Molecular dynamics simulation and essential dynamics study of mutated plastocyanin: structural, dynamical and functional effects of a disulfide bridge insertion at the protein surface

2001 ◽  
Vol 92 (3) ◽  
pp. 183-199 ◽  
Author(s):  
Caterina Arcangeli ◽  
Anna Rita Bizzarri ◽  
Salvatore Cannistraro
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Disulfide Bridge ◽  
Dynamics Simulation ◽  
Essential Dynamics ◽  
Protein Surface

Ligand Diffusion on Protein Surface Observed in Molecular Dynamics Simulation

2012 ◽  
Vol 3 (23) ◽  
pp. 3476-3479 ◽  
Author(s):  
Dmitry Nerukh ◽  
Noriaki Okimoto ◽  
Atsushi Suenaga ◽  
Makoto Taiji
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Protein Surface ◽  
Ligand Diffusion

scholarly journals Influence of Disulfide Bridge on the Structural Stability of Human Neuroglobin: A Molecular Dynamics Simulation Using Latest Data Entry

2016 ◽  
Vol 26 (2) ◽  
pp. 151
Author(s):  
Bui Thi Le Quyen ◽  
Nguyen Thi Lam Hoai ◽  
Ngo Van Thanh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Structural Stability ◽  
Data Entry ◽  
Disulfide Bridge ◽  
Dynamics Simulation ◽  
Wild Type ◽  
Heme Group ◽  
Classical Simulation

In this paper, we investigated the role of the disulfide bridge in the structural stability of wild-type human neuroglobin. The classical simulation of the neuroglobin without the disulfide bridge was performed for a long simulation run of 240~ns   using a new parameter set of Gromos96 force field and the latest data entry as the initial topologies. We used the analyzed data of original neuroglobin with the remained disulfide bridge to compare to the ones from this simulation. Our results showed that, the structure of neuroglobin was still very stable although the disulfide bridge was absent. There was only a few residues in B and C helices having a higher mobility. The most interesting result we obtained was that the increasing distance between the distal histidine and heme group could allow oxygen to bind more easily.

scholarly journals Homology Modeling, Molecular Dynamics Simulation and Essential Dynamics on Anopheles gambiae D7r1

2017 ◽  
Vol 5 (3) ◽  
pp. 65-77
Author(s):  
Chayanika Goswami ◽  
Manikandan Jayraman ◽  
Tamizhmathi Bakthavachalam ◽  
Guneswar Sethi ◽  
Ramadas Krishna
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Homology Modeling ◽  
Anopheles Gambiae ◽  
Dynamics Simulation ◽  
Essential Dynamics
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