One nanosecond molecular dynamics simulation of the N-terminal domain of the λ repressor protein

Biopolymers ◽  
2000 ◽  
Vol 53 (7) ◽  
pp. 596-605 ◽  
Author(s):  
David C. Kombo ◽  
Matthew A. Young ◽  
David L. Beveridge
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Repressor Protein ◽  
Terminal Domain

scholarly journals Molecular Dynamics simulation of the E.coli FtsZ dimer

2018 ◽  
Author(s):  
Vidyalakshmi C Muthukumar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Simulation Study ◽  
Homology Modelling ◽  
Initial Configuration ◽  
Dynamics Simulation ◽  
Initial Structure ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Intrinsically Disordered Region

AbstractFtsZ dimer was studied to gain insights into FtsZ protofilament formation. In a previous simulation study of the M.janaschii dimer it was found that the monomer-monomer contacts in the GDP bound dimer is lower which results in the high curvature of the GDP bound protofilaments. In this study, we have simulated the E.coli FtsZ dimer. The initial structure was obtained from our previous study in which we had simulated the E.coli FtsZ monomer with its C-terminal IDR (Intrinsically Disordered region) built by homology modelling. The M.janaschii FtsZ dimer subunit contacts were used in the initial configuration. Simulations of the dimer were performed with GTP, GDP and ATP. We observed that the C-terminal domain rotates considerably during dimerization. We also observed the different dynamics of the GTP, GDP and ATP bound dimers due to which assembly into straight protofilaments is favoured only in the presence of GTP.

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