title: patGPCR: a multitemplate approach for improving 3D structure prediction of transmembrane helices of G-protein-coupled receptors.
abstract: The structures of the seven transmembrane helices of G-protein-coupled receptors are critically involved in many aspects of these receptors, such as receptor stability, ligand docking, and molecular function. Most of the previous multitemplate approaches have built a "super" template with very little merging of aligned fragments from different templates. Here, we present a parallelized multitemplate approach, patGPCR, to predict the 3D structures of transmembrane helices of G-protein-coupled receptors. patGPCR, which employs a bundle-packing related energy function that extends on the RosettaMem energy, parallelizes eight pipelines for transmembrane helix refinement and exchanges the optimized helix structures from multiple templates. We have investigated the performance of patGPCR on a test set containing eight determined G-protein-coupled receptors. The results indicate that patGPCR improves the TM RMSD of the predicted models by 33.64% on average against a single-template method. Compared with other homology approaches, the best models for five of the eight targets built by patGPCR had a lower TM RMSD than that obtained from SWISS-MODEL; patGPCR also showed lower average TM RMSD than single-template and multiple-template MODELLER.
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou 215006, China.
authors.forename: Hongjie
authors.initials: H
authors.lastname: Wu
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lü
authors.forename: Lijun
authors.initials: L
authors.lastname: Quan
authors.forename: Peide
authors.initials: P
authors.lastname: Qian
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Xia
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D008024:Ligands; D008055:Lipids / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D015233:Models, Statistical; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000502:physiology*; D012984:Software
chemical_list: D008024:Ligands; D008055:Lipids; D043562:Receptors, G-Protein-Coupled
references.citation: Proteins. 2005;61 Suppl 7:99-105
references.pmid: 16187350
references.citation: Proteins. 2001;Suppl 5:39-46
references.pmid: 11835480
references.citation: J Mol Biol. 1993 Dec 5;234(3):779-815
references.pmid: 8254673
references.citation: Comput Appl Biosci. 1994 Dec;10(6):685-6
references.pmid: 7704669
references.citation: PLoS Comput Biol. 2006 Feb;2(2):e13
references.pmid: 16485037
references.citation: Bioinformatics. 2001 Sep;17(9):849-50
references.pmid: 11590105
references.citation: J Mol Biol. 1992 Jul 20;226(2):507-33
references.pmid: 1640463
references.citation: PLoS One. 2012;7(9):e44967
references.pmid: 23028708
references.citation: Proteins. 2008 Feb 15;70(3):834-43
references.pmid: 17729286
references.citation: Proteins. 2008 May 1;71(2):599-620
references.pmid: 17972285
references.citation: Bioinformatics. 2006 Mar 1;22(5):621-2
references.pmid: 16407320
references.citation: BMC Struct Biol. 2008 May 05;8:24
references.pmid: 18457597
references.citation: Proteins. 2003;53 Suppl 6:430-5
references.pmid: 14579332
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15682-7
references.pmid: 17905872
references.citation: Nat Cell Biol. 2000 Jul;2(7):E133-6
references.pmid: 10878827
references.citation: J Mol Biol. 2007 Oct 19;373(2):503-19
references.pmid: 17825317
references.citation: Proteins. 2006 Mar 1;62(4):1010-25
references.pmid: 16372357
references.citation: Drug Discov Today. 2009 Jul;14(13-14):676-83
references.pmid: 19422931
references.citation: Science. 2007 Nov 23;318(5854):1258-65
references.pmid: 17962520
references.citation: Nat Methods. 2009 Aug;6(8):551-2
references.pmid: 19644455
references.citation: Structure. 2011 Aug 10;19(8):1108-26
references.pmid: 21827947
references.citation: Proteins. 2006 Nov 1;65(2):438-52
references.pmid: 16927380
references.citation: Nature. 2012 Oct 18;490(7420):361-6
references.pmid: 23075985
references.citation: Cell. 2012 Jun 22;149(7):1607-21
references.pmid: 22579045
references.citation: Proteins. 2007 Oct 1;69(1):69-74
references.pmid: 17588228
references.citation: J Mol Biol. 2001 Jan 19;305(3):567-80
references.pmid: 11152613
references.citation: Proteins. 2010 Aug 1;78(10):2189-201
references.pmid: 20544957
references.citation: Proteins. 2010 Jan;78(1):197-211
references.pmid: 20063437
references.citation: J Mol Biol. 1994 Jun 3;239(2):249-75
references.pmid: 8196057
references.citation: Nat Protoc. 2009;4(1):1-13
references.pmid: 19131951
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W571-4
references.pmid: 19429894
references.citation: Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14796-801
references.pmid: 11752426
references.citation: Bioinformatics. 2008 Aug 1;24(15):1662-8
references.pmid: 18474507
references.citation: BMC Struct Biol. 2008 Mar 17;8:18
references.pmid: 18366648