Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel

2010 ◽  
pp. 747-755
Author(s):  
Lars Bock ◽  
Helmut Grubmüller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Peptide Chain ◽  
Nascent Peptide ◽  
Exit Tunnel

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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