scholarly journals 1P128 Molecular dynamics simulation of the 70S ribosome and nascent polypeptide passing through the exit tunnel(Nucleic acid,Poster Presentations)

2007 ◽  
Vol 47 (supplement) ◽  
pp. S55
Author(s):  
Hisashi Ishida ◽  
Kei Yura
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Nucleic Acid ◽  
Dynamics Simulation ◽  
Nascent Polypeptide ◽  
70S Ribosome ◽  
Exit Tunnel ◽  
Poster Presentations

scholarly journals Effects of ribosomal exit tunnel on protein's cotranslational folding

2013 ◽  
Vol 23 (3) ◽  
pp. 219 ◽  
Author(s):  
Bui Phuong Thuy ◽  
Trinh Xuan Hoang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hollow Cylinder ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Tertiary Structures ◽  
Coarse Grained Model ◽  
Cotranslational Folding ◽  
Exit Tunnel

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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