NDLI: Molecular modeling and molecular dynamics simulation-based structural analysis of GPR3

Content Provider	Springer Nature Link
Author	Kaushik, Aman Chandra Sahi, Shakti
Copyright Year	2017
Abstract	G protein-coupled receptor 3 (GPR3) is an orphan GPCR; GPR3 has been reported to play a key role in Alzheimer’s disease through modulation of amyloid-beta production. The understanding of molecular mechanism involved has been limited due to unavailability of crystal structure of GPR3 and lack of different specific agonists. In this paper, we report the modeled 3D structure of GPR3 using threading and ab initio techniques with an objective to understand the mechanism underlying its interaction with agonists. The predicted model was optimized through 50 ns molecular dynamics simulation. Molecular dynamics (MD) simulation for 50 ns was performed on the 3D model of GPR3 embedded in 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine (POPC) lipid bilayer with aqueous system using OPLS (optimized potentials for liquid simulations) force field. The MD trajectories were analyzed to optimize the helical bundle conformations, active site, and 7TM domain variability during production phase of simulation. Binding pocket gave an insight into the size and chemical nature of compounds which could be potential agonists. The optimized structure would be significant in screening potential ligands through virtual screening.
Starting Page	1
Ending Page	10
Page Count	10
File Format	PDF
ISSN	21926662
Journal	Network Modeling Analysis in Health Informatics and Bioinformatics
Volume Number	6
Issue Number	1
e-ISSN	21926670
Language	English
Publisher	Springer Vienna
Publisher Date	2017-04-28
Publisher Place	Vienna
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	MD simulation 7TM Computational Biology/Bioinformatics Molecular modeling POPC Health Informatics GPR3 OPLS Bioinformatics Applications of Graph Theory and Complex Networks
Content Type	Text
Resource Type	Article
Subject	Urology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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