BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 Figure 6 Electrostatic surface potential of the three complexes. A, B & C show the electrostatic surface potential on solvent accessible surface around PvPGIP1- FmPG, PvPGIP2-FmPG, GmPGIP3-FmPG docked complexes respectively at which the surface colors are clamped at red (-5) or blue (+5). B and C signify similar mode of binding and electrostatic interaction between the two PGIP molecules and FmPG whereas the mode of interaction between PvPGIP1 and FmPG shown in A is strikingly different from the other two. should be more than 2.52 Å, the distance in the complex with mutation was 2.47 Å. The complex bearing the mutation also showed the absence of the predicted hydrogen bond involving Q(224) of PvPGIP2 as obtained from PIC results. Even the ionic interaction that prevails in the wild type complex of PvPGIP2-FmPG vanishes with this single mutation. The in silico mutation study, confirms the importance of the Q(224) residue which has been experimentally found to give rise to a 70% reduction in the inhibition ability of the protein upon single mutation. The study also suggests probable reasons like a different electrostatic potential surface, steric clash or lack of hydrogen bonds that might explain why PvPGIP1 with only eight residues has a different mode of binding to FmPG. The above in silico study clearly portrays how a single mutation in PvPGIP2 results in disallowed hard sphere contact distances between the two protein molecules thus indicating the importance of van der Waals interaction in plant defense. Q at the 224th position which is also involved in forming hydrogen bonds, plays a substantial role in this interaction. Since GRAMM-X shows that the mode of binding of PvPGIP1 with FmPG is different from PvPGIP2 and GmPGIP3 and further more since GRAMM-X has a major involvement of smoothed Lennard-Jones potential in scoring, we infer that the discrimination in recognition has a significant contribution from van der Waals interaction. Role of van der Waals forces have already been shown to be important in offering stability to several protein-ligand and in some cases DNA-ligand complexes prevailing in biological systems. Molecular Dynamics studies have shown van der Waals interaction to play a vital role in groove binding of the repressor fragment of a bacter- iophage to its operator oligonucleotide [32]. In a study with proteins, it has been shown that the mouse major urinary protein (MUP) and its ligand show a binding thermodynamics that is dominated by dispersion inter- actions [33]. The involvement of the van der Waals forces in plant defense although not in specific recognition has also been reported. Many plants respond to pathogenic attack by producing defense proteins that bind to chitin, a polysaccharide present in the cell wall of the invading fungus or exoskeleton of infecting insects. NMR studies show the involvement of van der Waals interactions between the methyl acetamide group of the GlcNAc unit and a hydrophobic patch of the plant protein [34]. Studies on the characteristics of the sugar-binding sites in plant and animal lectin show van der Waals interaction and hydrogen bonds to contribute significantly. Selec- tivity for different sugars result from hydrogen bonds and unwanted recognition is prevented by steric exclu- sion [35]. Here in the case of plant defense through PGIP, the influence of van der Waals interaction there- fore does not seem to be atypical. In the present study, we have failed to address pertinent components like the change in the binding free energy Page 9 of 12 (page number not for citation purposes)