BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 specificity for PGs secreted by different pathogens [1]. Recognition specificity results from a few variations in the amino acid sequence of the PGIPs [16]. Plants successfully defend themselves from the attack of a wide range of PGs from pathogenic microorganisms through the role played by protein-protein interaction involving these PGIP proteins. Significant contributions have been made with experi- mental studies on the different isoforms of PGIP from a variety of plants. It has been seen that the overexpression of two PGIP genes, Atpgip1 and Atpgip2 genes from Arabidopsis thaliana limits the colonization by B. cinerea and also reduces the disease symptoms [17]. In transgenic tomato and grapevine plants, a significant increase of PG-inhibitory activity and a decrease in susceptibility to B. cinerea have been observed. Plant resistance have been successfully enhanced by the overexpression of pear PGIP in tomato [18] and Vitis vinifera [19], and also bean PGIP in tobacco [20]. Accumulation of information on several of the proper- ties exhibited by PGIPs have generated an interest in exploiting them as tools for enhancing plant resistance. In this regard, PGIPs of bean plant (Phaseolus vulgaris) needs special mention. Bean PGIPs are encoded by a family of genes [21], the products of which are PvPGIP1, PvPGIP2, PvPGIP3 and PvPGIP4. All of these show distinct regulation and specificity exhibiting different inhibitory capabilities against the PGs of Botrytis cinerea, Colletotrichum gloeos- porioides, Stenocarpella maydis, Fusarium moniliforme and Aspergillus niger [21]. The four mature products of the pgip genes have a very high extent of sequence similarity differing between 8 to 81 amino acids. Phylogenetic analysis indicates that Pvpgip1-Pvpgip2 groups with Gmpgip3 of soybean (Glycine max), a species of the Phaseoleae tribe close to bean, which suggests that these two genes are probably closer to the ancestral gene than are Pvpgip3 and Pvpgip4 [7]. Interestingly, although PGIP1 and PGIP2 from Phaseolus vulgaris share 99% sequence similarity, PvPGIP2 has been reported to inhibit PG from Fusarium moniliforme (Fm) while PvPGIP1 does not [16]. Strikingly, GmPGIP3 of soybean (Glycine max), shares a much lesser similarity of 88% with PvPGIP2 and yet has the ability to inhibit FmPG with an inhibition kinetics similar to that of PvPGIP2 [22]. It is thus evident that the ability of PGIP molecules to defend plants against infection is not buried in the extent of similarity shared between the sequences alone. Probable implications could be the presence of key structural features important for the necessary protein- protein interaction that need to be conserved to preserve the function. It would be interesting to study the molecular interaction of different PGIPs sharing different range of sequence variation, with the same PG molecule to elucidate the relation between the extent of sequence similarity and the corresponding ability/inability to inhibit PG. Three PGIPs, PvPGIP1 and PvPGIP2 from Phaseolus vulgaris and GmPGIP3 from Glycine max have been chosen for this purpose keeping in mind that they share a high level of sequence similarity and yet show distinct difference in their function as expressed through their ability/inability to inhibit the same PG from Fusarium moniliforme (FmPG). In this study, homology models of two PGIP molecules namely PvPGIP1 and GmPGIP3 have been built using the crystal structure of PvPGIP2 as the template. The crystal structure of FmPG being available, the three PGIPs have been subsequently docked to FmPG. In order to elucidate the mechanism underlying and the strategy undertaken by the plants in utilizing the different isoforms of PGIP, a comparative study of the interaction between these three pairs namely PvPGIP1 and FmPG, PvPGIP2 and FmPG and GmPGIP3 and FmPG have been accomplished. A comparison of the binding modes, the interacting residues and the electrostatic potential surface along the interface of the PGIP-PG complex have been investigated. Change in intermole- cular distances, hydrogen bond formation and electro- static surface potential upon in silico mutation of PvPGIP2 have also been explored. Results and discussion Sequence analysis Domain search Domain search using Pfam [23] discloses that the three PGIP molecules (two from P. vulgaris and one from G. max) studied here share identical domain architecture consisting of one LRR_NT2 (a domain found specifically at the N terminal ends of leucine-rich repeat proteins) at the N-terminal end and nine leucine-rich repeats (R1- R9) (Figure 2). Out of the nine LRRs, four have been identified as plant-specific (PS) LRRs (R3-R5, R9) using EMBOSS [24] with the pattern [ILVF]xx[ILVF]xx[ILVF]x [ILVF]xx[NTSC]x[ILVF] [TS]GxIPxx[ILVF]Gx. Pairwise alignment Pairwise alignment carried out in order to identify similarities between the PGIP molecules at the sequence level, shows only eight varying residue positions between PvPGIP1 and PvPGIP2 (shown by the vertical bars in Figure 2A) and 34 varying positions between PvPGIP2 and GmPGIP3 (shown in Figure 2C). Four out of the eight variations between PvPGIP1 and PvPGIP2 fall in the repeat regions and the rest reside in the non- LRR (intervening region between two repeats) region of Page 3 of 12 (page number not for citation purposes)