Computational approach to ensure the stability of the favorable ATP binding site in E. coli Hfq

Bacterial Hfq is a highly conserved thermostable protein of about 10 kDa. The Hfq protein was discovered in 1968 as an E. coli host factor that was essential for replication of the bacteriophage Q. It is now clear that Hfq has many important physiological roles. In E. coli, Hfq mutants show a multiple stress response related phenotypes. Hfq is now known to regulate the translation of two major stress transcription factors RpoS and RpoE in Enterobacteria and mediates its plieotrophic effects through several mechanisms. It interacts with regulatory sRNA and facilitates their antisense interaction with their targets. It also acts independently to modulate mRNA decay and in addition acts as a repressor of mRNA translation. Recent paper from Arluison et al. [9] provided the first evidence indicating that Hfq is an ATP-binding protein. They determined a plausible ATP-binding site in Hfq and tested Hfq’s ATP-binding affinity and stoichiometry. Experimental data suggest that the ATP-binding by the Hfq–RNA complex results in its significant destabilization of the protein and the result also proves important role of Tyr25 that flanks the cleft and stabilizes the adenine portion of ATP, possibly via aromatic stacking. In our study, the ATP molecule was docked into the predicted binding cleft using GOLD docking software. The binding nature of ATP and its effect on Hfq–RNA complex was studied using molecular dynamics simulations. Importance of Tyr25 residue was monitored and revealed using mutational study on the modeled systems. Our data and the corresponding results point to one of Hfq functional structural consequences due to ATP binding and Tyr25Ala mutation.