CHAP: A versatile tool for the structural and functional annotation of ion channel pores

Abstract

The regulation of ion channel and transporter function requires the modulation of energetic barriers or 'gates' within their transmembrane pathways. However, despite the ever-increasing number of available structures, our understanding of these barriers is often simply determined from calculating the physical dimensions of the pore. Such approaches (e.g. the HOLE program) have worked very well in the past, but there is now considerable evidence that the unusual behaviour of water within the narrow hydrophobic spaces found within many ion channel pores can also produce energetic barriers to ion conduction without requiring physical occlusion of the permeation pathway. Several different classes of ion channels have now been shown to exploit this principle of 'hydrophobic gating' to regulate ion flow. However, measurement of pore radius alone is unable to identify such barriers and new tools are required for more accurate functional annotation of an exponentially increasing number of ion channel structures. We have previously shown how molecular dynamics simulations of water behaviour can be used as a proxy to accurately predict hydrophobic gates. Here we now present a new and highly versatile computational tool, the Channel Annotation Package (CHAP) that implements this methodology to predict the conductive status of new ion channel structures.

A Heuristic Derived from Analysis of the Ion Channel Structural Proteome Permits the Rapid Identification of Hydrophobic Gates

“…A harmonic restraint with a force constant of 1000 kJ mol -1 nm -2 was placed on the protein backbone atoms during simulations. The Channel Annotation Package (CHAP; www.channotation.org; (28)) was used to analyse trajectory frames, with bandwidths of 0.14 nm and 0.45 nm, respectively, applied for estimating water density and hydrophobicity along each channel axis. SVM classification was conducted using the Caret package (45) in R version 3.4.4 (www.r-project.org).…”

“…1C), and subjected to three replicate 30 ns atomistic MD simulations to determine the behaviour of water within the transbilayer pore. Using our recently described channel annotation software (CHAP) (28), side chains that line the pore during simulations were identified and time-averaged profiles calculated for the pore radius, the local hydrophobicity, and the free energy of water as a function of position along the length of the pore ( Fig. 2 and SI Fig.…”

“…Schematic of a heuristic prediction approach for the permeation state of an ion channel structure based on analysis of hydrophobicity and pore radius profiles, both of which can be derived from a static structure using the CHAP analysis tool (28).…”

“…www.channotation.org) is now available for the analysis of channel pore dimensions, hydrophobicity profiles, and simulations of pore wetting/de-wetting (28). Thus, the ion channel structural proteome can now be subjected to a systematic examination of hydrophobic gating.…”

Automated cryo-EM Structure Refinement using Correlation-Driven Molecular Dynamics

“…We therefore compared the structure of the gating pathway in all of the models analyzed in Figure 10b,c. Specifically, we analyzed the structure and biophysical properties of the CorA gating pathway using the CHAP program (Rao et al, 2017;Klesse, 2019). This analysis yielded a surface representation of the gating pathway as well as its radius at every position along the pathway (Figure 10-figure supplement 2 and Figure 10-figure supplement 3).…”