Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

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.

Original publication

DOI

10.1016/j.jmb.2019.06.003

Type

Journal article

Journal

J Mol Biol

Publication Date

09/08/2019

Volume

431

Pages

3353 - 3365

Keywords

channel regulation, de-wetting, functional annotation, hydrophobic gating, ion channel, Biomimetics, Cell Membrane, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Ion Channel Gating, Ion Channels, Molecular Dynamics Simulation, Protein Conformation, Water