipot, Christophe Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1858, Issue 7 https://doi.org/10.1016/j.bbamem.2016.02.017	journal	July 2016
Divergent stalling sequences sense and control cellular physiology Ito, Koreaki; Chiba, Shinobu; Pogliano, Kit Biochemical and Biophysical Research Communications, Vol. 393, Issue 1 https://doi.org/10.1016/j.bbrc.2010.01.073	journal	February 2010
Structure of the Mammalian Ribosome-Sec61 Complex to 3.4 Å Resolution Voorhees, Rebecca M.; Fernández, Israel S.; Scheres, Sjors H. W. Cell, Vol. 157, Issue 7 https://doi.org/10.1016/j.cell.2014.05.024	journal	June 2014
Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation Zhang, Bin; Miller, Thomas F. Cell Reports, Vol. 2, Issue 4 https://doi.org/10.1016/j.celrep.2012.08.039	journal	October 2012
A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency Marshall, Stephen S.; Niesen, Michiel J. M.; Müller, Axel Cell Reports, Vol. 16, Issue 8 https://doi.org/10.1016/j.celrep.2016.07.042	journal	August 2016
Mechanisms of Integral Membrane Protein Insertion and Folding Cymer, Florian; von Heijne, Gunnar; White, Stephen H. Journal of Molecular Biology, Vol. 427, Issue 5 https://doi.org/10.1016/j.jmb.2014.09.014	journal	March 2015
Transmembrane helices before, during, and after insertion White, S.; Vonheijne, G. Current Opinion in Structural Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.sbi.2005.07.004	journal	August 2005
The Sec61p Complex Mediates the Integration of a Membrane Protein by Allowing Lipid Partitioning of the Transmembrane Domain Heinrich, Sven U.; Mothes, Walther; Brunner, Josef Cell, Vol. 102, Issue 2 https://doi.org/10.1016/s0092-8674(00)00028-3	journal	July 2000
Direct Simulation of Early-Stage Sec-Facilitated Protein Translocation Zhang, Bin; Miller, Thomas F. Journal of the American Chemical Society, Vol. 134, Issue 33 https://doi.org/10.1021/ja3034526	journal	August 2012
On the Nature of the Apparent Free Energy of Inserting Amino Acids into Membrane through the Translocon Rychkova, Anna; Warshel, Arieh The Journal of Physical Chemistry B, Vol. 117, Issue 44 https://doi.org/10.1021/jp406925y	journal	October 2013
X-ray structure of a protein-conducting channel Berg, Bert van den; Clemons, William M.; Collinson, Ian Nature, Vol. 427, Issue 6969 https://doi.org/10.1038/nature02218	journal	December 2003
Recognition of transmembrane helices by the endoplasmic reticulum translocon Hessa, Tara; Kim, Hyun; Bihlmaier, Karl Nature, Vol. 433, Issue 7024 https://doi.org/10.1038/nature03216	journal	January 2005
Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes Rapoport, Tom A. Nature, Vol. 450, Issue 7170 https://doi.org/10.1038/nature06384	journal	November 2007
Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion Gogala, Marko; Becker, Thomas; Beatrix, Birgitta Nature, Vol. 506, Issue 7486 https://doi.org/10.1038/nature12950	journal	February 2014
Lateral opening of the bacterial translocon on ribosome binding and signal peptide insertion Ge, Yan; Draycheva, Albena; Bornemann, Thomas Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6263	journal	October 2014
Dual-topology insertion of a dual-topology membrane protein Woodall, Nicholas B.; Yin, Ying; Bowie, James U. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9099	journal	August 2015
Experimentally determined hydrophobicity scale for proteins at membrane interfaces Wimley, William C.; White, Stephen H. Nature Structural & Molecular Biology, Vol. 3, Issue 10 https://doi.org/10.1038/nsb1096-842	journal	October 1996
