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Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

Molecular Modelling and Docking Studies of Glomalin Related Soil Protein from Rhizophagus irregularis .

Glomalin related soil protein (GRSP), is an insoluble glycoprotein, produced in copious amounts on hyphae of arbuscular mycorrhizal fungi (AMF). It provides unique properties to the soil such as mechanical stability, amelioration of salinity and aggregate water stability. Due to high sequence similarity of GRSP sequence identified from Rhizophagus irregularis, a mycorrhizal fungus, with heat shock proteins 60 (Hsp60) of various other species, this protein is said to be a putative, homolog of Hsp60. There is a lack of evidence both at the experimental and theoretical level with respect to the structural information of GRSP and its interaction with humic acid, one of the components of soil organic matter. Thus, the present study has focussed on evolutionary studies of Hsp60, followed by homology based 3D modelling and molecular docking of GRSP with humic acid. .

Based on the phylogenetic studies, it is evident that Hsp60 protein from R. irregularis, from Glomeromycota shares a very close evolutionary relationship with fungi belonging to Ascomycota and Basidiomycota, with classical α – Proteobacteria as the common ancestor. Comprehensive analysis of mitochondrial hsp6, 0 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Molecular clock analysis carried out by BEAST programme for the 14 common protein coding genes (inclusive of hsp60,), identified from 21 mitochondrial genomes belonging to fungal divisions Ascomycota, Basidiomycota and Glomeromycota estimates their time for diversification to be around 1425 Mya. Population genetics study credibly explains high genetic variability associated with fungal hsp60, presumably brought by random genetic recombination events. The results also confirm a high level of genetic differentiation of hsp60, among all the three fungal populations analysed. .

PsiBlast search and Swiss-Model server identified Hsp60 from Chlorobaculum tepidum, (5DA8_A) as the potential template for generating 3D model of GRSP. Accuracy of the 3D model was subsequently validated using Ramachandran plot analysis, ERRAT, ProCheck and Verify 3D. Among the two identified N-Linked glycosylation sites, the one that was present towards the C-terminal end was included in the truncated 94 residue fragment of the 3D model. Using Glycam Server, a glycoprotein model of GRSP was built by attaching the carbohydrate moiety rich in mannose, galactose and N-acetyl galactosamine to the asp94 residue of the truncated model. AutoDock software was successful in docking the standard 3D model of leonardite humic acid (chain L and U), onto the GRSP- carbohydrate complex. This was followed by docking the “GRSP glycoprotein – humic acid” complex with 50 water molecules. These findings open up new avenues for exploring the interactions of glomalin related soil protein with the soil organic matter, and its influence in aggregating the water molecules in improving soil productivity. .

    Gadkar, V., & Rillig, M. C. (2006). The arbuscular mycorrhizal fungal protein glomalin is a putative homolog of heat shock protein 60. FEMS Microbiology Letters, 263(1), 93-101.

    Petrov, D., Tunega, D., Gerzabek, M. H., & Oostenbrink, C. (2017). Molecular dynamics simulations of the standard leonardite humic acid: Microscopic analysis of the structure and dynamics. Environmental Science & Technology, 51(10), 5414-5424.

Dipti Mothay and
K. V. Ramesh


Dipti, a doctoral student of Prof. K. V. Ramesh, Jain Univ.,Bangalore, India, will deliver a short oral from the platform

Department of Biotechnology
Jain Univ., School of Sciences
#18/3, 9th Main Road
Jayanagar East
Jaya Nagar 3rd Block
Bengaluru, Karnataka 560041 India.

Email: m.dipti@jainuniversity.ac.in
ORCID ID: 0000-0003-0432-8655; Ph#: 9980155197

*Email: kv.ramesh@jainuniversity.ac.in
ORCID ID: 0000-0002-6787-5050; Ph#: 9448619022