Molecular dynamics calculations were performed on the 27mer protein tail of mouse apoSAA2.   A right alpha helix was chosen as the initial conformation of the 27mers.  The wildtype and 6 mutant variations, where the basic residues were replaced by alanine, underwent energy minimisation.   Once optimised structures were obtained, these were oriented in co-ordinate space, such that, all conformations could be compared.

The minimised conformations described the extents of a 3D grid.  Evaluation of the electrostatic interaction energy involved stepping a probe atom through this grid in 2A increments.

An sp3 carbon atom, with a negative charge, was used as the probe. The resuling grid of electrostatic energies were contoured using InsightII.   The energies of the contours were colour coded.  

The work was instigated by Robert Kisilevsky and carried out with the amazing help and guidance of Heather Gordon. Thanks also to Marian Zlomislic and Chunghang Gong for support and friendship.