The folding mechanism and key metastable state identification of the PrP127–147 monomer studied by molecular dynamics simulations and Markov state model analysis

2017 ◽  
Vol 19 (18) ◽  
pp. 11249-11259 ◽  
Author(s):  
Shuangyan Zhou ◽  
Qianqian Wang ◽  
Yuwei Wang ◽  
Xiaojun Yao ◽  
Wei Han ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Structural Dynamics ◽  
Md Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Folding Mechanism ◽  
State Identification ◽  
Dynamics Simulations

MD simulation combined with MSM analysis was employed to investigate the structural dynamics and the folding mechanism of the key fragment 127–147 monomer of prion protein.

The Synergistic Mechanism of Apo-Ferritin Structural Transitions and Au(III) ions Transportation: A Molecular Dynamics Simulations with Markov State Model

2021 ◽  
Author(s):  
Xue Peng ◽  
Chenlin Lu ◽  
Zheng Liu ◽  
Diannan Lu
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Transport Mechanism ◽  
Markov State Model ◽  
Markov State ◽  
Unique Structure ◽  
Synergistic Mechanism ◽  
Nanomaterials Synthesis ◽  
Dynamics Simulations

Due to its unique structure, recent years witness the use of apo-ferritin to accumulate various non-natural metal ions as a scaffold for nanomaterials synthesis. However, the transport mechanism of metal...

scholarly journals Dominant-negative effects in prion diseases: insights from molecular dynamics simulations on mouse prion protein chimeras

2013 ◽  
Vol 31 (8) ◽  
pp. 829-840 ◽  
Author(s):  
Xiaojing Cong ◽  
Salvatore Bongarzone ◽  
Gabriele Giachin ◽  
Giulia Rossetti ◽  
Paolo Carloni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Prion Diseases ◽  
Dominant Negative ◽  
Negative Effects ◽  
Dynamics Simulations

Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

2005 ◽  
Vol 351 (4) ◽  
pp. 731-748 ◽  
Author(s):  
Maryna V. Krasovska ◽  
Jana Sefcikova ◽  
Nad'a Špačková ◽  
Jiří Šponer ◽  
Nils G. Walter
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamics ◽  
Hepatitis Delta Virus ◽  
Hepatitis Delta ◽  
Dynamics Simulations ◽  
Delta Virus

scholarly journals Misfolding Pathways of the Prion Protein Probed by Molecular Dynamics Simulations

2005 ◽  
Vol 88 (2) ◽  
pp. 1334-1343 ◽  
Author(s):  
Alessandro Barducci ◽  
Riccardo Chelli ◽  
Piero Procacci ◽  
Vincenzo Schettino
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Prion Protein ◽  
Dynamics Simulations
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