Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis

2019 ◽  
Vol 59 (5) ◽  
pp. 2359-2366 ◽  
Author(s):  
Jingwei Weng ◽  
Wenning Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Outer Membrane ◽  
Structural Features ◽  
State Model ◽  
Dynamics Simulation ◽  
Membrane Channel ◽  
Markov State Model ◽  
Markov State ◽  
Outer Membrane Channel

scholarly journals Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaojun Zeng ◽  
Liyun Zhang ◽  
Xiuchan Xiao ◽  
Yuanyuan Jiang ◽  
Yanzhi Guo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State

scholarly journals Molecular dynamics simulation of outer membrane channel protein, maltoporin of E.coli

2003 ◽  
Vol 43 (supplement) ◽  
pp. S49
Author(s):  
K. Seki ◽  
A. Suenaga ◽  
T. Narumi ◽  
M. Taiji ◽  
C. Danelon ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Outer Membrane ◽  
Dynamics Simulation ◽  
Membrane Channel ◽  
Channel Protein ◽  
Outer Membrane Channel

scholarly journals Molecular Dynamics Simulation and Markov State Model Reveal Irregular Metastable Conformation and Allostery In DNAJB-PKAc

2016 ◽  
Vol 110 (3) ◽  
pp. 51a-52a
Author(s):  
Yingjie Wang ◽  
Alessandro Cembran ◽  
Jiali Gao ◽  
Gianluigi Veglia ◽  
Susan S. Taylor ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State

The misfolding mechanism of the key fragment R3 of tau protein: a combined molecular dynamics simulation and Markov state model study

2020 ◽  
Vol 22 (19) ◽  
pp. 10968-10980 ◽  
Author(s):  
Hongli Liu ◽  
Haiyang Zhong ◽  
Zerong Xu ◽  
Qianqian Zhang ◽  
Syed Jawad Ali Shah ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Tau Protein ◽  
Md Simulation ◽  
Structural Characteristics ◽  
Protein A ◽  
State Model ◽  
Dynamics Simulation ◽  
Markov State Model ◽  
Markov State ◽  
Model Study

All-atom molecular dynamics (MD) simulation combined with Markov state model (MSM) were used to uncover the structural characteristics and misfolding mechanism of the key R3 fragment of tau protein at the atomic level.

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