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.

scholarly journals Free-energy landscape of a hyperstable RNA tetraloop

2016 ◽  
Vol 113 (24) ◽  
pp. 6665-6670 ◽  
Author(s):  
Jacob C. Miner ◽  
Alan A. Chen ◽  
Angel E. García
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
High Performance ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Left Handed ◽  
Rna Conformation ◽  
Dynamics Simulations ◽  
Secondary Structure Motif

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

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 Characterization of Protein Kinase a Free Energy Landscape by NMR-Restrained Metadynamics

2017 ◽  
Vol 112 (3) ◽  
pp. 50a ◽  
Author(s):  
Yingjie Wang ◽  
Carlo Camilloni ◽  
Jonggul Kim ◽  
Michele Vendruscolo ◽  
Jiali Gao ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Kinase ◽  
Protein Kinase A ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Kinase A

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.

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