Molecular dynamics study on water and ions transport mechanism in nanometer channel of 13X zeolite

2021 ◽  
Vol 420 ◽  
pp. 129975
Author(s):  
Dongshuai Hou ◽  
Gang Qiao ◽  
Pan Wang
Keyword(s):  
Molecular Dynamics ◽  
Transport Mechanism ◽  
13X Zeolite ◽  
Ions Transport

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>

scholarly journals Proton Transport Mechanism and Pathways in the Superprotonic Phase of M3H(AO4)2 Solid Acids from Ab Initio Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Boris Merinov ◽  
Sergey Morozov
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Dynamics Simulations ◽  
Experimental And Theoretical Studies ◽  
Superprotonic Phase

The proton transport mechanism in superprotonic phases of solid acids is a subject of experimental and theoretical studies for a number of years. Despite this, details of the mechanism still...

Molecular Dynamics Study on Energy Transport Mechanism in Liquid with Nanoparticle Suspension

2019 ◽  
Vol 2019 (0) ◽  
pp. 0024
Author(s):  
Yukihiro Yamamoto ◽  
Kunio Fujiwara ◽  
Yoshitaka Ueki ◽  
Taku Ohara ◽  
Masahiko Shibahara
Keyword(s):  
Molecular Dynamics ◽  
Transport Mechanism ◽  
Energy Transport ◽  
Nanoparticle Suspension

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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