scholarly journals Predicting Ion Channel Conductance via Dissipation-Corrected Targeted Molecular Dynamics and Langevin Equation Simulations

2021 ◽  
Author(s):  
Miriam Jäger ◽  
Thorsten Koslowski ◽  
Steffen Wolf
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Langevin Equation ◽  
Channel Conductance ◽  
Targeted Molecular Dynamics

Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance

2014 ◽  
Vol 141 (22) ◽  
pp. 22D519 ◽  
Author(s):  
Michael A. Wilson ◽  
Thuy Hien Nguyen ◽  
Andrew Pohorille
Keyword(s):  
Molecular Dynamics ◽  
Ion Channel ◽  
Channel Conductance

Perturbation of Ion Channel Conductance Alters the Hypnotic Response to the α2-Adrenergic Agonist Dexmedetomidine in the Locus Coeruleus of the Rat

1994 ◽  
Vol 81 (6) ◽  
pp. 1527-1534 ◽  
Author(s):  
Carla Nacif-Coelho ◽  
Christiane Correa-Sales ◽  
Louise Lenoir Chang ◽  
Mervyn Maze
Keyword(s):  
Ion Channel ◽  
Locus Coeruleus ◽  
Channel Conductance ◽  
Adrenergic Agonist

scholarly journals Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

2020 ◽  
Vol 55 (S3) ◽  
pp. 14-45
Keyword(s):  
Artificial Intelligence ◽  
Molecular Dynamics ◽  
Ion Channels ◽  
Ion Channel ◽  
Computational Methods ◽  
Homology Modelling ◽  
Channel Structure ◽  
Learning Approaches ◽  
Qsar Analysis ◽  
Wide Range

Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods have evolved into important and invaluable approaches for studying ion channels and their functions. This is mainly due to their demanding mechanism of action where a static picture of an ion channel structure is often insufficient to fully understand the underlying mechanism. Therefore, the use of computational methods is as important as chemical-biological based experimental methods for a better understanding of ion channels. This review provides an overview on a variety of computational methods and software specific to the field of ion-channels. Artificial intelligence (or more precisely machine learning) approaches are applied for the sequence-based prediction of ion channel family, or topology of the transmembrane region. In case sufficient data on ion channel modulators is available, these methods can also be applied for quantitative structureactivity relationship (QSAR) analysis. Molecular dynamics (MD) simulations combined with computational molecular design methods such as docking can be used for analysing the function of ion channels including ion conductance, different conformational states, binding sites and ligand interactions, and the influence of mutations on their function. In the absence of a three-dimensional protein structure, homology modelling can be applied to create a model of your ion channel structure of interest. Besides highlighting a wide range of successful applications, we will also provide a basic introduction to the most important computational methods and discuss best practices to get a rough idea of possible applications and risks.

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 Molecular Dynamics Simulation of Transmembrane Transport of Chloride Ions in Mutants of Channelrhodopsin

Biomolecules ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 852
Author(s):  
Wenying Zhang ◽  
Ting Yang ◽  
Shuangyan Zhou ◽  
Jie Cheng ◽  
Shuai Yuan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ion Channel ◽  
Ion Selectivity ◽  
Potential Of Mean Force ◽  
Chloride Ions ◽  
Dynamics Simulation ◽  
Mutant Proteins ◽  
Transmembrane Channel ◽  
Anion Conduction

Channelrhodopsins (ChRs) are light-gated transmembrane cation channels which are widely used for optogenetic technology. Replacing glutamate located at the central gate of the ion channel with positively charged amino acid residues will reverse ion selectivity and allow anion conduction. The structures and properties of the ion channel, the transport of chloride, and potential of mean force (PMF) of the chimera protein (C1C2) and its mutants, EK-TC, ER-TC and iChloC, were investigated by molecular dynamics simulation. The results show that the five-fold mutation in E122Q-E129R-E140S-D195N-T198C (iChloC) increases the flexibility of the transmembrane channel protein better than the double mutations in EK-TC and ER-TC, and results in an expanded ion channel pore size and decreased steric resistance. The iChloC mutant was also found to have a higher affinity for chloride ions and, based on surface electrostatic potential analysis, provides a favorable electrostatic environment for anion conduction. The PMF free energy curves revealed that high affinity Cl− binding sites are generated near the central gate of the three mutant proteins. The energy barriers for the EK-TC and ER-TC were found to be much higher than that of iChloC. The results suggest that the transmembrane ion channel of iChloC protein is better at facilitating the capture and transport of chloride ions.

scholarly journals Mutation-induced changes of transmembrane pore size revealed by combined ion-channel conductance and single vesicle permeabilization analyses

2018 ◽  
Vol 1860 (5) ◽  
pp. 1015-1021 ◽  
Author(s):  
Eneko Largo ◽  
Douglas P. Gladue ◽  
Johana Torralba ◽  
Vicente M. Aguilella ◽  
Antonio Alcaraz ◽  
...  
Keyword(s):  
Ion Channel ◽  
Pore Size ◽  
Channel Conductance ◽  
Induced Changes ◽  
Single Vesicle

scholarly journals Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance

2011 ◽  
Vol 100 (10) ◽  
pp. 2394-2402 ◽  
Author(s):  
Michael A. Wilson ◽  
Chenyu Wei ◽  
Pär Bjelkmar ◽  
B.A. Wallace ◽  
Andrew Pohorille
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ion Channel ◽  
Dynamics Simulation
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