Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 431, Issue 17, Pages 3353-3365Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jmb.2019.06.003
Keywords
ion channel; channel regulation; hydrophobic gating; functional annotation; de-wetting
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Funding
- BBSRC
- EPSRC
- Wellcome Trust - EPSRC
- BBSRC [BB/N000145/1] Funding Source: UKRI
- EPSRC [EP/L000253/1, EP/R029407/1, EP/M022609/1, EP/R004722/1] Funding Source: UKRI
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The control of ion channel permeation requires the modulation of energetic barriers or gates within their pores. However, such barriers are often simply identified from the physical dimensions of the pore. Such approaches have worked well in the past, but there is now evidence that the unusual behavior of water within narrow hydrophobic pores can produce an energetic barrier to permeation without requiring steric occlusion of the pathway. Many different ion channels have now been shown to exploit hydrophobic gating to regulate ion flow, and it is clear that new tools are required for more accurate functional annotation of the increasing number of ion channel structures becoming available. We have previously shown how molecular dynamics simulations of water can be used as a proxy to predict hydrophobic gates, and we now present a new and highly versatile computational tool, the Channel Annotation Package (CHAP) that implements this methodology. (C) 2019 The Authors. Published by Elsevier Ltd.
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