In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protei
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ORIGINAL PAPER
In silico studies on the interaction of phage displayed biorecognition element (TFQAFDLSPFPS) with the structural protein VP28 of white spot syndrome virus Snehal Jamalpure 1 & Gauri Panditrao 2 & Prabir Kumar Kulabhusan 1 & A. S. Sahul Hameed 3 & K. M. Paknikar 1,4 & Manali Joshi 2 & J. M. Rajwade 1 Received: 7 April 2020 / Accepted: 26 August 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
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. Keywords pep28 . VP28 . WSSV . Phage display . MD simulation . Docking
Snehal Jamalpure and Gauri Panditrao contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00894-020-04524-z) contains supplementary material, which is available to authorized users. * Manali Joshi [email protected] * J. M. Rajwade [email protected] 1
Nanobioscience Group, Agharkar Research Institute, Pune 411004, India
2
Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune 411007, India
3
OIE Reference Laboratory for WTD, C. Abdul Hakeem College, Melvisharam, Tamil Nadu 632509, India
4
Department of Chemistry, Indian Institute of Technology, Powai, Mumbai 400076, India
Abbreviations WSSV WSD OPLS GROMACS VMD MM-PBSA RMSD RMSF
White spot syndrome virus White spot disease Optimized potentials for liquid simulations GROningen MAchine for Chemical Simulations Visual molecular dynamics Molecular mechanics Poisson– Boltzmann surface area Root mean square deviation Root mean square fluctuation
Introduction White spot disease (WSD) caused by the white spot sy
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