ArticleProteins2010
Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors.
Article in Proteins, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 29 citations in OpenAlex.
- Modelling three-dimensional protein structures for applications in drug design.Drug discovery today · 2014Review
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
- Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking.BMC biophysics · 2014Article
- Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program.Journal of chemical theory and computation · 2013Article
- Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors.PloS one · 2013Article
- FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.Molecular pharmaceutics · 2012Article
- Article
- Conserved residues in the extracellular loops of short-wavelength cone visual pigments.Biochemistry · 2011Article
- Difference between restoring and predicting 3D structures of the loops in G-protein-coupled receptors by molecular modeling.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Successful prediction of the intra- and extracellular loops of four G-protein-coupled receptors.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor.Proteins · 2011Article
- Modeling G Protein-Coupled Receptors: a Concrete Possibility.Chimica oggi · 2010Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
This study presents the results of a de novo approach modeling possible conformational dynamics of the extracellular (EC) loops in G-protein-coupled receptors (GPCRs), specifically in bovine rhodopsin (bRh), squid rhodopsin (sRh), human beta-2 adrenergic receptor (beta2AR), turkey beta-1 adrenergic receptor (beta1AR), and human A2 adenosine receptor (A2AR). The approach deliberately sacrificed a detailed description of any particular 3D structure of the loops in GPCRs in favor of a less precise description of many possible structures. Despite this, the approach found ensembles of the low-energy conformers of the EC loops that contained structures close to the available X-ray snapshots. For the smaller EC1 and EC3 loops (6-11 residues), our results were comparable with the best recent results obtained by other authors using much more sophisticated techniques. For the larger EC2 loops (25-34 residues), our results consistently yielded structures significantly closer to the X-ray snapshots than the results of the other authors for loops of similar size. The results suggested possible large-scale movements of the EC loops in GPCRs that might determine their conformational dynamics. The approach was also validated by accurately reproducing the docking poses for low-molecular-weight ligands in beta2AR, beta1AR, and A2AR, demonstrating the possible influence of the conformations of the EC loops on the binding sites of ligands. The approach correctly predicted the system of disulfide bridges between the EC loops in A2AR and elucidated the probable pathways for forming this system.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.