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Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies

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Abstract

White spot disease is a devastating disease of shrimp Penaeus monodon in which the shrimp receptor protein PmRab7 interacts with viral envelop protein VP28 to form PmRab7–VP28 complex, which causes initiation of the disease. The molecular mechanism implicated in the disease, the dynamic behavior of proteins as well as interaction between both the biological counterparts that crafts a micro-environment feasible for entry of virus into the shrimp is still unknown. In the present study, we applied molecular modeling (MM), molecular dynamics (MD) and docking to compute surface mapping of infective amino acid residues between interacting proteins. Our result showed that α-helix of PmRab7 (encompassing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) interacts with β-sheets of VP28 (containing Ser74, Ile143, Thr184, Arg53, Asn144, Thr184, Arg53, Arg79) and Arg69-Ser74, Val75-Ile143, Leu73-Ile143, Arg79-Asn144, Ala198-Ala182 bonds contributed in the formation of PmRab7–VP28 complex. Further studies on the amino acid residues and bonds may open new possibilities for preventing PmRab7–VP28 complex formation, thus reducing chances of WSD. The quantitative predictions provide a scope for experimental testing in future as well as endow with a straightforward evidence to comprehend cellular mechanisms underlying the disease.

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Acknowledgments

Authors are thankful to National Agricultural Bioinformatics Grid Project under National Agricultural Innovation Project, Indian Council of Agricultural Research, New Delhi for providing financial support. We also gratefully acknowledge the necessary facilities provided by the Director, National Bureau of Fish Genetic Resources, Lucknow and the Chief Executive Officer, Biotech Park, Lucknow.

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Authors and Affiliations

  1. Molecular Biology and Biotechnology Division, National Bureau of Fish Genetic Resources, Indian Council of Agricultural Research, Canal Ring Road, P.O. Dilkusha, Lucknow, 226002, Uttar Pradesh, India

    Arunima Kumar Verma, N. S. Nagpure, Ajey Kumar Pathak, Uttam Kumar Sarkar, Shri Prakash Singh & Mahender Singh

  2. Bioinformatics Centre, Biotech Park, Sector-G, Jankipuram, Lucknow, 226021, Uttar Pradesh, India

    Shipra Gupta & Prahlad Kishore Seth

  3. Department of Zoology, Autonomous Government P.G. College, Satna, Madhya Pradesh, India

    Shivesh Pratap Singh

  4. School of Biochemical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India

    Sharad Verma & Abha Mishra

  5. Amity Institute of Biotechnology, Amity University Haryana, Amity Education Valley, Manesar, Gurgaon, 122 413, Haryana, India

    Shipra Gupta

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  1. Arunima Kumar Verma
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  2. Shipra Gupta
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  3. Sharad Verma
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  9. Shri Prakash Singh
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Correspondence to N. S. Nagpure.

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Verma, A.K., Gupta, S., Verma, S. et al. Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies. J Mol Model 19, 1285–1294 (2013). https://doi.org/10.1007/s00894-012-1672-0

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  • DOI: https://doi.org/10.1007/s00894-012-1672-0

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