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Migration of PIP2 on KCNQ2 Surface Revealed by Molecular Dynamics Simulations

Part of the Methods in Molecular Biology book series (MIMB,volume 1684)

Abstract

Lipids and membrane proteins are the main components of cell membranes. Lipid-protein interactions are dynamic because these interactions typically occur on shallow protein surface clefts. Molecular dynamics (MD) simulations provide a tool for studying the dynamics of these interactions. Here, we describe the interactions of phosphatidylinositol-4,5-bisphosphate (PIP2) with both the open and closed states of a KCNQ2 channel. Through these methods, we show that a lipid can migrate between different binding sites in a protein and this migration modulates protein functions.

Key words

  • Potassium channel
  • Lipid
  • Molecular dynamics simulation
  • Migration
  • PIP2
  • Lipid-protein interaction
  • Lipid-binding site

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Acknowledgments

The research was supported in part by Ministry of Science and Technology of the People’s Republic of China (2013CB910604), National Natural Science Foundation of China (21422208), and Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase). We also thank National Supercomputing Center in Tianjin (Tianhe) for computational resources.

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Correspondence to Huaiyu Yang .

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Zhang, Q., Yang, H. (2018). Migration of PIP2 on KCNQ2 Surface Revealed by Molecular Dynamics Simulations. In: Shyng, SL., Valiyaveetil, F., Whorton, M. (eds) Potassium Channels. Methods in Molecular Biology, vol 1684. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7362-0_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7362-0_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7361-3

  • Online ISBN: 978-1-4939-7362-0

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