Calculating the ion solvation energy along the permeation pathway of an ion channel

UPDATE: this functionality is now built into APBSmem, our interface for electrostatics calculations on membrane proteins.


Although this functionality will be built into our APBSmem interface very soon, in this tutorial we will use a script with our draw_membrane Java tool that models the membrane as a low dielectric slab to calculate the ion solvation permeation pathway.

For more details and the theory behind these calculations, please see my paper in PLoS ONE: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012722

Requirements:

• APBS: http://www.poissonboltzmann.org/
• Linux, OS X, or Windows with Cygwin
• Java v1.4.2 or greater

1. Download and extract the following archive to a new directory: http://mem.bio.pitt.edu/sites/default/files/permeation.zip

2. Verify that the tools work for the test case on KcsA by executing this command in a terminal:

./ion_permeation -1.000 1 3

This will move an ion through the pore from -1 to +3 in steps of 1 angstrom.

3. Prepare your protein by converting it to the PQR format. You can use the PDB2PQR server: http://kryptonite.nbcr.net/pdb2pqr/

4. The protein should also be oriented with its principal axis oriented along the z-axis.
This can be done in VMD: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/
PyMOL: http://www.pymolwiki.org/index.php/Orient
or using MODELLER: http://salilab.org/modeller/9v6/manual/node180.html

5. Open the ion_permeation script in a text editor. At the top of the script are a series of parameters that specify the membrane geometry and dielectrics. For more details on what these parameters signify, please see our PLoS ONE paper. Change the line that reads cat K1K2K3_protein.pqr ion.pqr > K1K2K3_protein.pqr.withion.pqr to reflect your own protein pqr file names.

6. Open the permeation.dummy.in and permeation.solv.in input files in a text editor. First make sure the file locations reflect the locations of your pqr files. Now modify the settings to reflect your system. This can be made easier using APBSmem. Details on the parameters are available here: http://www.poissonboltzmann.org/apbs/user-guide/running-apbs/input-files

7. Run the script using the following syntax:

./ion_permeation -1.000 1 3

The arguments are: Starting Z position, Step distance, Stop Z position.
Please note, the number format of the first argument needs to be 6 characters for the pqr columns to line up properly.

8. Results will be saved in results.out.

Please feel free to contact me with any questions or help performing these calculations.