Abstract
Hyposidra talaca is a vicious pest of tea plants in the Eastern Himalayan’s Darjeeling foothills and NE India. The infestation of this pest leads to crop loss, as early instars prefer to feed the young harvestable leaves and late instars feed the matured leaves, which leads to loss of photosynthetic capacity of the entire tea bush. Among the few accessible methods to control H. talaca is the baculovirus H. talaca nucleopolyhedrovirus (HytaNPV). DNA-binding protein (DBP) plays a significant role in HytaNPV during viral replication and transcription. The present study attempted to predict the structure and the functional analysis of two crucial DNA-binding proteins (DBP-1 and DBP-2) in the absence of experimental structures. Analysis of sequence, prediction of structure, functional characterization, and evolutionary analysis based on UniProtKB studied the amino acid sequences of DBP-1 and DBP-2 proteins. Modeling of these two proteins was presented using ab-initio modeling. QMEANDisCo 4.0.0 global and local per-residue quality estimates verified the structure as high quality. Phylogenetic analysis of both HytaNPV DBP-1 and DBP-2 proteins revealed a close evolutionary relationship with Buzura suppressaria nucleopolyhedrovirus. Tunnel analysis revealed multiple tunnels in DBP-1 (six) and DBP-2 (eleven), indicating a large number of transport pathways for small ligands that influence their reactivity. The theoretical structures and statistical verifications were successfully deposited in the Model Archive. They will be useful for advanced computational analysis of each protein’s interactions for detailed functional analysis and understanding of viral pathogenesis in the absence of a complete experimental structure.
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Abbreviations
- NPV:
-
nucleopolyhedrovirus
- HytaNPV:
-
Hyposidra talaca nucleopolyhedrovirus
- Bp:
-
base pair
- DBP:
-
DNA-binding protein
- BmNPV:
-
Bombyx mori nucleopolyhedrovirus
- DBP-1:
-
DNA-binding protein-1
- DBP-2:
-
DNA-binding protein-2
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Acknowledgments
The authors are grateful to the Deputy Director (Research) North Bengal Regional R&D Centre, Nagrakata, West Bengal India and the Principal, Darrang College (Gauhati University), Tezpur (Assam), India, for supporting the research laboratory facility.
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Supplementary Information
ESM 1
Structure of the DBP-1 protein along with major active sites (PNG 289 kb)
ESM 2
Structure of the DBP-2 protein along with major active sites (PNG 239 kb)
ESM 3
Secondary structure of DBP-1protein (GIF 74 kb)
ESM 4
Secondary structure of DBP-2 protein (GIF 72 kb)
ESM 5
Hydropathicity plot for DBP-1 protein of HytaNPV [Kyte-Doolittle scale, (Kyte and Doolittle 1982)] (GIF 24 kb)
ESM 6
Hydropathicity plot for DBP-2 protein of HytaNPV [Kyte-Doolittle scale, (Kyte and Doolittle 1982)] (GIF 22 kb)
ESM 7
Local quality estimate of DBP-1 (PNG 122 kb)
ESM 8
Local quality estimate of DBP-2 (PNG 134 kb)
ESM 9
Structure assessment of DBP-1 and DBP-2 of HytaNPV (DOCX 12 kb)
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Deka, B., Baruah, C. & Barthakur, M. In silico tertiary structure prediction and evolutionary analysis of two DNA-binding proteins (DBP-1 and DBP-2) from Hyposidra talaca nucleopolyhedrovirus (HytaNPV). Biologia 76, 1075–1086 (2021). https://doi.org/10.2478/s11756-020-00665-x
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DOI: https://doi.org/10.2478/s11756-020-00665-x