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In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus

Journal of Molecular Modeling volume 26, Article number: 264 (2020) Cite this article

Abstract

White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (designated as pep28) with high affinity for VP28, the structural protein of the white spot syndrome virus (WSSV). The peptide pep28 was successfully used as a biorecognition probe in the lateral flow assay developed for rapid, on-site detection of WSSV. To unravel the structural determinants for the selective binding between VP28 and pep28, we used bioinformatics, structural modeling, protein-protein docking, and binding-free energy studies. We performed atomistic molecular dynamics simulations of pep28-pIII model totaling 300 ns timescale. The most representative pep28-pIII structure from the simulation was used for docking with the crystal structure of VP28. Our results reveal that pep28 binds in a surface groove of the monomeric VP28 β-barrel and makes several hydrogen bonds and non-polar interactions. Ensemble-based binding-free energy studies reveal that the binding is dominated by non-polar interactions. Our studies provide molecular level insights into the binding mechanism of pep28 with VP28, which explain why the peptide is selective and can assist in modifying pep28 for its practical use, both as a biorecognition probe and a therapeutic.

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Abbreviations

WSSV:

White spot syndrome virus

WSD:

White spot disease

OPLS:

Optimized potentials for liquid simulations

GROMACS:

GROningen MAchine for Chemical Simulations

VMD:

Visual molecular dynamics

MM-PBSA:

Molecular mechanics Poisson–Boltzmann surface area

RMSD:

Root mean square deviation

RMSF:

Root mean square fluctuation

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Acknowledgments

MJ thanks DST-PURSE for HPC facility and Bioinformatics Centre for infrastructure support. MJ also thanks the generous support from Biovia for the work-from-home use of Discovery Studio Academic Research Suite and PARAM Yuva II cluster of CDAC, Pune, for computational time.

Funding

SJ acknowledges the award of Ph. D fellowship (Award no. 09/670(0079)/2017-EMR-1) to Council of Scientific & Industrial Research (CSIR), India.

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Author notes

  1. Snehal Jamalpure and Gauri Panditrao contributed equally to this work.

Authors and Affiliations

  1. Nanobioscience Group, Agharkar Research Institute, Pune, 411004, India

    Snehal Jamalpure, Prabir Kumar Kulabhusan, K. M. Paknikar & J. M. Rajwade

  2. Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, 411007, India

    Gauri Panditrao & Manali Joshi

  3. OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, Tamil Nadu, 632509, India

    A. S. Sahul Hameed

  4. Department of Chemistry, Indian Institute of Technology, Powai, Mumbai, 400076, India

    K. M. Paknikar

Authors
  1. Snehal Jamalpure
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  2. Gauri Panditrao
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  3. Prabir Kumar Kulabhusan
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  4. A. S. Sahul Hameed
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  5. K. M. Paknikar
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  6. Manali Joshi
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Contributions

SJ, GP performed the simulations and drafted the manuscript, GP worked extensively for the computational study, PK conducted lab experiments, ASS, KMP supervised the work and edited the manuscript, MJ, JMR conceived the idea, analyzed the results and finalized the manuscript.

Corresponding authors

Correspondence to Manali Joshi or J. M. Rajwade.

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Jamalpure, S., Panditrao, G., Kulabhusan, P.K. et al. In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus. J Mol Model 26, 264 (2020). https://doi.org/10.1007/s00894-020-04524-z

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