Comparative modeling of lipid receptors

Methods in Molecular Biology

Volumn 914, Issue , 2012, Pages 207-218

  Parrill, Abby L ^a  

^a University of Memphis   (United States)

Author keywords

Comparative modeling; GPCR; Homology modeling; Lipid receptors; Sequence alignment

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIPID RECEPTOR; RECEPTOR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; COMPARATIVE MODELING; COMPUTER PROGRAM; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT;

EID: 84934442769     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-23-6_12     Document Type: Article

References (67)

1. Esposito EX, Tobi D, Madura JD (2006) Comparative protein modeling. In: Lipkowitz KB, Cundari TR, Gillet VJ (eds) Reviews in computational chemistry. Wiley, Hoboken, N. J, pp 57-167
2. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp R, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739-745
3. Parrill AL, Baker DL, Wang D, Fischer DJ, Bautista DL, van Brocklyn J, Spiegel S, Tigyi G (2000) Structural features of EDG1 receptor-ligand complexes revealed by computational modeling and mutagenesis. In: Goetzl EJ, Lynch KR (eds) Lysophospholipids and eicosanoids in biology and pathophysiology. New York Academy of Sciences, New York, pp 330-339
4. Parrill AL, Wang D-A, Bautista DL, Van Brocklyn JR, Lorincz Z, Fischer DJ, Baker DL, Liliom K, Spiegel S, Tigyi G (2000) Identification of Edg1 receptor residues that recognize sphingosine 1-phosphate. J Biol Chem 275:39379-39384
5. Wang D, Lorincz Z, Bautista DL, Liliom K, Tigyi G, Parrill AL (2001) A single amino acid determines ligand specificity of the S1P 1 (EDG1) and LPA 1 (EDG2) phospholipid growth factor receptors. J Biol Chem 276: 49213-49220
6. Holdsworth G, Osborne DA, Pham TT, Fells JI, Hutchinson G, Milligan G, Parrill AL (2004) A single amino acid determines preference between phospholipids and reveals length restriction for activation of the S1P4 receptor. BMC Biochem 5:12
7. Fujiwara Y, Sardar V, Tokumura A, Baker D, Murakami-Murofushi K, Parrill A, Tigyi G (2005) Identification of residues responsible for ligand recognition and regioisomeric selectivity of lysophosphatidic acid receptors expressed in mammalian cells. J Biol Chem 280:35038-35050
8. Inagaki Y, Pham TT, Fujiwara Y, Kohno T, Osborne DA, Igarashi Y, Tigyi G, Parrill AL (2005) Sphingosine-1-phosphate analog recognition and selectivity at S1P 4 within the endothelial differentiation gene family of receptors. Biochem J 389:187-195
9. Fujiwara Y, Osborne DA, Walker MD, Wang DA, Bautista DA, Liliom K, Van Brocklyn JR, Parrill AL, Tigyi G (2007) Identification of the hydrophobic ligand binding pocket of the S1P1 receptor. J Biol Chem 282:2374-2385
10. Valentine WJ, Fells JI, Perygin DH, Mujahid S, Yokoyama K, Fujiwara Y, Tsukahara R, Van Brocklyn JR, Parrill AL, Tigyi G (2008) Subtype-specific residues involved in ligand activation of the endothelial differentiation gene family lysophosphatidic acid receptors. J Biol Chem 283:12175-12187
11. Hurst DP, Grossfield A, Lynch DL, Feller S, Romo TD, Gawrisch K, Pitman MC, Reggio PH (2010) A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor. J Biol Chem 285:17954-17964
12. Ruan KH, Wijaya C, Cervantes V, Wu J (2008) Characterization of the prostaglandin H2 mimic: binding to the purified human thromboxane A2 receptor in solution. Arch Biochem Biophys 477:396-403
13. Stitham J, Stojanovic A, Merenick BL, OHara KA, Hwa J (2003) The unique ligand-binding pocket for the human prostacyclin receptor. Site-directed mutagenesis and molecular modeling. J Biol Chem 278:4250-4257
14. Jo E, Sanna MG, Gonzalez-Cabrera PJ, Thangada S, Tigyi G, Osborne DA, Hla T, Parrill AL, Rosen H (2005) S1P 1 -Selective in vivo -active agonists from high throughput screening: off-the-shelf chemical probes of receptor interactions, signaling and fate. Chem Biol 12:703-715
15. Fells JI, Tsukahara R, Fujiwara Y, Liu J, Perygin DH, Osborne DA, Tigyi G, Parrill AL (2008) Identification of non-lipid LPA3 antagonists by virtual screening. Bioorg Med Chem 16:6207-6217