A biphasic pulling force acts on transmembrane helices during translocon-mediated membrane integration Ismail, Nurzian; Hedman, Rickard; Schiller, Nina Nature Structural & Molecular Biology, Vol. 19, Issue 10 https://doi.org/10.1038/nsmb.2376	journal	September 2012
Cotranslational folding of spectrin domains via partially structured states Nilsson, Ola B.; Nickson, Adrian A.; Hollins, Jeffrey J. Nature Structural & Molecular Biology, Vol. 24, Issue 3 https://doi.org/10.1038/nsmb.3355	journal	January 2017
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments Dudko, O. K.; Hummer, G.; Szabo, A. Proceedings of the National Academy of Sciences, Vol. 105, Issue 41 https://doi.org/10.1073/pnas.0806085105	journal	October 2008
Hydrophobically stabilized open state for the lateral gate of the Sec translocon Zhang, B.; Miller, T. F. Proceedings of the National Academy of Sciences, Vol. 107, Issue 12 https://doi.org/10.1073/pnas.0914752107	journal	March 2010
Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes Egea, P. F.; Stroud, R. M. Proceedings of the National Academy of Sciences, Vol. 107, Issue 40 https://doi.org/10.1073/pnas.1012556107	journal	September 2010
Cotranslational folding of membrane proteins probed by arrest-peptide–mediated force measurements Cymer, Florian; von Heijne, Gunnar Proceedings of the National Academy of Sciences, Vol. 110, Issue 36 https://doi.org/10.1073/pnas.1306787110	journal	August 2013
Functional asymmetry within the Sec61p translocon Demirci, E.; Junne, T.; Baday, S. Proceedings of the National Academy of Sciences, Vol. 110, Issue 47 https://doi.org/10.1073/pnas.1318432110	journal	November 2013
Improving membrane protein expression by optimizing integration efficiency Niesen, Michiel J. M.; Marshall, Stephen S.; Miller, Thomas F. Journal of Biological Chemistry, Vol. 292, Issue 47 https://doi.org/10.1074/jbc.M117.813469	journal	September 2017
Mutations in the Sec61p Channel Affecting Signal Sequence Recognition and Membrane Protein Topology Junne, Tina; Schwede, Torsten; Goder, Veit Journal of Biological Chemistry, Vol. 282, Issue 45 https://doi.org/10.1074/jbc.M707219200	journal	September 2007
Improving membrane protein expression by optimizing integration efficiency Niesen, Michiel J. M.; Marshall, Stephen S.; Miller, Thomas F. Journal of Biological Chemistry, Vol. 292, Issue 47 https://doi.org/10.1074/jbc.m117.813469	journal	September 2017
Mutations in the Sec61p Channel Affecting Signal Sequence Recognition and Membrane Protein Topology Junne, Tina; Schwede, Torsten; Goder, Veit Journal of Biological Chemistry, Vol. 282, Issue 45 https://doi.org/10.1074/jbc.m707219200	journal	September 2007
A gating motif in the translocation channel sets the hydrophobicity threshold for signal sequence function Trueman, Steven F.; Mandon, Elisabet C.; Gilmore, Reid Journal of Cell Biology, Vol. 199, Issue 6 https://doi.org/10.1083/jcb.201207163	journal	December 2012
Protein translocation mutants defective in the insertion of integral membrane proteins into the endoplasmic reticulum. Stirling, C. J.; Rothblatt, J.; Hosobuchi, M. Molecular Biology of the Cell, Vol. 3, Issue 2 https://doi.org/10.1091/mbc.3.2.129	journal	February 1992
The Hydrophobic Core of the Sec61 Translocon Defines the Hydrophobicity Threshold for Membrane Integration Junne, Tina; Kocik, Lucyna; Spiess, Martin Molecular Biology of the Cell, Vol. 21, Issue 10 https://doi.org/10.1091/mbc.e10-01-0060	journal	May 2010
