English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

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

MPS-Authors
/persons/resource/persons15407

Kutzner,  C.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons59321

Köpfer,  D.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons145385

Machtens,  J. P.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons14970

de Groot,  B. L.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons86738

Song,  C.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

/persons/resource/persons16069

Zachariae,  U.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

Fulltext (public)

2249662.pdf
(Publisher version), 4MB

Supplementary Material (public)
There is no public supplementary material available
Citation

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.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0029-B474-1
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.