scholarly journals Determining the free energy landscape of α-synuclein (35-97) using molecular dynamics

2020 ◽  
Author(s):  
Karnesh Jain ◽  
Othman Ghribi ◽  
Jerome Delhommelle
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape

Free Energy Landscape of a DNA−Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics

Nano Letters ◽  
2009 ◽  
Vol 9 (2) ◽  
pp. 537-541 ◽  
Author(s):  
Robert R. Johnson ◽  
Axel Kohlmeyer ◽  
A. T. Charlie Johnson ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Carbon Nanotube ◽  
Energy Landscape ◽  
Replica Exchange ◽  
Free Energy Landscape ◽  
Replica Exchange Molecular Dynamics

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.

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