Structure prediction of Bestrophin for the induced - fit docking of anthocyanins

Bestrophin, an integral membrane protein existing in basolateral region of the retina is a propitious target for drug discovery.Mutations in the Bestrophin protein cause Best Vitelliform Macular Dystrophy (BVMD) leading to retinal damages and loss ofvisual acuity. Owing to the lack of three dimensional structure and related structural homologs in the protein data bank, wemodeled the bestrophin protein using Robetta ab initio method. Further, no treatment is available for the disease. In this situation,anthocyanins from natural sources are reported to combat retinal damages. Hence, we identified anthocyanins from Syzygiumcumini fruit skin using Electrospray Ionization tandem mass spectrometry. These compounds were docked into the predictedbestrophin model to study the interactions within the active site. The results may provide a valuable insight into the structure ofbestrophin and efficacy of anthocyanins in molecular docking studies.

Abbreviations

PTP - Putative transmembrane proteins, VMD - Vitelliform macular dystrophy, BVMD - Best''s vitelliform macular dystrophy, RPE - Retinal pigment epithelium, ESI-MS/MS - Electrospray Ionization Tandem Mass Spectrometry, UNIPROT - Universal Protein Resource, PSIPRED - Protein secondary structure prediction, TMH - Transmembrane Helices, SCFS - Syzygium cumini fruit skinDP - Declustering PotentialIFD - Induced Fit Docking.