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.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Jamalpure S,Panditrao G,Kulabhusan PK,Hameed ASS,Paknikar KM,Joshi M,Rajwade JMdoi
10.1007/s00894-020-04524-zsubject
Has Abstractpub_date
2020-09-10 00:00:00pages
264issue
10eissn
1610-2940issn
0948-5023pii
10.1007/s00894-020-04524-zjournal_volume
26pub_type
杂志文章abstract：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...
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