16. Fells JI, Tsukahara R, Liu J, Tigyi G, Parrill AL (2009) Structure-based drug design identifies novel LPA3 antagonists. Bioorg Med Chem 17:7457-7464
17. Fells JI, Tsukahara R, Liu J, Tigyi G, Parrill AL (2010) 2D binary QSAR modeling of LPA3 receptor antagonism. J Mol Graph Model 28:828-833
18. Guindon J, Hohmann AG (2009) The endocannabinoid system and pain. CNS Neurol Disord Drug Targets 8:403-421
19. Martin-Moreno AM, Reigada D, Ramirez BG, Mechoulam R, Innamorato N, Cuadrado A, de Ceballos ML (2011) Cannabidiol and other cannabinoids reduce microglial activation in vitro and in vivo: relevance to Alzheimers disease. Mol Pharmacol 79(6):964-973
20. Parrill AL (2008) Lysophospholipid interactions with protein targets. Biochim Biophys Acta 1781:540-546
21. Im DS (2009) New intercellular lipid mediators and their GPCRs: an update. Prostaglandins Other Lipid Mediat 89:53-56
22. Murph M, Mills GB (2007) Targeting the lipids LPA and S1P and their signalling pathways to inhibit tumour progression. Expert Rev Mol Med 9:1-18
23. Pua TL, Wang FQ, Fishman DA (2009) Roles of LPA in ovarian cancer development and progression. Future Oncol 5:1659-1673
24. Inoue M, Rashid MH, Fujita R, Contos JJA, Chun J, Ueda H (2004) Initiation of neuropathic pain requires lysophosphatidic acid receptor signaling. Nat Med 10:712-718
25. Inoue M, Ma L, Aoki J, Chun J, Ueda H (2008) Autotaxin, a synthetic enzyme of lysophosphatidic acid (LPA), mediates the induction of nerve-injured neuropathic pain. Mol Pain 4:6
26. Inoue M, Xie W, Matsushita Y, Chun J, Aoki J, Ueda H (2008) Lysophosphatidylcholine induces neuropathic pain through an action of autotaxin to generate lysophosphatidic acid. Neuroscience 152:296-298
27. Okudaira S, Yukiura H, Aoki J (2010) Biological roles of lysophosphatidic acid signaling through its production by autotaxin. Biochimie 92:698-706
28. Brinkmann V, Davis MD, Heise CE, Albert R, Cottens S, Hof R, Bruns C, Prieschl E, Baumruker T, Hiestand P, Foster CA, Zollinger M, Lynch KR (2002) The immune modulator, FTY720, targets sphingosine 1-phosphate receptors. J Biol Chem 277:21453-21457
29. Hammack BN, Fung KY, Hunsucker SW, Duncan MW, Burgoon MP, Owens GP, Gilden DH (2004) Proteomic analysis of multiple sclerosis cerebrospinal fluid. Mult Scler 10: 245-260
30. Herr DR, Chun J (2007) Effects of LPA and S1P on the nervous system and implications for their involvement in disease. Curr Drug Targets 8:155-167
31. Brinkmann V, Billich A, Baumruker T, Heining P, Schmouder R, Francis G, Aradhye S, Burtin P (2010) Fingolimod (FTY720): discovery and development of an oral drug to treat multiple sclerosis. Nat Rev Drug Discov 9:883-897
32. Fechteler T, Dengler U, Schomburg D (1995) Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria. J Mol Biol 253:114-131
33. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28:235-242
34. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G proteincoupled receptor. Science 318:1258-1265
35. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol 342:571-583
36. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, Schertler GF (2008) Structure of a beta1-adrenergic G-proteincoupled receptor. Nature 454:486-491
37. Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, Stevens RC (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322: 1211-1217
38. Rasmussen SG, Choi HJ, Fung JJ, Pardon E, Casarosa P, Chae PS, Devree BT, Rosenbaum DM, Thian FS, Kobilka TS, Schnapp A, Konetzki I, Sunahara RK, Gellman SH, Pautsch A, Steyaert J, Weis WI, Kobilka BK (2011) Structure of a nanobody-stabilized active state of the beta(2) adrenoceptor. Nature 469:175-180
39. Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SG, Choi HJ, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011) Structure and function of an irreversible agonist-beta(2) adrenoceptor complex. Nature 469:236-240
40. Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, Ernst OP (2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature 455:497-502
