BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 interactions were studied for the three complexes namely PvPGIP2-FmPG, PvPGIP1-FmPG and GmPGIP3-FmPG. Table 2 shows that whereas this kind of interaction plays a vital role both in PvPGIP2-FmPG and GmPGIP3-FmPG complexes, it is not so for the PvPGIP1-FmPG complex. Electrostatic surface potential of individual PGIPs and the complexes Adaptive Poisson-Boltzmann Solver (APBS) package [29] was used to generate the electrostatic surface potential for each of PvPGIP1, PvPGIP2, GmPGIP3 and FmPG, as shown in Figure 5A, B, C and 5D respectively. It is evidently clear that the electrostatic surface potential for PvPGIP2 and GmPGIP3 (Figure 5B &5C) show similarity along the surface at the concave face which is the site for interaction with FmPG. PvPGIP1 shows a distinctly different potential surface at a region in this face, even though it bears very few variations at the sequence level when compared to PvPGIP2. Figure 6 shows the electrostatic potential surface and the mode of binding for the three complexes namely PvPGIP1-FmPG (Figure 6A), PvPGIP2-FmPG (Figure 6B) and GmPGIP3-FmPG (Figure 6C). The potential surface of the complex in PvPGIP1-FmPG is undoubtedly dissimilar from the other two complexes and so is the mode of binding. Interestingly, the mode of binding of GmPGIP3 with FmPG very much resembles that of PvPGIP2 and FmPG although the sequence variation between the two PGIPs is significant. In silico mutation of PvPGIP2 and PvPGIP2-FmPG complex PvPGIP2 was mutated at six positions, with the amino acid present in PvPGIP1 at that position, using WHAT IF [30]. Electrostatic surface potential was generated for all the six mutated PvPGIP2 molecules. The surface drawn with the Q224K mutation showed considerable change from the wild type protein (Additional file 2). The other single mutations did not show much of a significant Figure 5 Electrostatic surface potential of the individual proteins. A, B, C & D show the electrostatic surface potential on solvent accessible surface around PvPGIP1, PvPGIP2, GmPGIP3 and FmPG respectively at which the surface colors are clamped at red (-5) or blue (+5). The negatively charged region marked in B and C signify the area where they interact with their partner FmPG. The corresponding region in A is distinctly different with less electronegativity in surface electrostatics in comparison to B and C. change in the electrostatic surface potential. It may be mentioned that when these mutated PvPGIP2 molecules were docked to FmPG, none of the complexes showed any resemblance to the conformation found for the PvPGIP1-FmPG complex, shown in Figure 6A. When in the PvPGIP2-FmPG complex, Q (224) of PvPGIP2 was mutated to K, using WHAT IF, the resultant complex showed quite a few of the following deviations from the complex with the wild type protein. Hard sphere contact distances [31] between heavy atoms revealed an existence of steric clash between the Nζ of Q224K of the mutated PvPGIP2 and Cε of K(300) of FmPG. Whereas the contact distance between the atoms Table 2: Ionic interaction in PvPGIP2-FmPG, PvPGIP1-FmPG and GmPGIP3-FmPG complexes: The ionic interaction as obtained from Protein Interaction Calculator, showing the positions of the residue pairs in PvPGIP2-FmPG, PvPGIP1-FmPG and GmPGIP3-FmPG docked complexes Ionic interaction showing the positions of residue pairs in the PvPGIP2-FmPG complex for Ionic interaction showing the positions of residue pairs in the PvPGIP1-FmPG complex for Ionic interaction showing the positions of residue pairs in the GmPGIP3-FmPG complex for PvPGIP2 46 110 203 FmPG 336 146 183 PvPGIP1 46 FmPG 292 GmPGIP3 56 85 131 225 294 FmPG 152 146 183 180 116 Page 8 of 12 (page number not for citation purposes)