Electrostatic Potential Calculations of Pentameric Ligand-Gated Ion-Channel Proteins


Principal Investigator

Shoba Ranganathan

Division of Biochemistry and Molecular Biology,


The ligand-gated ion-channel (LGIC) superfamily of neurotransmitter receptors provide a vital link
in the transmission of neural signals. The LGIC receptors are composed of five identical or similar subunits, with an integral membrane channel. Binding of small neurotransmitter molecules such as acetylcholine, nicotine and glycine to the extracellular (EC) part of the receptor causes the membrane channel to open, permitting ions to traverse the membrane. Using a model for the EC region, we have used electrostatic potential (EP) calculations to understand which specific component amino acids of the EC region are involved in receptor assembly and ion selectivity of the channel.


Drew Whitehouse


Jill Gready

Division of Biochemistry and Molecular Biology,





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What are the results to date and the future of the work?

EP calculations were carried out on homopentameric EC models of the human a-1 glycine receptor (GlyR, selective to anions) and the chicken neuronal a-7 acetylcholine receptor (ACh7, selective to cations).

1. Grid spacing in EP calculations: Results from GRASP lead to artefacts due to the variable size of the cubic grid spacing used in the computation. The surface EPs from GRASP are asymmetric for symmetric molecular assemblies. MOLMOL results, using a fixed grid spacing resulted in symmetric surface EPs for identical subunits.

2. Channel polarity and patterns of residue conservation: The polarity of the channel pore is consistent with the ion selectivity of the channel, i.e. the ACh7 channel pore has a negatively charged surface while that of the GlyR pore has a positively charged surface. From the present study, there appears to be no consistent patterns of conservation of charged residues.

3. Intersubunit contact regions and subunit assembly: The subunit interfaces are charged, contrary to the hydrophobhic surfaces expected for protein-protein contact regions. Initial EP studies using GRASP seemed to indicate a potentiation of surface EP upon subunit assembly. However, detailed MOLMOL calculations have shown that such an effect was an artefact.

- Appendix A


Further computation would be required to determine the overall patterns of charge conservation in the anion-selective and cation-selective families of LGIC receptors.

The results for the GlyR pentamer have been used to generate the images and animations depicting subunit assembly and dissection, by Drew Whitehouse (available at http://anusf.anu.edu.au/anusf_visualization/viz_showcase/shoba_ranganathan/)

What computational techniques are used?

The electrostatic potential on the molecular surface is computed using the finite-difference Poisson-Boltzmann (Delphi) methodology as implemented in the two most commonly used computation and graphic visualisation software packages GRASP (A. Nicholls and B. Honig, Science, 268, 1144-1149, 1995 & J. Comput. Chem., 12, 435-445, 1991) and in MOLMOL ((R. Koradi, M. Billeter and K. Wuthrich, J. Mol. Graphics, 14, 51-55, 1996). Computed EP values are mapped onto the molecular surface with a colour scale.


S. Ranganathan, 1997. http://biocomp.anu.edu.au/~sra/asbmb/ep.html

D. Whitehouse, and S. Ranganathan, 1997. http://anusf.anu.edu.au/anusf_visualization/viz_showcase/shoba_ranganathan/



Appendix A -