GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome

Structure

Volumn 23, Issue 8, 2015, Pages 1538-1549

  Zhang, Jian ^a   Yang, Jianyi ^a,b   Jang, Richard ^a   Zhang, Yang ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b NANKAI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINE; G PROTEIN COUPLED RECEPTOR; MELANOCORTIN; NEUROPEPTIDE Y RECEPTOR; PROSTANOID; RELEASING FACTOR; VASOPRESSIN;

AB INITIO CALCULATION; ALGORITHM; ANALYTIC METHOD; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DISULFIDE BOND; G PROTEIN COUPLED RECEPTOR ITERATIVE THREADING ASSEMBLY METHOD; HUMAN GENOME; HYDROGEN BOND; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS; CELL MEMBRANE; CHEMISTRY; GENE EXPRESSION; GENETICS; HUMAN; MOLECULAR MODEL; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY; THERMODYNAMICS;

ALGORITHMS; CELL MEMBRANE; DATABASES, PROTEIN; GENE EXPRESSION; GENOME, HUMAN; HUMANS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, G-PROTEIN-COUPLED; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS;

EID: 84938745406     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.06.007     Document Type: Article

References (61)

1. E. Archer, B. Maigret, C. Escrieut, L. Pradayrol, and D. Fourmy Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol. Sci. 24 2003 36 40
2. T.J. Baranski, P. Herzmark, O. Lichtarge, B.O. Gerber, J. Trueheart, E.C. Meng, T. Iiri, S.P. Sheikh, and H.R. Bourne C5a receptor activation. Genetic identification of critical residues in four transmembrane helices J. Biol. Chem. 274 1999 15757 15765
3. P. Barth, B. Wallner, and D. Baker Prediction of membrane protein structures with complex topologies using limited constraints Proc. Natl. Acad. Sci. USA 106 2009 1409 1414
4. M. Berthold, U. Kahl, A. Jureus, K. Kask, G. Nordvall, U. Langel, and T. Bartfai Mutagenesis and ligand modification studies on galanin binding to its GTP-binding-protein-coupled receptor GalR1 Eur. J. Biochem. 249 1997 601 606
5. R.M. Breyer, C.K. Bagdassarian, S.A. Myers, and M.D. Breyer Prostanoid receptors: subtypes and signaling Annu. Rev. Pharmacol. Toxicol. 41 2001 661 690
6. S.P. Brothers, and C. Wahlestedt Therapeutic potential of neuropeptide Y (NPY) receptor ligands EMBO Mol. Med. 2 2010 429 439
7. H. Chen, F. Ji, V. Olman, C.K. Mobley, Y. Liu, Y. Zhou, J.H. Bushweller, J.H. Prestegard, and Y. Xu Optimal mutation sites for PRE data collection and membrane protein structure prediction Structure 19 2011 484 495
8. E.Y. Chien, W. Liu, Q. Zhao, V. Katritch, G.W. Han, M.A. Hanson, L. Shi, A.H. Newman, J.A. Javitch, V. Cherezov, and et al. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist Science 330 2010 1091 1095
9. M.S. Cline, M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, and et al. Integration of biological networks and gene expression data using Cytoscape Nat. Protoc. 2 2007 2366 2382
10. R.M. Eglen, R. Bosse, and T. Reisine Emerging concepts of guanine nucleotide-binding protein-coupled receptor (GPCR) function and implications for high throughput screening Assay Drug Dev. Technol. 5 2007 425 451
11. F. Fanelli, and P.G. De Benedetti Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors Chem. Rev. 111 2011 PR438 PR535
12. L. Fu, B. Niu, Z. Zhu, S. Wu, and W. Li CD-HIT: accelerated for clustering the next-generation sequencing data Bioinformatics 28 2012 3150 3152
13. E. Giannini, L. Brouchon, and F. Boulay Identification of the major phosphorylation sites in human C5a anaphylatoxin receptor in vivo J. Biol. Chem. 270 1995 19166 19172
14. S. Granier, A. Manglik, A.C. Kruse, T.S. Kobilka, F.S. Thian, W.I. Weis, and B.K. Kobilka Structure of the delta-opioid receptor bound to naltrindole Nature 485 2012 400 404
15. G.S. Harrison, M.E. Wierman, T.M. Nett, and L.M. Glode Gonadotropin-releasing hormone and its receptor in normal and malignant cells Endocr. Relat. Cancer 11 2004 725 748