41. Pogozheva ID, Lomize AL, Mosberg HI (1997) The transmembrane 7-a-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J 70:1963-1985
42. Ballesteros JA, Weinstein H (1995) Chapter 19. Integrated methods for the construction of three-dimensional models and computational probing of structure function relations in 6 protein-coupled receptors. In: Conn PM, Sealfon SC (eds) Methods in neurosciences. Academic, San Diego, pp 366-428
43. Sardar VM, Bautista DL, Fischer DJ, Yokoyama K, Nusser N, Virag T, Wang D, Baker DL, Tigyi G, Parrill AL (2002) Molecular basis for lysophosphatidic acid receptor antagonist selectivity. Biochim Biophys Acta 1582:309-317
44. Zhang D, Weinstein H (1994) Polarity conserved positions in transmembrane domains of G-protein coupled receptors and bacteriorhodopsin. FEBS Lett 337:207-212
45. Naor MM, Walker MD, Van Brocklyn JR, Tigyi G, Parrill AL (2007) Sphingosine 1-phosphate pKa and binding constants: intramolecular and intermolecular in fluences. J Mol Graph Model 26:519-528
46. Ye S, Zaitseva E, Caltabiano G, Schertler GF, Sakmar TP, Deupi X, Vogel R (2010) Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature 464:1386-1389
47. Ye S, Huber T, Vogel R, Sakmar TP (2009) FTIR analysis of GPCR activation using azido probes. Nat Chem Biol 5:397-399
48. Ulfers AL, McMurry JL, Kendall DA, Mierke DF (2002) Structure of the third intracellular loop of the human cannabinoid 1 receptor. Biochemistry 41(38):11344-11350
49. Ulfers AL, McMurry JL, Miller A, Wang L, Kendall DA, Mierke DF (2002) Cannabinoid receptor-G protein interactions: G(alphai1)-bound structures of IC3 and a mutant with altered G protein specificity. Protein Sci 11:2526-2531
50. Pham TT, Kriwacki RW, Parrill AL (2007) Peptide design and structural characterization of a GPCR loop mimetic. Biopolymers 86:298-310
51. Muegge I, Rarey M (2001) Small molecule docking and scoring. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry. Wiley, New York
52. Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y (2002) Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc Natl Acad Sci U S A 99:5982-5987
53. Li J, Edwards PC, Burghammer M, Villa C, Schertler GF (2004) Structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol 343:1409-1438
54. Standfuss J, Xie G, Edwards PC, Burghammer M, Oprian DD, Schertler GF (2007) Crystal structure of a thermally stable rhodopsin mutant. J Mol Biol 372:1179-1188
55. Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K (2006) Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Proc Natl Acad Sci U S A 103:16123-16128
56. Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP (2008) Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454:183-187
57. Murakami M, Kouyama T (2008) Crystal structure of squid rhodopsin. Nature 453:363-367
58. Shimamura T, Hiraki K, Takahashi N, Hori T, Ago H, Masuda K, Takio K, Ishiguro M, Miyano M (2008) Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J Biol Chem 283:17753-17756
59. Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383-387
60. Hanson MA, Cherezov V, Griffith MT, Roth CB, Jaakola VP, Chien EY, Velasquez J, Kuhn P, Stevens RC (2008) A specific cholesterol binding site is established by the 2.8 A structure of the human beta2-adrenergic receptor. Structure 16:897-905
61. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330: 1066-1071
62. Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, Stevens RC (2010) Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science 330:1091-1095
63. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 37:D387-D392
64. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201
65. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2006) Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics Chapter 5, Unit 5.6
66. Ginalski K, Elofsson A, Fischer D, Rychlewski L (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19:1015-1018
67. Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Yao XJ, Weis WI, Stevens RC, Kobilka BK (2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science 318:1266-1273