Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study

Biotechnology and Bioengineering
Lydia M Contreras MartínezMatthew P DeLisa

Abstract

Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular ...Continue Reading

References

Mar 1, 1973·Proceedings of the National Academy of Sciences of the United States of America·D B Wetlaufer
Jul 3, 1995·Proceedings of the National Academy of Sciences of the United States of America·W ChenA Helenius
Jan 9, 1996·Biochemistry·C D SfatosE I Shakhnovich
Aug 6, 1996·Proceedings of the National Academy of Sciences of the United States of America·S ChattopadhyayC Dasgupta
Feb 1, 1997·Current Opinion in Structural Biology·A R Fersht
Jan 1, 1996·Folding & Design·E I Shakhnovich
Jan 1, 1996·Folding & Design·V I AbkevichE I Shakhnovich
Apr 18, 1997·The Journal of Biological Chemistry·A A KomarA S Spirin
Jan 1, 1997·Folding & Design·W KudlickiB Hardesty
Oct 23, 1997·Biochemical and Biophysical Research Communications·R J Ellis
Feb 27, 1999·Current Opinion in Structural Biology·B HardestyG Kramer
Feb 27, 1999·Current Opinion in Structural Biology·R J Ellis, F U Hartl
Jun 13, 1994·Physical Review Letters·E I Shakhnovich
Jul 22, 1996·Physical Review Letters·W Sung, P J Park
Mar 27, 1999·Journal of Molecular Biology·M R Betancourt, D Thirumalai
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·A R Fersht
Apr 29, 2000·Cell·B BukauE A Craig
Oct 29, 2000·Progress in Nucleic Acid Research and Molecular Biology·B Hardesty, G Kramer
Apr 3, 2001·Science·M M YusupovH F Noller
Apr 6, 2001·Physical Review Letters·M Muthukumar
May 8, 2001·Annual Review of Biophysics and Biomolecular Structure·L Mirny, E Shakhnovich
May 30, 2001·The International Journal of Biochemistry & Cell Biology·G KramerB Hardesty
Jun 8, 2001·Annual Review of Biochemistry·J Frydman
Sep 19, 2001·Biochemistry·H X Zhou, K A Dill
Mar 9, 2002·Science·F Ulrich Hartl, Manajit Hayer-Hartl
Mar 15, 2002·Cell·Tanel Tenson, Måns Ehrenberg
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·D K KlimovD Thirumalai
Sep 13, 2002·Nature·Günter KramerBernd Bukau
Aug 30, 2003·Proceedings of the National Academy of Sciences of the United States of America·Fumiko TakagiShoji Takada
Dec 20, 2003·Nature·Christopher M Dobson
Apr 8, 2004·Molecular Cell·Robert J C GilbertDavid I Stuart
Aug 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·A I JewettJ-E Shea
Nov 20, 2004·The Journal of Chemical Physics·Serdal KirmizialtinDmitrii E Makarov
Mar 15, 2005·Critical Reviews in Biochemistry and Molecular Biology·Elke Deuerling, Bernd Bukau

❮ Previous
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Citations

Mar 28, 2008·European Biophysics Journal : EBJ·Mohammad M Mohammad, Liviu Movileanu
Jul 16, 2008·The Journal of Chemical Physics·Ernesto E Borrero, Fernando A Escobedo
Nov 6, 2007·The Journal of Chemical Physics·Ernesto E Borrero, Fernando A Escobedo
Mar 26, 2008·The Journal of Chemical Physics·Lei Huang, Dmitrii E Makarov
Nov 10, 2006·The Journal of Chemical Physics·Ernesto E Borrero, Fernando A Escobedo
Apr 19, 2011·The Journal of Chemical Physics·Wenwei ZhengCecilia Clementi
Feb 18, 2012·Current Opinion in Structural Biology·Karissa Y Sanbonmatsu
Nov 11, 2008·Trends in Biochemical Sciences·Anton A Komar
Apr 22, 2011·Biotechnology Journal·Rhodri SaundersCharlotte M Deane
Nov 13, 2007·Biophysical Journal·Lydia M Contreras MartínezMatthew P DeLisa
Nov 23, 2013·Critical Reviews in Biochemistry and Molecular Biology·Kevin C Baldridge, Lydia M Contreras
Jun 15, 2016·Annual Review of Biophysics·Fabio Trovato, Edward P O'Brien
Feb 18, 2020·The Journal of Chemical Physics·Sarwar Hussain, Amir Haji-Akbari
May 28, 2019·Current Opinion in Structural Biology·Karissa Y Sanbonmatsu
Dec 17, 2008·Accounts of Chemical Research·Dmitrii E Makarov
Mar 5, 2020·Journal of the American Chemical Society·Michiel J M NiesenThomas F Miller
Mar 29, 2007·The Journal of Physical Chemistry. B·Carl P GoodrichLiviu Movileanu

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