16. T.A. Hopf, L.J. Colwell, R. Sheridan, B. Rost, C. Sander, and D.S. Marks Three-dimensional structures of membrane proteins from genomic sequencing Cell 149 2012 1607 1621
17. V.P. Jaakola, M.T. Griffith, M.A. Hanson, V. Cherezov, E.Y. Chien, J.R. Lane, A.P. Ijzerman, and R.C. Stevens The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist Science 322 2008 1211 1217
18. D.T. Jones, W.R. Taylor, and J.M. Thornton A model recognition approach to the prediction of all-helical membrane protein structure and topology Biochemistry 33 1994 3038 3049
19. K. Kask, M. Berthold, U. Kahl, G. Nordvall, and T. Bartfai Delineation of the peptide binding site of the human galanin receptor EMBO J. 15 1996 236 244
20. L.F. Kolakowski Jr., B. Lu, C. Gerard, and N.P. Gerard Probing the "message:address" sites for chemoattractant binding to the C5a receptor. Mutagenesis of hydrophilic and proline residues within the transmembrane segments J. Biol. Chem. 270 1995 18077 18082
21. A. Krogh, B. Larsson, G. von Heijne, and E.L. Sonnhammer Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 305 2001 567 580
22. I. Kufareva, M. Rueda, V. Katritch, R.C. Stevens, and R. Abagyan Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment Structure 19 2011 1108 1126
23. A. Lala, A. Sharma, H.T. Sojar, S.J. Radel, R.J. Genco, and E. De Nardin Recombinant expression and partial characterization of the human formyl peptide receptor Biochim. Biophys. Acta 1178 1993 302 306
24. H.S. Lee, and Y. Zhang BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures Proteins 80 2012 93 110
25. A.L. Lomize, I.D. Pogozheva, M.A. Lomize, and H.I. Mosberg Positioning of proteins in membranes: a computational approach Protein Sci. 15 2006 1318 1333
26. J.S. Mills, H.M. Miettinen, D. Cummings, and A.J. Jesaitis Characterization of the binding site on the formyl peptide receptor using three receptor mutants and analogs of Met-Leu-Phe and Met-Met-Trp-Leu-Leu J. Biol. Chem. 275 2000 39012 39017
27. T. Nugent, and D.T. Jones Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis Proc. Natl. Acad. Sci. USA 109 2012 E1540 E1547
28. M.W. Panas, Z. Xie, H.N. Panas, M.C. Hoener, E.J. Vallender, and G.M. Miller Trace amine associated receptor 1 signaling in activated lymphocytes J. Neuroimmune Pharmacol. 7 2012 866 876
29. S. Perlman, H.T. Schambye, R.A. Rivero, W.J. Greenlee, S.A. Hjorth, and T.W. Schwartz Non-peptide angiotensin agonist. Functional and molecular interaction with the AT1 receptor J. Biol. Chem. 270 1995 1493 1496
30. S. Perlman, C.M. Costa-Neto, A.A. Miyakawa, H.T. Schambye, S.A. Hjorth, A.C. Paiva, R.A. Rivero, W.J. Greenlee, and T.W. Schwartz Dual agonistic and antagonistic property of nonpeptide angiotensin AT1 ligands: susceptibility to receptor mutations Mol. Pharmacol. 51 1997 301 311
31. E.R. Prossnitz, T.L. Gilbert, S. Chiang, J.J. Campbell, S. Qin, W. Newman, L.A. Sklar, and R.D. Ye Multiple activation steps of the N-formyl peptide receptor Biochemistry 38 1999 2240 2247
32. U. Raffetseder, D. Roper, L. Mery, C. Gietz, A. Klos, J. Grotzinger, A. Wollmer, F. Boulay, J. Kohl, and W. Bautsch Site-directed mutagenesis of conserved charged residues in the helical region of the human C5a receptor. Arg2O6 determines high-affinity binding sites of C5a receptor Eur. J. Biochem. 235 1996 82 90
33. S.G. Rasmussen, H.J. Choi, D.M. Rosenbaum, T.S. Kobilka, F.S. Thian, P.C. Edwards, M. Burghammer, V.R. Ratnala, R. Sanishvili, R.F. Fischetti, and et al. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor Nature 450 2007 383 387
34. A. Roy, A. Kucukural, and Y. Zhang I-TASSER: a unified platform for automated protein structure and function prediction Nat. Protoc. 5 2010 725 738
35. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
36. H.T. Schambye, B. von Wijk, S.A. Hjorth, W. Wienen, M. Entzeroth, D.J. Bergsma, and T.W. Schwartz Mutations in transmembrane segment VII of the AT1 receptor differentiate between closely related insurmountable and competitive angiotensin antagonists Br. J. Pharmacol. 113 1994 331 333
37. M. Schushan, Y. Barkan, T. Haliloglu, and N. Ben-Tal C(alpha)-trace model of the transmembrane domain of human copper transporter 1, motion and functional implications Proc. Natl. Acad. Sci. USA 107 2010 10908 10913
38. L. Shi, and J.A. Javitch The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop Annu. Rev. Pharmacol. Toxicol. 42 2002 437 467
39. T. Shimamura, M. Shiroishi, S. Weyand, H. Tsujimoto, G. Winter, V. Katritch, R. Abagyan, V. Cherezov, W. Liu, G.W. Han, and et al. Structure of the human histamine H1 receptor complex with doxepin Nature 475 2011 65 70
40. K.T. Simons, R. Bonneau, I. Ruczinski, and D. Baker Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins Suppl 3 1999 171 176
41. S. Takeda, S. Kadowaki, T. Haga, H. Takaesu, and S. Mitaku Identification of G protein-coupled receptor genes from the human genome sequence FEBS Lett. 520 2002 97 101
42. G.E. Tusnady, and I. Simon Principles governing amino acid composition of integral membrane proteins: application to topology prediction J. Mol. Biol. 283 1998 489 506
43. N. Vaidehi, W.B. Floriano, R. Trabanino, S.E. Hall, P. Freddolino, E.J. Choi, G. Zamanakos, and W.A. Goddard 3rd Prediction of structure and function of G protein-coupled receptors Proc. Natl. Acad. Sci. USA 99 2002 12622 12627
44. G. Vassart, and S. Costagliola G protein-coupled receptors: mutations and endocrine diseases Nat. Rev. Endocrinol. 7 2011 362 372
45. C. Wang, Y. Jiang, J. Ma, H. Wu, D. Wacker, V. Katritch, G.W. Han, W. Liu, X.P. Huang, E. Vardy, and et al. Structural basis for molecular recognition at serotonin receptors Science 340 2013 610 614
46. S. Wu, and Y. Zhang LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res. 35 2007 3375 3382
47. B. Wu, E.Y. Chien, C.D. Mol, G. Fenalti, W. Liu, V. Katritch, R. Abagyan, A. Brooun, P. Wells, F.C. Bi, and et al. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists Science 330 2010 1066 1071
48. J. Xu, and Y. Zhang How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26 2010 889 895
49. Z. Xue, D. Xu, Y. Wang, and Y. Zhang ThreaDom: extracting protein domain boundary information from multiple threading alignments Bioinformatics 29 2013 i247 i256
50. J. Yang, R. Jang, Y. Zhang, and H.B. Shen High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling Bioinformatics 29 2013 2579 2587
51. J. Yang, R. Yan, A. Roy, D. Xu, J. Poisson, and Y. Zhang The I-TASSER Suite: protein structure and function prediction Nat. Methods 12 2015 7 8
52. Y. Zhang I-TASSER server for protein 3D structure prediction BMC Bioinformatics 9 2008 40
53. Y. Zhang Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10 Proteins 82 Suppl 2 2014 175 187
54. Y. Zhang, and J. Skolnick Automated structure prediction of weakly homologous proteins on a genomic scale Proc. Natl. Acad. Sci. USA 101 2004 7594 7599
55. Y. Zhang, and J. Skolnick Scoring function for automated assessment of protein structure template quality Proteins 57 2004 702 710
56. Y. Zhang, and J. Skolnick SPICKER: a clustering approach to identify near-native protein folds J. Comput. Chem. 25 2004 865 871
57. Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309
58. J. Zhang, and Y. Zhang GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation Bioinformatics 26 2010 3004 3005
59. J. Zhang, and Y. Zhang A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction PLoS One 5 2010 e15386
60. Y. Zhang, M.E. Devries, and J. Skolnick Structure modeling of all identified G protein-coupled receptors in the human genome PLoS Comput. Biol. 2 2006 e13
61. J. Zhang, Y. Liang, and Y. Zhang Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling Structure 19 2011 1784 1795