A double bilayer to study the nonequilibrium environmental response of GIRK2 in complex states

Weng, Junben; Wang, Anhui; Zhang, Dinglin; Liao, Chenyi; Li, Guohui

doi:10.1039/d1cp01785c

Cited by 3 publications

(4 citation statements)

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“…We constructed the double-layer systems (Fig. 3 ) with two aqueous compartments in which ion concentration difference was generated by swapping K + and/or Cl − in one compartment with water molecules in the other 51 . The coordinates of a single-layer system were translated along the z-axis and then merged with another single-layer system as a double-layer system with two aqueous compartments using the TCL scripts implemented in VMD 52 and further processed with ParmEd in AMBER18 49 .…”

Section: Methodsmentioning

confidence: 99%

“…The double-layer systems were relaxed in ~100 ns MD simulation under NVT ensemble (298 Kelvin, 1 bar, Langevin dynamics thermostat) to reach equilibrated states, then went through a series of ion-water swapping and MD relaxing processes to study the ion transport in Zn-, Cr-, and Fe- PBI systems. In the ion-water swapping protocol 51 , we exchange the coordinates of K + or Cl − in one aqueous compartment with water molecules in the other compartment. We defined the exchange regions as the water regions 5~10 Å away from the PBI membrane.…”

Section: Methodsmentioning

confidence: 99%

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Metal-coordinated polybenzimidazole membranes with preferential K+ transport

Liao

et al. 2023

Nat Commun

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Membranes with fast and selective ion transport are essential for separations and electrochemical energy conversion and storage devices. Metal-coordinated polymers are promising for fabricating ion-conducting membranes with molecular channels, however, the structures and ion transport channels remain poorly understood. Here, we reported mechanistic insights into the structures of metal-ion coordinated polybenzimidazole membranes and the preferential K+ transport. Molecular dynamics simulations suggested that coordination between metal ions and polybenzimidazole expanded the free volume, forming subnanometre molecular channels. The combined physical confinement in nanosized channels and electrostatic interactions of membranes resulted in a high K+ transference number up to 0.9 even in concentrated salt and alkaline solutions. The zinc-coordinated polybenzimidazole membrane enabled fast transport of charge carriers as well as suppressed water migration in an alkaline zinc-iron flow battery, enabling the battery to operate stably for over 340 hours. This study provided an alternative strategy to regulate the ion transport properties of polymer membranes by tuning polymer chain architectures via metal ion coordination.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Metal-coordinated polybenzimidazole membranes with preferential K+ transport

Liao

et al. 2023

Nat Commun

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“…[24][25][26] Thus, MD simulation and related methods have been widely used to study the structure-function relationship of K + channels. [27][28][29] Furthermore, drug discovery targeting K + channels is always an area of intense research interest since the dysfunction of K + channels is highly related to the occurrence of many diseases. The computer-aided methods, including virtual screening, quantitative structure-activity F I G U R E 1 Phylogenetic tree of potassium (K + ) channels and typical structural feature of each subfamily.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, the enhanced sampling and coarse‐grained molecular dynamics (CG‐MD) methods allow for exploring much wider conformational space and longer simulation scales 24–26 . Thus, MD simulation and related methods have been widely used to study the structure–function relationship of K + channels 27–29 . Furthermore, drug discovery targeting K + channels is always an area of intense research interest since the dysfunction of K + channels is highly related to the occurrence of many diseases.…”

Section: Introductionmentioning

confidence: 99%

Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design

Wang,

Zhang,

Tong

et al. 2024

WIREs Comput Mol Sci

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Potassium (K+) channels play vital roles in various physiological functions, including regulating K+ flow in cell membranes, impacting nervous system signal transduction, neuronal firing, muscle contraction, neurotransmitters, and enzyme secretion. Their activation and switch‐off are directly linked to diseases like arrhythmias, atrial fibrillation, and pain etc. Although the experimental methods play important roles in the studying the structure and function of K+ channels, they are still some limitations to enclose the dynamic molecular processes and the corresponding mechanisms of conformational changes during ion transport, permeation, and gating control. Relatively, computational methods have obvious advantages in studying such problems compared with experimental methods. Recently, more and more three‐dimensional structures of K+ channels have been disclosed based on experimental methods and in silico prediction methods, which provide a good chance to study the molecular mechanism of conformational changes related to the functional regulations of K+ channels. Based on these structural details, molecular dynamics simulations together with related methods such as enhanced sampling and free energy calculations, have been widely used to reveal the conformational dynamics, ion conductance, ion channel gating, and ligand binding mechanisms. Additionally, the accessibility of structures also provides a large space for structure‐based drug design. This review mainly addresses the recent progress of computational methods in the structure, mechanism, and drug design of K+ channels. After summarizing the progress in these fields, we also give our opinion on the future direction in the area of K+ channel research combined with the cutting edge of computational methods.This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Biochemistry and Biophysics Data Science > Chemoinformatics

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Dynamics and functions of membrane proteins

2024

Chemical Theory and Multiscale Simulation in Biomolecules

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A double bilayer to study the nonequilibrium environmental response of GIRK2 in complex states

Abstract: G protein-gated inwardly rectifying potassium (GIRK) channels play essential roles in electrical signaling in neurons and muscle cells. Nonequilibrium environment provide crucial driving forces behind many cellular events. Here, we...

Cited by 3 publications

References 43 publications

Metal-coordinated polybenzimidazole membranes with preferential K+ transport

Metal-coordinated polybenzimidazole membranes with preferential K+ transport

Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design

Dynamics and functions of membrane proteins

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