A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein–protein interaction with an all-atom model in explicit solvent

2013 ◽  
Vol 138 (18) ◽  
pp. 184106 ◽  
Author(s):  
Junichi Higo ◽  
Koji Umezawa ◽  
Haruki Nakamura
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Protein Interaction ◽  
Energy Landscape ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Protein Protein Interaction ◽  
Explicit Solvent ◽  
Virtual System

scholarly journals Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation

2007 ◽  
Vol 3 ◽  
pp. 757-766
Author(s):  
Masakazu Sekijima ◽  
Jun Doi ◽  
Shinya Honda ◽  
Tamotsu Noguchi ◽  
Shigenori Shimizu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Parallel Molecular Dynamics ◽  
Analysis System

scholarly journals Free-energy landscape of molecular interactions between endothelin 1 and human endothelin type B receptor: fly-casting mechanism

2019 ◽  
Vol 32 (7) ◽  
pp. 297-308 ◽  
Author(s):  
Junichi Higo ◽  
Kota Kasahara ◽  
Mitsuhito Wada ◽  
Bhaskar Dasgupta ◽  
Narutoshi Kamiya ◽  
...  
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Binding Pocket ◽  
Free Energy Landscape ◽  
Type B ◽  
Endothelin 1 ◽  
Reaction Coordinates ◽  
Explicit Solvent ◽  
Virtual System ◽  
G Protein Coupled

Abstract The free-energy landscape of interaction between a medium-sized peptide, endothelin 1 (ET1), and its receptor, human endothelin type B receptor (hETB), was computed using multidimensional virtual-system coupled molecular dynamics, which controls the system’s motions by introducing multiple reaction coordinates. The hETB embedded in lipid bilayer was immersed in explicit solvent. All molecules were expressed as all-atom models. The resultant free-energy landscape had five ranges with decreasing ET1–hETB distance: completely dissociative, outside-gate, gate, binding pocket, and genuine-bound ranges. In the completely dissociative range, no ET1–hETB interaction appeared. In the outside-gate range, an ET1–hETB attractive interaction was the fly-casting mechanism. In the gate range, the ET1 orientational variety decreased rapidly. In the binding pocket range, ET1 was in a narrow pathway with a steep free-energy slope. In the genuine-bound range, ET1 was in a stable free-energy basin. A G-protein-coupled receptor (GPCR) might capture its ligand from a distant place.

Discovery and identification of Cdc37-derived peptides targeting the Hsp90–Cdc37 protein–protein interaction

RSC Advances ◽  
2015 ◽  
Vol 5 (116) ◽  
pp. 96138-96145 ◽  
Author(s):  
Lei Wang ◽  
Qi-Chao Bao ◽  
Xiao-Li Xu ◽  
Fen Jiang ◽  
Kai Gu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Protein Interaction ◽  
Peptide Inhibitors ◽  
Dynamics Simulation ◽  
Protein Protein Interaction ◽  
Binding Interface ◽  
Combined Strategy ◽  
Key Residues

In order to explore the key residues of the Hsp90–Cdc37 binding interface for further design of peptide inhibitors, a combined strategy of molecular dynamics simulation and MM-PBSA analysis was performed.

scholarly journals Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

RSC Advances ◽  
2017 ◽  
Vol 7 (46) ◽  
pp. 28580-28590 ◽  
Author(s):  
Peng Sang ◽  
Xing Du ◽  
Li-Quan Yang ◽  
Zhao-Hui Meng ◽  
Shu-Qun Liu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Cold Adaptation ◽  
Energy Landscape ◽  
Serine Proteinase ◽  
Dynamics Simulation ◽  
Proteinase K ◽  
Free Energy Landscape ◽  
Molecular Motions ◽  
Underlying Mechanisms

The physicochemical bases for enzyme cold-adaptation remain elusive.

Energetics and structural characterization of the “DFG-flip” conformational transition of B-RAF kinase: a SITS molecular dynamics study

2017 ◽  
Vol 19 (2) ◽  
pp. 1257-1267 ◽  
Author(s):  
Qiang Shao ◽  
Zhijian Xu ◽  
Jinan Wang ◽  
Jiye Shi ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Conformational Transition ◽  
Energy Landscape ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Raf Kinase ◽  
Kinase A

A combination of a homology modeling technique and an enhanced sampling molecular dynamics simulation implemented using the SITS method is employed to compute a detailed map of the free-energy landscape and explore the conformational transition pathway of B-RAF kinase.

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