Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations

2011 ◽  
Vol 2 (19) ◽  
pp. 2504-2508 ◽  
Author(s):  
Vincenzo Carnevale ◽  
Werner Treptow ◽  
Michael L. Klein
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Sodium Ion ◽  
Ion Binding ◽  
Ion Binding Sites ◽  
Dynamics Simulations

scholarly journals Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations

2019 ◽  
Vol 20 (15) ◽  
pp. 3780 ◽  
Author(s):  
Ting Yang ◽  
Wenying Zhang ◽  
Jie Cheng ◽  
Yanhong Nie ◽  
Qi Xin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Binding Sites ◽  
Electrostatic Interactions ◽  
Potential Of Mean Force ◽  
Dynamics Simulation ◽  
Cationic Channel ◽  
Dynamics Simulations

Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuroscience research, the molecular mechanism of cation channel formation following retinal photoisomerization in ChR2 is not well understood. In this paper, studies of the closed and opened state ChR2 structures are presented. The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal (ChR2-trans) configuration of ChR2 and its isomerization products, 13-cis-retinal (ChR2-cis) configuration, respectively. Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues (e.g., E90, E82, N258, and R268) around the channel and the extended H-bond network mediated by numerous water molecules, which opens the pore. Steering molecular dynamics (SMD) simulations show that the electrostatic interactions at the binding sites in intracellular gate (ICG) and central gate (CG) can influence the transmembrane transport of Na+ in ChR2-cis obviously. Potential of mean force (PMF) constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+. These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel. This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation.

scholarly journals Hydrophobic Gating and Functional Annotation of Ion Channel Structures by Molecular Dynamics Simulations

2017 ◽  
Vol 112 (3) ◽  
pp. 417a
Author(s):  
Gianni Klesse ◽  
Jemma Trick ◽  
Sivapalan Chelvaniththilan ◽  
Prafulla Aryal ◽  
Jayne Wallace ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Molecular Dynamics Simulations ◽  
Functional Annotation ◽  
Dynamics Simulations ◽  
Channel Structures

scholarly journals Quantum and All-Atom Molecular Dynamics Simulations of Protonation and Divalent Ion Binding to Phosphatidylinositol 4,5-Bisphosphate (PIP2)

2013 ◽  
Vol 104 (2) ◽  
pp. 79a
Author(s):  
David R. Slochower ◽  
Peter J. Huwe ◽  
Ryan Bradley ◽  
Ravi Radhakrishnan ◽  
Paul A. Janmey
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Binding ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations of Kir2.2 and Cholesterol Reveal State- and Concentration-Dependent Binding Sites

2019 ◽  
Vol 116 (3) ◽  
pp. 41a
Author(s):  
Nicolas Barbera ◽  
Manuela A. Ayee ◽  
Belinda S. Akpa ◽  
Irena Levitan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Dynamics Simulations

scholarly journals Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

2020 ◽  
Vol 53 (3) ◽  
pp. 654-661 ◽  
Author(s):  
Antonija Kuzmanic ◽  
Gregory R. Bowman ◽  
Jordi Juarez-Jimenez ◽  
Julien Michel ◽  
Francesco L. Gervasio
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Cryptic Binding Sites ◽  
Dynamics Simulations
Sign in / Sign up

Export Citation Format

Share Document