Molecular dynamics simulation of homology modeled glomalin related soil protein ( Rhizophagus irregularis ) complexed wi
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ORIGINAL ARTICLE
Molecular dynamics simulation of homology modeled glomalin related soil protein (Rhizophagus irregularis) complexed with soil organic matter model Dipti Mothay 1
&
Kureeckal Vasudev Ramesh 1
Received: 4 June 2020 / Accepted: 30 August 2020 # Institute of Molecular Biology, Slovak Academy of Sciences 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 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. Keywords Heat shock protein 60 . Protein modelling . PyRED server . DOCK6 . Molecular dynamics simulation . Binding free energy
Abbreviations GRSP Glomalin related soil protein GiHsp60 Glomalin related soil protein produced by mycorrhizal fungus Rhizophagus irregularis Electronic supplementary material The online version of this article (https://doi.org/10.2478/s11756-020-00590-z) contains supplementary material, which is available to authorized users. * Kureeckal Vasudev Ramesh [email protected] Dipti Mothay [email protected] 1
Department of Biotechnology, School of Sciences, Jain University, #18/3, 9th Main Road, Jayanagar East, Jaya Nagar 3rd Block, Bengaluru, Karnataka 560041, India
SOM AMF t-SOM MD VdWaals Py-FIMS Py-GC/MS SPDBV 3D RMSF RMSD VMD MM/GBSA
Soil organic matter Arbuscular mycorrhizal fungi Gaussian optimized and truncated soil organic matter Molecular dynamics Van der Waal’s energy Pyr
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