Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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A Novel Unified Ab Initio and Template-Based Approach to GPCR Modeling: Case of EDG-LPA Receptors.

Author(s): Olaposi I. Omotuyi, Hiroshi Ueda.

Abstract:

G-protein-coupled receptors (GPCRs) mediate diverse biological functions through intracellular signal cascades initiated by intracellular G-protein coupling following extracellular agonist binding. GPCRs are quintessential targets for drug design due to their involvement in pathophysiological conditions. The difficulty associated with GPCR crystallization and lack of accurate computational method for GPCR modeling constitutes the major setbacks for GPCRbased drug development. Here, we reported the combination of previously known ab initio and template-based methods as a novel approach applicable for modeling geometrically optimized full-length GPCR. First, geometry-optimized transmembrane helices (7Tms) of full-length GPCR are modeled using the GPCR server (http://gpcr.usc.es) followed by loop-refinement. A second structure is generated via the Iterative approach as implemented on I-TASSER (http://zhanglab.ccmb.med.umich.edu/I-TASSER/) server. The best Structures are then selected from the servers based on DOPE-score (GPCR server) and C-score (I-TASSER server) and piped into ModRefiner algorithm as initial and reference models respectively. ModRefiner drives the folding of the N- and C-termini regions of the initial model towards the reference model without altering the local geometries of the 7Tms and the loop regions as evaluated by Local-Global Alignment (LGA) algorithm. Finally, atomic clashes in the ModelRefiner output are resolved using Fragment-Guided Molecular Dynamics (FG-MD) simulation. Comparatively, FG-MD output structures of our test proteins (Endothelial Differentiation Gene-class (EDG) Lysophosphatidic acid receptors) have better model qualities than the initial and reference structures as evaluated by the QmeanScore6 algorithm.

Keywords: C-and N-terminal optimization, EDG-LPAs, GPCR modeling, mod refiner, I-TASSER.

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Article Details

VOLUME: 8
ISSUE: 5
Year: 2013
Page: [603 - 610]
Pages: 8
DOI: 10.2174/1574893611308050603
Price: $58