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Journal of Molecular Modeling

, Volume 19, Issue 4, pp 1651–1666 | Cite as

Targeted molecular dynamics (TMD) of the full-length KcsA potassium channel: on the role of the cytoplasmic domain in the opening process

  • Yan Li
  • Florent Barbault
  • Michel Delamar
  • Ruisheng Zhang
  • Rongjing Hu
Original Paper

Abstract

Some recent papers clearly indicate that the cytoplasmic domain of KcsA plays a role in pH sensing. We have performed, for the first time, a targeted molecular dynamics (TMD) simulation of the opening of full-length KcsA at pH 4 and pH 7, with a special interest for the cytoplasmic domain. Association energy calculations show a stabilization at pH 7 confirming that the protonation of some amino-acids at pH 4 in this domain plays a role in the opening process. A careful analysis of the pH dependent charges borne by residues in the cytoplasmic domain and their interactions confirms some literature experimental data and permits to give further insight into the role played by some of them in the opening process.

Keywords

Cytoplasmic domain Full-length KcsA pH sensor Targeted molecular dynamics (TMD) 

Notes

Acknowledgments

The China Scholarship Council is gratefully acknowledged for granting a PhD scholarship to Yan LI.

Supplementary material

894_2012_1726_MOESM1_ESM.doc (419 kb)
ESM 1 (DOC 419 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Yan Li
    • 1
    • 3
  • Florent Barbault
    • 3
  • Michel Delamar
    • 3
  • Ruisheng Zhang
    • 1
    • 2
  • Rongjing Hu
    • 2
  1. 1.Department of ChemistryLanzhou UniversityLanzhouPeople’s Republic of China
  2. 2.School of Information Science and EngineeringLanzhou UniversityLanzhouPeople’s Republic of China
  3. 3.Univ Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR CNRS 7086ParisFrance

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