Molecular mechanism of signal sequence orientation in the endoplasmic reticulum Goder, V. The EMBO Journal, Vol. 22, Issue 14 https://doi.org/10.1093/emboj/cdg361	journal	July 2003
XSEDE: Accelerating Scientific Discovery Towns, John; Cockerill, Timothy; Dahan, Maytal Computing in Science & Engineering, Vol. 16, Issue 5 https://doi.org/10.1109/MCSE.2014.80	journal	September 2014
XSEDE: Accelerating Scientific Discovery Towns, John; Cockerill, Timothy; Dahan, Maytal Computing in Science & Engineering, Vol. 16, Issue 5 https://doi.org/10.1109/mcse.2014.80	journal	September 2014
Mechanical force releases nascent chain-mediated ribosome arrest in vitro and in vivo Goldman, D. H.; Kaiser, C. M.; Milin, A. Science, Vol. 348, Issue 6233 https://doi.org/10.1126/science.1261909	journal	April 2015
Energetics of Membrane Protein Folding Fleming, Karen G. Annual Review of Biophysics, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-biophys-051013-022926	journal	May 2014
Membrane Protein Insertion at the Endoplasmic Reticulum Shao, Sichen; Hegde, Ramanujan S. Annual Review of Cell and Developmental Biology, Vol. 27, Issue 1 https://doi.org/10.1146/annurev-cellbio-092910-154125	journal	November 2011
Protein Translocation Across the Bacterial Cytoplasmic Membrane Driessen, Arnold J. M.; Nouwen, Nico Annual Review of Biochemistry, Vol. 77, Issue 1 https://doi.org/10.1146/annurev.biochem.77.061606.160747	journal	June 2008
Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration Niesen, Michiel J. M.; Wang, Connie Y.; Van Lehn, Reid C. PLOS Computational Biology, Vol. 13, Issue 3 https://doi.org/10.1371/journal.pcbi.1005427	journal	March 2017
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads Wick, Ryan R.; Judd, Louise M.; Gorrie, Claire L. PLOS Computational Biology, Vol. 13, Issue 6 https://doi.org/10.1371/journal.pcbi.1005595	journal	June 2017
Cotranslational folding of spectrin domains via partially structured states. Nilsson, Ob; Nickson, Aa; Hollins, Jj Nature Publishing Group https://doi.org/10.17863/cam.8181	journalarticle	January 2017
The hydrophobic core of the Sec61 translocon defines the hydrophobicity threshold for membrane integration Junne, T.; Kocik, L.; Spiess, M. American Society for Cell Biology https://doi.org/10.5451/unibas-ep19096	text	January 2010
Regulation of multispanning membrane protein topology via post-translational annealing Van Lehn, Reid C.; Zhang, Bin; Miller, Thomas F. eLife, Vol. 4 https://doi.org/10.7554/eLife.08697	journal	September 2015
Mutational scanning reveals the determinants of protein insertion and association energetics in the plasma membrane Elazar, Assaf; Weinstein, Jonathan; Biran, Ido eLife, Vol. 5 https://doi.org/10.7554/eLife.12125	journal	January 2016
Regulation of multispanning membrane protein topology via post-translational annealing Van Lehn, Reid C.; Zhang, Bin; Miller, Thomas F. eLife, Vol. 4 https://doi.org/10.7554/elife.08697	journal	September 2015

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Domain topology, stability, and translation speed determine mechanical force generation on the ribosome Leininger, Sarah E.; Trovato, Fabio; Nissley, Daniel A. Proceedings of the National Academy of Sciences, Vol. 116, Issue 12 https://doi.org/10.1073/pnas.1813003116	journal	March 2019
Cotranslational folding stimulates programmed ribosomal frameshifting in the alphavirus structural polyprotein Harrington, Haley R.; Zimmer, Matthew H.; Chamness, Laura M. Journal of Biological Chemistry, Vol. 295, Issue 20 https://doi.org/10.1074/jbc.ra120.012706	journal	May 2020
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