Exploring the Viral Channel KcvPBCV-1 Function via Computation

The Journal of Membrane Biology
Alma E V AnderssonLucie Delemotte

Abstract

Viral potassium channels (Kcv) are homologous to the pore module of complex [Formula: see text]-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of [Formula: see text] conduction and channel gating. In this work, we construct a homology model of the [Formula: see text] open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of [Formula: see text] with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 1, 1994·Quarterly Reviews of Biophysics·F J Sigworth
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 13, 2001·Bioinformatics·S MöllerR Apweiler
May 25, 2002·The Journal of Membrane Biology·S GazzarriniA Moroni
Apr 24, 2004·The Journal of Biological Chemistry·Sabrina GazzarriniAnna Moroni
Jul 21, 2004·Journal of Computational Chemistry·Eric F PettersenThomas E Ferrin
Apr 20, 2005·Structure·Simon Bernèche, Benoît Roux
Dec 31, 2005·Nucleic Acids Research·David S WishartJennifer Woolsey
Feb 10, 2006·Nature·Ning ShiYouxing Jiang
Nov 1, 2006·Protein Science : a Publication of the Protein Society·Min-Yi Shen, Andrej Sali
Dec 1, 2007·Nucleic Acids Research·David S WishartMurtaza Hassanali
Mar 21, 2008·Journal of Computational Chemistry·Sunhwan JoWonpil Im
Oct 28, 2008·Journal of the American Chemical Society·Ruhma SyedaHagan Bayley
Jan 27, 2009·Biophysical Journal·Sascha TayefehStefan M Kast
Apr 25, 2009·European Biophysics Journal : EBJ·Brigitte HertelStefan M Kast
Sep 2, 2009·The Journal of General Physiology·Alessandra AbenavoliAnna Moroni
May 26, 2010·The Journal of Physical Chemistry. B·Jeffery B KlaudaRichard W Pastor
Nov 10, 2010·Nucleic Acids Research·Craig KnoxDavid S Wishart
Feb 12, 2011·The Journal of Biological Chemistry·Manuela GebhardtGerhard Thiel
Mar 30, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lucie DelemotteWerner Treptow
Sep 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·David B SauerYouxing Jiang
Mar 28, 2012·The Journal of General Physiology·Qiulin TanLi-Qun Gu
Feb 27, 2013·The Journal of General Physiology·Cristina ArrigoniAnna Moroni
Apr 13, 2013·Biochemistry·Indra SchroederAnna Moroni
Nov 10, 2013·Nucleic Acids Research·Vivian LawDavid S Wishart
Oct 18, 2014·Science·David A KöpferBert L de Groot
May 9, 2015·Science·Cristian CosentinoAnna Moroni
Sep 26, 2015·Biochimica Et Biophysica Acta·F HoffgaardK Hamacher
Oct 22, 2015·Biophysical Journal·Robert T McGibbonVijay S Pande
Jan 1, 2008·Journal of Chemical Theory and Computation·Berk Hess
Apr 22, 2017·Cell·Weiwei Wang, Roderick MacKinnon
May 13, 2017·Journal of the American Chemical Society·Oliver RauhIndra Schroeder

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Citations

Apr 24, 2019·Channels·Denise EckertGerhard Thiel
Jul 1, 2018·The Journal of Membrane Biology·Ana-Nicoleta Bondar, Sandro Keller
Feb 2, 2021·European Biophysics Journal : EBJ·Michael SchmidtKay Hamacher
Jun 25, 2021·Molecular Cell·Andrea SaponaroAnna Moroni

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