Three-dimensional rearrangements – in which two different parts of the channel protein change their proximity during conformational changes – are probed by cross-linking or bridging together two cysteine side-chains. Two-dimensional structural rearrangements, such as changes in the accessibility of different parts of the channel protein to the bulk solution on either side of the membrane, are used to define movements within the permeation pathway, such as those that open and close ion channel gates.
Several functional approaches have been used to understand two- and three-dimensional dynamic structures of ion channels, based on the reactivity of the cysteine side-chain.
The molecular underpinnings of these dynamic conformational rearrangements are difficult to ascertain using current structural methods. Ion channels are integral membrane proteins that undergo important conformational changes as they open and close to control transmembrane flux of different ions.
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