Effects of ribosomal exit tunnel on protein's cotranslational folding

Bui Phuong Thuy, Trinh Xuan Hoang

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.

Keywords


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

Full Text:

PDF

References


C. B. Anfinsen, Science 181 (1973) 223-230.

A. Matouschek, J. T. Kellis, L. Serrano and A. R. Fersht, Nature 340 (1989) 122-126.

K. A. Dill, H. S. Chan, Nat. Struct. Biol. 4 (1997) 10-19.

J. N. Onuchic, P. G. Wolynes, Curr. Opin. Struct. Biol. 14 (2004) 70-75.

T. X. Hoang, A. Trovato, F. Seno, J. R. Banavar, and A. Maritan, Proc. Natl. Acad. Sci. USA. 101 (2004) 7960-7964.

R. D. Schaeffer, A. Fersht, V. Daggett, Curr. Opin. Struct. Biol. 18 (2008) 4-9.

M. S. Cheung, D. Klimov, and D. Thirmalai, Proc. Natl. Acad. Sci. USA 102 (2005) 4753-4758.

F. Ulrich Hartl, and M. Hayer-Hartl, Nat. Struct. Mol. Biol. 16 (2009) 574-581.

A. A. Komar, Trends Biochem. Sci. 34 (2009) 16-24.

G. Kramer, D. Boehringer, N. Ban, B. Bukau, Nat. Struct. Mol. Biol. 16 (2009) 589-597.

L. D. Cabrita, C. M. Dobson, J. Christodoulou, Curr. Opin. Struct. Biol. 20 (2010) 33-45.

C. M. Kaiser, D. H. Goldman, J. D. Chodera, I. Tinoco Jr., C. Bustamante, Science 334 (2011) 1723.

D. Marenduzzo, T. X. Hoang, F. Seno, M. Vendruscolo and A. Maritan, Phys. Rev. Lett. 95 (2005) 098103.

D. N. Wilson, R. Beckmann, Curr. Opin. Struct. Biol. 21 (2011) 274-282.

N. Ban, P. Nissen, J. Hansen, P. B. Moore, T. A. Steitz, Science 289 (2000) 905-920.

A. Kosolapov, C. Deutsch, Nat. Struct. Mol. Biol. 16 (2009) 405-411.

N. Go and H. Abe, Biopolymers, 20 (1981) 991.

T. X. Hoang and M. Cieplak, J. Chem. Phys., 113 (2000) 8319.

D. Baker, Nature (London), 405 (2002) 39.

C. Clementi, H. Nymeyer, J. N. Onuchic, J. Mol. Biol. 298 (2000) 937-953.

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.

S. Fulle, H. Gohlke, J. Mol. Biol. 387 (2009) 502-517.




DOI: https://doi.org/10.15625/0868-3166/23/3/3119 Display counter: Abstract : 171 views. PDF : 71 views.

Refbacks

  • There are currently no refbacks.




Editorial Office:

Communications in Physics

1st Floor, A16 Building, 18B Hoang Quoc Viet Street, Cau Giay District, Hanoi, Vietnam

Tel: (+84) 024 3791 7102 

Email: cip@vjs.ac.vn

Copyright by