Effects of ribosomal exit tunnel on protein's cotranslational folding

Bui Phuong Thuy, Trinh Xuan Hoang
Author affiliations

Authors

  • Bui Phuong Thuy Nam Dinh University of Technology Education
  • Trinh Xuan Hoang Institute of Physics, Vietnam Academy of Science and Technology

DOI:

https://doi.org/10.15625/0868-3166/23/3/3119

Keywords:

cotranslational folding, nascent proteins, ribosomal exit tunnel, molecular dynamics

Abstract

In vivo, folding of many proteins occurs during their synthesis in the ribosomeand continues after they have escaped from the ribosomal exit tunnel. Inthis research, we investigate the confinement effects of the ribosome on thecotranslational folding of three proteins, of PDB codes 1PGA, 1CRN and 2RJX,by using a coarse-grained model and molecular dynamics simulation. The exittunnel is modeled as a hollow cylinder attached to a flat wall, whereas aGo-like model is adopted for the proteins. Our results show that theexit tunnel has a strong effect on the folding mechanism by setting an order bywhich the secondary and tertiary structures are formed. For protein 1PGA, thefolding follows two different folding routes. The presence of the tunnel alsoimproves the foldability of protein.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

C. B. Anfinsen, Science 181 (1973) 223-230. DOI: https://doi.org/10.1126/science.181.4096.223

A. Matouschek, J. T. Kellis, L. Serrano and A. R. Fersht, Nature 340 (1989) 122-126. DOI: https://doi.org/10.1038/340122a0

K. A. Dill, H. S. Chan, Nat. Struct. Biol. 4 (1997) 10-19. DOI: https://doi.org/10.1038/nsb0197-10

J. N. Onuchic, P. G. Wolynes, Curr. Opin. Struct. Biol. 14 (2004) 70-75. DOI: https://doi.org/10.1016/j.sbi.2004.01.009

T. X. Hoang, A. Trovato, F. Seno, J. R. Banavar, and A. Maritan, Proc. Natl. Acad. Sci. USA. 101 (2004) 7960-7964. DOI: https://doi.org/10.1073/pnas.0402525101

R. D. Schaeffer, A. Fersht, V. Daggett, Curr. Opin. Struct. Biol. 18 (2008) 4-9. DOI: https://doi.org/10.1016/j.sbi.2007.11.007

M. S. Cheung, D. Klimov, and D. Thirmalai, Proc. Natl. Acad. Sci. USA 102 (2005) 4753-4758. DOI: https://doi.org/10.1073/pnas.0409630102

F. Ulrich Hartl, and M. Hayer-Hartl, Nat. Struct. Mol. Biol. 16 (2009) 574-581. DOI: https://doi.org/10.1038/nsmb.1591

A. A. Komar, Trends Biochem. Sci. 34 (2009) 16-24. DOI: https://doi.org/10.1016/j.tibs.2008.10.002

G. Kramer, D. Boehringer, N. Ban, B. Bukau, Nat. Struct. Mol. Biol. 16 (2009) 589-597. DOI: https://doi.org/10.1038/nsmb.1614

L. D. Cabrita, C. M. Dobson, J. Christodoulou, Curr. Opin. Struct. Biol. 20 (2010) 33-45. DOI: https://doi.org/10.1016/j.sbi.2010.01.005

C. M. Kaiser, D. H. Goldman, J. D. Chodera, I. Tinoco Jr., C. Bustamante, Science 334 (2011) 1723. DOI: https://doi.org/10.1126/science.1209740

D. Marenduzzo, T. X. Hoang, F. Seno, M. Vendruscolo and A. Maritan, Phys. Rev. Lett. 95 (2005) 098103. DOI: https://doi.org/10.1103/PhysRevLett.95.098103

D. N. Wilson, R. Beckmann, Curr. Opin. Struct. Biol. 21 (2011) 274-282. DOI: https://doi.org/10.1016/j.sbi.2011.01.007

N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz, Science 289 (2000) 905-920. DOI: https://doi.org/10.1126/science.289.5481.905

A. Kosolapov, C. Deutsch, Nat. Struct. Mol. Biol. 16 (2009) 405-411. DOI: https://doi.org/10.1038/nsmb.1571

N. Go and H. Abe, Biopolymers, 20 (1981) 991. DOI: https://doi.org/10.1002/bip.1981.360200511

T. X. Hoang and M. Cieplak, J. Chem. Phys., 113 (2000) 8319. DOI: https://doi.org/10.1063/1.1314868

D. Baker, Nature (London), 405 (2002) 39. DOI: https://doi.org/10.1038/35011000

C. Clementi, H. Nymeyer, J. N. Onuchic, J. Mol. Biol. 298 (2000) 937-953. DOI: https://doi.org/10.1006/jmbi.2000.3693

R.J. Gilbert, P. Fucini, S. Connell, S. D. Fuller, K. H. Nierhaus,

C. V. Robinson, C. M. Dobson, D. I. Stuart, Mol. Cell 14 (2004) 57-66. DOI: https://doi.org/10.1016/S1097-2765(04)00163-7

S. Fulle, H. Gohlke, J. Mol. Biol. 387 (2009) 502-517. DOI: https://doi.org/10.1016/j.jmb.2009.01.037

Downloads

Published

26-09-2013

How to Cite

[1]
B. P. Thuy and T. X. Hoang, Effects of ribosomal exit tunnel on protein’s cotranslational folding, Comm. Phys. 23 (2013) 219. DOI: https://doi.org/10.15625/0868-3166/23/3/3119.

Issue

Vol. 23 No. 3 (2013)

Section

Papers

License

Authors who publish with CIP agree with the following terms:
  1. The manuscript is not under consideration for publication elsewhere. When a manuscript is accepted for publication, the author agrees to automatic transfer of the copyright to the editorial office.
  2. The manuscript should not be published elsewhere in any language without the consent of the copyright holders. Authors have the right to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal’s published version of their work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
  3. Authors are encouraged to post their work online (e.g., in institutional repositories or on their websites) prior to or during the submission process, as it can lead to productive exchanges or/and greater number of citation to the to-be-published work (See The Effect of Open Access).
Crossref
Scopus
Google Scholar
Europe PMC
Received 12-07-2013
Accepted 28-08-2013
Published 26-09-2013