Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

2007 ◽  
Vol 157 (3) ◽  
pp. 444-453 ◽  
Author(s):  
M. Dal Peraro ◽  
Katrin Spiegel ◽  
Guillaume Lamoureux ◽  
Marco De Vivo ◽  
William F. DeGrado ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Charge Distribution ◽  
Dynamics Simulations

scholarly journals Phosphorylation of interfacial phosphosite leads to increased binding of Rap-Raf complex

2021 ◽  
Author(s):  
Devanand T ◽  
Susmita Ghosh ◽  
Prasanna Venkatraman ◽  
Satyavani Vemparala
Keyword(s):  
Molecular Dynamics ◽  
Network Analysis ◽  
Molecular Dynamics Simulations ◽  
Charge Distribution ◽  
Electrostatic Interactions ◽  
Salt Bridge ◽  
Complex Stability ◽  
Serine Residue ◽  
Entire Region ◽  
Dynamics Simulations

The effect of phosphorylation of a serine residue in the Rap protein, residing at the complex interface of Rap-Raf complex is studied using atomistic molecular dynamics simulations. As the phosphosite of interest (SER39) is buried at the interface of the Rap-Raf complex, phosphorylation of only Rap protein was simulated and then complexed with the RBD of Raf for further analysis of complex stability. Our simulations reveal that the phosophorylation increases the binding of complex through strong electrostatic interactions and changes the charge distribution of the interface significantly. This is manifested as an increase in stable salt-bridge interactions between the Rap and Raf of the complex. Network analysis clearly shows that the phosphorylation of SER39 reorganizes the community network to include the entire region of Raf chain, including, Raf L4 loop potentially affecting downstream signalling.

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