Molecular dynamics simulation of homology modeled glomalin related soil protein (Rhizophagus irregularis) complexed with soil organic matter model (original) (raw)

2020

Abstract

Glomalin related soil protein produced by mycorrhizal fungus such as Rhizophagus irregularis (GiHsp60) has been termed as a miracle protein for soil sustainability. In this study we propose an integrative in silico approach to explain the mode of interaction between GiHsp60 and the soil organic matter (SOM). In the first step of the study, the three-dimensional (3D) structure of GiHsp60 was constructed using the SWISS-MODEL server; while in the second step, the SOM model was optimized using the Gaussian program, followed by docking-molecular dynamics simulation studies to investigate the stability and interactions of GiHsp60_SOM complex, using Dock and Amber packages respectively. The quality of the modeled 3D structure of GiHsp60 was reasonably good based on reports generated by different validation servers. The docking results suggested that both Van der Waals ( grid_vdw = −34.73 kcal mol −1 ) and electrostatic interactions ( grid_es = −3.28 kcal mol −1 ) were responsible for th...

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