title: Interaction between shrimp and white spot syndrome virus through PmRab7-VP28 complex: an insight using simulation and docking studies.
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.
authors.affiliation: 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.
authors.forename: Arunima Kumar
authors.initials: AK
authors.lastname: Verma
authors.forename: Shipra
authors.initials: S
authors.lastname: Gupta
authors.forename: Sharad
authors.initials: S
authors.lastname: Verma
authors.forename: Abha
authors.initials: A
authors.lastname: Mishra
authors.forename: N S
authors.initials: NS
authors.lastname: Nagpure
authors.forename: Shivesh Pratap
authors.initials: SP
authors.lastname: Singh
authors.forename: Ajey Kumar
authors.initials: AK
authors.lastname: Pathak
authors.forename: Uttam Kumar
authors.initials: UK
authors.lastname: Sarkar
authors.forename: Shri Prakash
authors.initials: SP
authors.lastname: Singh
authors.forename: Mahender
authors.initials: M
authors.lastname: Singh
authors.forename: Prahlad Kishore
authors.initials: PK
authors.lastname: Seth
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D033561:Penaeidae / Q000821:virology*; D011485:Protein Binding; D025941:Protein Interaction Mapping; D014759:Viral Envelope Proteins / Q000737:chemistry / Q000378:metabolism*; D046848:White spot syndrome virus 1 / Q000378:metabolism*; D020691:rab GTP-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D000090802:rab7 GTP-Binding Proteins
chemical_list: C548473:VP28 protein, white spot syndrome virus; D014759:Viral Envelope Proteins; D000090802:rab7 GTP-Binding Proteins; D020691:rab GTP-Binding Proteins