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  Insights into the function of ion channels by computational electrophysiology simulations.

Kutzner, C., Köpfer, D., Machtens, J. P., de Groot, B. L., Song, C., & Zachariae, U. (2016). Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et Biophysica Acta - Biomembranes, 1858(7, B), 1741-1752. doi:10.1016/j.bbamem.2016.02.006.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0029-B474-1 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002C-DE38-E
Genre: Journal Article

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 Creators:
Kutzner, C.1, Author              
Köpfer, D.2, Author              
Machtens, J. P.2, Author              
de Groot, B. L.2, Author              
Song, C.2, Author              
Zachariae, U.2, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              
2Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              

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Free keywords: molecular dynamics; GROMACS; electrophysiology; ion channels; conductance; selectivity
 Abstract: Ion channels are of universal importance for all cell types and play key roles in cellular physiology and pathology. Increased insight into their functional mechanisms is crucial to enable drug design on this important class of membrane proteins, and to enhance our understanding of some of the fundamental features of cells. This review presents the concepts behind the recently developed simulation protocol CompEL, which facilitates the atomistic simulation of ion channels in action. In addition, the review provides guidelines for its application in conjunction with the molecular dynamics software package GROMACS. We first lay out the rationale for designing CompEL as a method that models the driving force for ion permeation through channels the way it is established in cells, i.e. by electrochemical ion gradients across the membrane. This is followed by an outline of its implementation and a description of key settings and parameters helpful to users wishing to set up and conduct such simulations. In recent years, key mechanistic and biophysical insights have been obtained by employing the CompEL protocol to address a wide range of questions on ion channels and permeation. We summarize these recent findings on membrane proteins, which span a spectrum from highly ion-selective, narrow channels to wide diffusion pores. Finally we discuss the future potential of CompEL in light of its limitations and strengths. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

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Language(s): eng - English
 Dates: 2016-02-102016-07
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.bbamem.2016.02.006
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Title: Biochimica et Biophysica Acta - Biomembranes
Source Genre: Journal
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Pages: - Volume / Issue: 1858 (7, B) Sequence Number: - Start / End Page: 1741 - 1752 Identifier: -