Journal of Molecular Modeling

, Volume 18, Issue 5, pp 2117–2133 | Cite as

Structural insights into human GPCR protein OA1: a computational perspective

  • Anirban Ghosh
  • Uddhavesh Sonavane
  • Sai Krishna Andhirka
  • Gopala Krishna Aradhyam
  • Rajendra Joshi
Original Paper


Human ocular albinism type 1 protein (OA1)—a member of the G-protein coupled receptor (GPCR) superfamily—is an integral membrane glycoprotein expressed exclusively by intracellular organelles known as melanocytes, and is responsible for the proper biogenesis of melanosomes. Mutations in the Oa1 gene are responsible for the disease ocular albinism. Despite its clinical importance, there is a lack of in-depth understanding of its structure and mechanism of activation due to the absence of a crystal structure. In the present study, homology modeling was applied to predicting OA1 structure following thorough sequence analysis and secondary structure predictions. The predicted model had the signature residues and motifs expected of GPCRs, and was used for carrying out molecular docking studies with an endogenous ligand, l-DOPA and an antagonist, dopamine; the results agreed quite well with the available experimental data. Finally, three sets of explicit molecular dynamics simulations were carried out in lipid bilayer, the results of which not only confirmed the stability of the predicted model, but also helped witness some differences in structural features such as rotamer toggle switch, helical tilts and hydrogen bonding pattern that helped distinguish between the agonist- and antagonist-bound receptor forms. In place of the typical “D/ERY”-motif-mediated “ionic lock”, a hydrogen bond mediated by the “DAY” motif was observed that could be used to distinguish the agonist and antagonist bound forms of OA1. In the absence of a crystal structure, this study helped to shed some light on the structural features of OA1, and its behavior in the presence of an agonist and an antagonist, which might be helpful in the future drug discovery process for ocular albinism.


G-protein coupled receptor Ocular albinism l-DOPA Dopamine Homology modeling Molecular docking Molecular dynamics simulation 



A.G., U.B.S. and R.R.J. gratefully acknowledge the Department of Information Technology (DIT), Government of India, New Delhi, for providing financial support. This work was performed using the “Bioinformatics Resources and Applications Facility (BRAF)” at C-DAC, Pune, funded by DIT, New Delhi. A.G.K. and A.S.K. gratefully acknowledge funding support from IIT Madras, Department of Science and Technology (DST) and Department of Biotechnology (DBT), Government of India.

Supplementary material

894_2011_1228_MOESM1_ESM.pdf (235 kb)
Supplementary Fig. 1 (PDF 235 kb)
894_2011_1228_MOESM2_ESM.pdf (267 kb)
Supplementary Fig. 2 (PDF 267 kb)
894_2011_1228_MOESM3_ESM.pdf (104 kb)
Supplementary Fig. 3 (PDF 103 kb)
894_2011_1228_MOESM4_ESM.pdf (252 kb)
Supplementary Fig. 4 (PDF 252 kb)
894_2011_1228_MOESM5_ESM.pdf (116 kb)
Supplementary Table 1 (PDF 115 kb)


  1. 1.
    Schöneberg T, Schulz A, Gudermann T (2002) The structural basis of G-protein-coupled receptor function and dysfunction in human diseases. Rev Physiol Biochem Pharmacol 144:143–227Google Scholar
  2. 2.
    Lundstrom K (2009) An overview on GPCRs and drug discovery: structure-based drug design and structural biology on GPCRs. Methods Mol Biol 552:51–66CrossRefGoogle Scholar
  3. 3.
    Wilson S, Bergsma D (2000) Orphan G-protein coupled receptors: novel drug targets for the pharmaceutical industry. Drug Des Discov 17:105–114Google Scholar
  4. 4.
    Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5:993–996CrossRefGoogle Scholar
  5. 5.
    Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H et al (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739–745CrossRefGoogle Scholar
  6. 6.
    Ballesteros J, Palczewski K (2001) G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr Opin Drug Discov Dev 4:561–574Google Scholar
  7. 7.
    Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS et al (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383–387CrossRefGoogle Scholar
  8. 8.
    Rasmussen SG, Choi HJ, Fung JJ, Pardon E, Casarosa P et al (2011) Structure of a nanobody-stabilized active state of the β(2) adrenoceptor. Nature 469:175–180CrossRefGoogle Scholar
  9. 9.
    Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D et al (2011) Structure and function of an irreversible agonist-β(2) adrenoceptor complex. Nature 469:236–240CrossRefGoogle Scholar
  10. 10.
    Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY et al (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322:1211–1217CrossRefGoogle Scholar
  11. 11.
    Murakami M, Kouyama T (2008) Crystal structure of squid rhodopsin. Nature 453:363–367CrossRefGoogle Scholar
  12. 12.
    Wu B, Chien EY, Mol CD, Fenalti G, Liu W et al (2010) Structures of the CXCR4 chemokine GPCR with small molecule and cyclic peptide antagonists. Science 330:1066–1071CrossRefGoogle Scholar
  13. 13.
    Choe HW, Kim YJ, Park JH, Morizumi T, Pai EF et al (2011) Crystal structure of metarhodopsin II. Nature 471:651–655CrossRefGoogle Scholar
  14. 14.
    Patny A, Desai PV, Avery MA (2006) Homology modelling of G-protein coupled receptors and implications in drug design. Curr Med Chem 13:1667–1691CrossRefGoogle Scholar
  15. 15.
    Kanagarajadurai K, Malini M, Bhattacharya A, Panicker M, Sowdhamini R (2009) Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding. Mol BioSys 5:1877–1888CrossRefGoogle Scholar
  16. 16.
    Miedlich SU, Gama L, Seuwen K, Wolf RM, Breitwieser GE (2004) Homology modeling of the transmembrane domain of the human calcium sensing receptor and localization of an allosteric binding site. J Biol Chem 279:7254–7263CrossRefGoogle Scholar
  17. 17.
    Dastmalchi S, Church WB, Morris MB (2008) Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. BMC Bioinforma 9:S14CrossRefGoogle Scholar
  18. 18.
    Niv MY, Skrabanek L, Filizola M, Weinstein H (2006) Modeling activated states of GPCRs: the rhodopsin template. J Comput Aided Mol Des 20:437–448CrossRefGoogle Scholar
  19. 19.
    Costanzi S (2008) On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the β2-adrenergic receptor. J Med Chem 51:2907–2914CrossRefGoogle Scholar
  20. 20.
    Lavecchia A, Cosconati S, Novellino E (2005) Architecture of the human urotensin II receptor: comparison of the binding domains of peptide and non-peptide urotensin II agonists. J Med Chem 48:2480–2492CrossRefGoogle Scholar
  21. 21.
    Periole X, Weinstein H (2002) Key issues in computational simulation of GPCR function. J Comput Aided Mol Des 16:841–853CrossRefGoogle Scholar
  22. 22.
    Ivetac A, Sansom MS (2008) Molecular dynamics simulations and membrane protein structure quality. Eur Biophys J 37:403–409CrossRefGoogle Scholar
  23. 23.
    Fan H, Mark AE (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 13:211–220CrossRefGoogle Scholar
  24. 24.
    Kobilka B, Schertler GF (2008) New G-protein-coupled receptor crystal structures: insights and limitations. Trends Pharmacol Sci 29:79–83CrossRefGoogle Scholar
  25. 25.
    Klein-Seetharaman J (2002) Dynamics in rhodopsin. ChemBioChem 3:981–986CrossRefGoogle Scholar
  26. 26.
    Vilardaga JP, Bünemann M, Krasel C, Castro M, Lohse MJ (2003) Measurement of the millisecond activation switch of G protein-coupled receptors in living cells. Nat Biotechnol 21:807–812CrossRefGoogle Scholar
  27. 27.
    Shen B, Samaraweera P, Rosenberg B, Orlow SJ (2001) Ocular albenism type I: more than meets the eye. Pigment Cell Res 14:243–248CrossRefGoogle Scholar
  28. 28.
    Incerti B, Cortese K, Pizzigoni A, Surace EM, Varani S et al (2000) Oa1 knock-out: new insights on the pathogenesis of ocular albinism type I. Hum Mol Genet 9:2781–2788CrossRefGoogle Scholar
  29. 29.
    Bassi MV, Schiaffino MV, Renieri A, De Nigris F, Galli L et al (1995) Cloning of the gene for ocular albinism type I from the distal short arm of the X chromosome. Nat Genet 10:13–19CrossRefGoogle Scholar
