Computational Studies of GiHsp60 from Arbuscular Mycorrhizal Fungi a putative glomalin related soil protein

Abstract

Glomalin related soil protein produced by mycorrhizal fungus such as Rhizophagus newlineirregularis (GiHsp60) has been termed as a miracle protein for soil sustainability. In newlinethe current study, an attempt has been made to elucidate the evolutionary history, time newlineof divergence followed mutation analysis of Gihsp60 using R. irregularis as a model newlineorganism. Further we propose an integrative in silico approach to explain the mode of newlineinteraction between GiHsp60 and the soil organic matter (SOM). In the first step of the newlinestudy, the evolutionary history and the mutation study was carried out. This was newlinefollowed by the construction of the three-dimensional (3D) structure of GiHsp60 using newlinethe SWISS-MODEL server; while in the final step, the SOM model was optimized newlineusing the Gaussian program, followed by docking-molecular dynamics simulation newlinestudies to investigate the stability and interactions of GiHsp60_SOM complex, using newlineDock and Amber packages respectively. Evolutionary study results presented here newlinebased on computational approach, stands as a testimony for explaining the possibility newlineof increased genetic differentiation experienced by Gihsp60. The quality of the modeled newline3D structure of GiHsp60 was reasonably good based on reports generated by different newlinevalidation servers. The docking results suggested that both Van der Waals and newlineelectrostatic interactions were responsible for the interaction between the protein and newlinethe ligand. Molecular dynamics simulation was used to compute the free energy of newlinebinding of GiHsp60_SOM complex under explicit conditions. The study further newlinerevealed that H-bonding, electrostatic, and Van der Waals forces, followed by newlinehydrophilic and hydrophobic interactions were the forces responsible for the binding of newlineGiHsp60 with SOM. The present investigation is perhaps a benchmark study, which newlineexplains the interaction between GiHsp60 and SOM at the molecular level using newlinecomputational approach. Results from this study can enable agricultural molecular newlinebiologists in their efforts to explore GiHsp60 as a potential soil conditioner, which in newlineturn will lead ways to enhance inputs for sustainable agricultural systems and boost newlineagricultural productivity. newline