Z-docking reported 3600 docked poses for all of the inputted protein pairs. The interface cut-off distance was set at 6 with a surface area probe radius of 0.6. The maximum hydrogen bond distance, weak hydrogen bond distance and salt bridge distance parameters were set at 3.4, 3.8 and 4.0 respectively.
The docked proteins were analysed for their interactions and the resulting interactions are reported in Tables 2i and 2ii. The docked poses of the various protein complexes are given in Fig. 2i.
Table 2
i: Interaction of Hyaluronidase with the H.pylori proteins.
| Cag A | Cag L | GGT | Cag D | Urease |
H- Bond interactions | 36 | 7 | 7 | 17 | 12 |
Pi interactions | 10 | 3 | 3 | 3 | 2 |
Salt bridge interactions | 5 | | | | 2 |
Table 2
ii: Interaction of PV toxin-a with the H.pylori proteins.
| Cag A | Cag L | GGT | Cag D | Urease |
H- Bond interactions | 16 | 29 | 7 | 8 | 57 |
Pi interactions | 4 | | 1 | 5 | 8 |
Salt bridge interactions | | 1 | | | 6 |
Protein-protein interaction depends upon the formation of a bond between the proteins. The binding of proteins involves the formation of weak non-covalent bonds, hydrogen bonds, ionic bonds, Vander Waal’s and hydrophobic interactions. One protein can bind with another protein by the specific affinity of one rigid surface with that of another (19). There is a change in the structure of proteins when they bind with each other, and these changes play an important role in altering the cell regulatory process. The results of this study show that the interaction of the H. pylori proteins is more with the venom protein Hyaluronidase than that of the PV Toxin-a of P. volitans.
When few bonds form between proteins, they dissociate rapidly but when there is an increase in the number of bonds the interactions are stronger (20). It has been observed in this study that Cag A protein has a stronger interaction with the venom protein Hyaluronidase with 51 bonds (Fig. 2i). The 266th Lysine in the B chain of the Cag A protein forms an H-bond interaction at a distance of 1.6 Å with the 273rd Methionine in the A chain of the venom protein Hyaluronidase. The 953rd Histamine in the E chain of the Cag A protein forms a Pi interaction at a distance of 3.6 Å with the 214th Proline in the A chain of the venom protein Hyaluronidase. The 955th Lysine in the B chain of the Cag A protein forms a salt bridge interaction at a distance of 1.78 Å with the 193rd Aspartic acid in the A chain of the venom protein Hyaluronidase. Similarly, 35 other H-bond interactions, 9 other Pi interactions and 4 other salt bridge interactions have been observed within a maximum distance of 2.9 Å, 5.4 Å and 2.6 Å respectively.
Likewise, the urease protein has a stronger interaction with the venom protein PV toxin-a with 71 bonds (Fig. 2ii). It has been observed that the 22nd Arginine in the B chain of the Urease protein forms an H-bond at a distance of 1.7 Å with the 110th glutamic acid in the A chain of venom protein PV-Toxin a. The 60th asparagine in the B chain of the urease protein forms a Pi interaction at a distance of 2.3 Å with the 196th phenylalanine in the B chain of the venom protein PV toxin-a. The 1st methionine in B chain of the Urease protein forms a salt bridge interaction at a distance of 1.8 Å with the 167th aspartic acid in A chain of the venom protein PV-toxin a. Similarly, 56 other H-bond interactions, 7 other Pi interactions and 5 more salt bridge interactions are observed within a maximum distance of 2.8 Å, 5.2 Å and 2.7 Å respectively.