Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li+Usingab InitioQuantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations

2018 ◽  
Vol 14 (12) ◽  
pp. 6443-6459 ◽  
Author(s):  
Niko Prasetyo ◽  
Philippe H. Hünenberger ◽  
Thomas S. Hofer
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
First Principles ◽  
Electrode Potential ◽  
First Principles Calculation ◽  
Hydration Free Energy ◽  
The Absolute ◽  
Dynamics Simulations

Effects of thermodynamic inhibitors on the dissociation of methane hydrate: a molecular dynamics study

2015 ◽  
Vol 17 (48) ◽  
pp. 32347-32357 ◽  
Author(s):  
Takuma Yagasaki ◽  
Masakazu Matsumoto ◽  
Hideki Tanaka
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Methane Hydrate ◽  
Bubble Formation ◽  
Hydration Free Energy ◽  
Hydrate Dissociation ◽  
Dynamics Simulations

Bubble formation and the hydration free energy of methane play important roles in the hydrate dissociation. The effects of methanol and NaCl on them are investigated using molecular dynamics simulations.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

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