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Title |
Structure prediction of Bestrophin for the induced - fit docking of anthocyanins |
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Authors |
Sathyan Sri Lavvanya Priya1*, Ponnuswamy Renuka Devi1, Palanisami Eganathan2 & Nishith Saurav Topno3 |
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Affiliation |
1Department of Biotechnology, Anna University of Technology, Coimbatore- 641 047, Tamilnadu, India; 2Plant Tissue Culture and Bioprospecting Laboratory, M. S. Swaminathan Research Foundation, 3rd Cross Road, Institutional Area, Taramani, Chennai- 600 113. India; 3Department of Bioinformatics, Pondicherry University, Kalapet, Puducherry- 605 014, India.
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lavanya19@yahoo.com; *Corresponding author
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Article Type |
Hypothesis
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Date |
Received July 26, 2012; Accepted August 13, 2012; Published August 24, 2012
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Abstract |
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 of visual acuity. Owing to the lack of three dimensional structure and related structural homologs in the protein data bank, we modeled 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 Syzygium cumini fruit skin using Electrospray Ionization tandem mass spectrometry. These compounds were docked into the predicted bestrophin model to study the interactions within the active site. The results may provide a valuable insight into the structure of bestrophin and efficacy of anthocyanins in molecular docking studies.
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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 skin, DP - Declustering Potential, IFD- Induced Fit Docking
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Keywords |
Bestrophin, Ab initio, Anthocyanin, Induced Fit Docking
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Citation |
Priya et al.
Bioinformation 8(16): 742-748 (2012) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |