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 the interaction between the protein and the ligand. Molecular dynamics simulation was used to compute the free energy of binding of GiHsp60_SOM complex under explicit conditions. The study further revealed that H-bonding, electrostatic, and Van der Waals forces, followed by hydrophilic and hydrophobic interactions were the forces responsible for the binding of GiHsp60 with SOM. The present investigation is perhaps a benchmark study, which explains the interaction between GiHsp60 and SOM at the molecular level using computational approach. Results from this study can enable agriculture molecular biologists in their efforts to explore GiHsp60 as a potential soil conditioner, which in turn will lead ways to enhance inputs for sustainable agricultural systems and boost agricultural productivity.
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Abbreviations
- GRSP:
-
Glomalin related soil protein
- GiHsp60:
-
Glomalin related soil protein produced by mycorrhizal fungus Rhizophagus irregularis
- SOM:
-
Soil organic matter
- AMF:
-
Arbuscular mycorrhizal fungi
- t-SOM :
-
Gaussian optimized and truncated soil organic matter
- MD:
-
Molecular dynamics
- VdWaals:
-
Van der Waal’s energy
- Py-FIMS:
-
Pyrolysis-field ionization mass spectrometry
- Py-GC/MS:
-
Pyrolysis gas chromatography mass spectrometry
- SPDBV:
-
Swiss-Pdb Viewer
- 3D:
-
Three-dimensional
- RMSF:
-
Root mean square fluctuation
- RMSD:
-
Root mean square deviation
- VMD:
-
Visual Molecular Dynamics
- MM/GBSA:
-
Molecular mechanics / generalized Born surface area
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Fig. S1
Docking of the best pose of the truncated SOM (ligand) onto the 3D model of GiHsp60 (receptor) using rigid docking method as implemented in DOCK software (grid_vdw = − 34.73 kcal mol−1 and grid_es = −3.28 kcal mol−1). While the secondary structure of the receptor is represented as cartoon, the ligand is shown as spheres. Box dimension of x = 38.487 Å; y = 47.249 Å; and z = 41.766 Å (coloured as red) enclosing the docked complex was generated with the box length set to 16 Å in the input file showbox.in. The image was generated using PyMOL package. (PNG 913 kb)
Fig. S2
Lowest energy structure of GiHsp60_t-SOM complex generated at the end of 3021 ps of simulation using AMBER package (energy of −216,120.6504 kcal mol−1). Note the homology modelled protein- ligand complex is surrounded by water molecules. The image was generated using PyMol. (PNG 3174 kb)
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Mothay, D., Ramesh, K.V. Molecular dynamics simulation of homology modeled glomalin related soil protein (Rhizophagus irregularis) complexed with soil organic matter model. Biologia 76, 699–709 (2021). https://doi.org/10.2478/s11756-020-00590-z
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DOI: https://doi.org/10.2478/s11756-020-00590-z