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Structural analysis and molecular dynamics simulations of novel δ-endotoxin Cry1Id from Bacillus thuringiensis to pave the way for development of novel fusion proteins against insect pests of crops

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Abstract

The theoretical three-dimensional structure of a novel δ-endotoxin Cry1Id (81 kDa) belonging to Cry1I class, toxic to many of the lepidopteran pests has been investigated through comparative modeling. Molecular dynamics (MD) simulations was carried out to characterize its structural and dynamical features at 10 ns in explicit solvent using the GROMACS version 4.5.4. Finally the simulated model was validated by the SAVES, WHAT IF, MetaMQAP, ProQ, ModFOLD and MolProbity servers. Despite low sequence identity with its structural homologs, Cry1Id not only resembles the previously reported Cry structures but also shares the common five conserved blocks of amino acid residues. Although the domain II of Cry1Id superpose well with its closest structural homolog Cry8Ea1, variation of amino acids and length in the apical loop2 of domain II was observed. In this work, we have hypothesized that the variations in apical loop2 might be the sole factor for providing variable surface accessibility to Cry1Id protein that could be important in receptor recognition. MD simulation showed the proposed endotoxin retains its stable conformation in aqueous solution. The result from this study is expected to aid in the development hybrid Cry proteins and new potent fusion proteins with novel specificities against different insect pests for improved pest management of crop plants.

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Acknowledgments

This work was financially supported by the grant of Bioinformatics Initiative Division, Department of Electronics and Informatics Technology (DEITY), Ministry of Communications and Information Technology, Government of India. We also gratefully acknowledge the financial support by Biotechnology Information System Network (BTISNET), Department of Biotechnology, Government of India.

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  1. Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, 785013, Assam, India

    Budheswar Dehury, Mousumi Sahu, Jagajjit Sahu, Kishore Sarma, Priyabrata Sen, Mahendra K. Modi & Madhumita Barooah

  2. Department of Life Science and Bioinformatics, Assam University, Silchar, 788011, Assam, India

    Budheswar Dehury & Manabendra Dutta Choudhury

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  1. Budheswar Dehury
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  2. Mousumi Sahu
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Correspondence to Madhumita Barooah.

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Dehury, B., Sahu, M., Sahu, J. et al. Structural analysis and molecular dynamics simulations of novel δ-endotoxin Cry1Id from Bacillus thuringiensis to pave the way for development of novel fusion proteins against insect pests of crops. J Mol Model 19, 5301–5316 (2013). https://doi.org/10.1007/s00894-013-2010-x

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