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.

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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., vol. 23, no. 3, p. 219, Sep. 2013.

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Vol. 23 No. 3 (2013)

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Papers

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Received 12-07-2013
Accepted 28-08-2013
Published 26-09-2013