  30. 30.
    Schiaffino MV, Bassi MV, Galli L, Renieri A, Bruttini M et al (1995) Analysis of the OA1 gene reveals mutations in only one-third of the patients with X linked ocular albinism. Hum Mol Genet 4:2319–2325CrossRefGoogle Scholar
  31. 31.
    Schiaffino MV, d’Addio M, Alloni A, Baschirotto C, Valetti C et al (1999) Ocular albinism: evidence for a defect in an intracellular signal transduction system. Nat Genet 23:108–112CrossRefGoogle Scholar
  32. 32.
    Schiaffino MV, Tacchetti C (2005) The Ocular Albinism type I (OA1) protein and the evidence for an intracellular signal transduction system involved in melanosome biogenesis. Pigment Cell Res 18:227–233CrossRefGoogle Scholar
  33. 33.
    Innamorati G, Piccirillo R, Bagnato P, Palmisano I, Schiaffino MV (2006) The melanosome/lysosomal protein OA1 has properties of a G protein coupled receptor. Pigment Cell Res 19:125–135CrossRefGoogle Scholar
  34. 34.
    d’Addio M, Pizzigoni A, Bassi MT, Baschirotto C, Valetti C et al (2000) Defective intracellular transport and processing of OA1 is a major cause of ocular albinism type 1. Human Mol Genet 9:3011–3018CrossRefGoogle Scholar
  35. 35.
    Palmisano I, Bagnato P, Palmigiano A, Innamorati G, Rotondo G et al (2008) The ocular albinism type 1 protein, an intracellular G protein coupled receptor, regulates melanosome transport in pigment cells. Human Mol Genet 17:3487–3501CrossRefGoogle Scholar
  36. 36.
    Lopez VM, Decatur CL, Stamer WD, Lynch RM, MacKay BS (2008) l-DOPA is an endogenous ligand for OA1. PLoS Biol 6:e236CrossRefGoogle Scholar
  37. 37.
    Bairoch A, Apweiler R (1998) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res 26:38–42CrossRefGoogle Scholar
  38. 38.
    Bateman A, Coin L, Durbin R, Finn RD, Hollich V et al (2004) The Pfam protein families database. Nucleic Acids Res 32:138–141CrossRefGoogle Scholar
  39. 39.
    Altschul SF, Madden TL, Schäffer AA (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefGoogle Scholar
  40. 40.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948CrossRefGoogle Scholar
  41. 41.
    Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305:567–580CrossRefGoogle Scholar
  42. 42.
    Rost B, Yachdav G, Liu J (2004) The PredictProtein Server. Nucleic Acids Res 32:W321–W326CrossRefGoogle Scholar
  43. 43.
    Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS et al (2007) High-resolution crystal structure of an engineered human β2-adrenergic G protein-coupled receptor. Science 318:1258–1265CrossRefGoogle Scholar
  44. 44.
    Okada T, Sugihara M, Bondar AN, Elstner M, Entel P et al (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J Mol Biol 342:571–583CrossRefGoogle Scholar
  45. 45.
    Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Series 41:95–98Google Scholar
  46. 46.
    Šali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815CrossRefGoogle Scholar
  47. 47.
    Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291CrossRefGoogle Scholar
  48. 48.
    Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404CrossRefGoogle Scholar
  49. 49.
    Schrödinger Suite (2009) QM-polarized ligand docking protocol; Glide version 5.5; Jaguar version 7.6; QSite version 5.5. Schrödinger, LLC, New York, NYGoogle Scholar
  50. 50.
    Chung JY, Hah JM, Cho AE (2009) Correlation between performance of QM/MM docking and simple classification of binding sites. J Chem Inf Model 49:2382–2387CrossRefGoogle Scholar
  51. 51.
    Hess B, Kutzner C, van der Spoel D, Lindahl EJ (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Chem Theor Comput 4:435–447CrossRefGoogle Scholar
  52. 52.
    Schuettelkopf AW, van Aalten DMF (2004) PRODRG—a tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica D60:1355–1363Google Scholar
  53. 53.
    Kandt C, Ash WL, Tieleman DP (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods 41:475–488CrossRefGoogle Scholar
  54. 54.
    Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101CrossRefGoogle Scholar
  55. 55.
    Hess B (2008) P-LINCS: a parallel linear constraint solver for molecular simulations. J Chem Theor Comput 4:116–122CrossRefGoogle Scholar
  56. 56.
    Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Prot Eng 8:127–134CrossRefGoogle Scholar
  57. 57.
  58. 58.
    Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38CrossRefGoogle Scholar
  59. 59.
    DeLano WL (2003) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CAGoogle Scholar
  60. 60.
    Schnur RE, Gao M, Wick PA, Keller M, Benke PJ et al (1998) OA1 mutations and deletions in X-linked ocular albinism. Am J Hum Genet 62:800–809CrossRefGoogle Scholar
  61. 61.
    Unal H, Jagannathan R, Bhat MB, Karnik SS (2010) Ligand-specific conformation of extracellular loop-2 in the angiotensin II type 1 receptor. J Biol Chem 285:16341–16350CrossRefGoogle Scholar
  62. 62.
    Conner M, Hawtin SR, Simms J, Wootten D, Lawson Z et al (2007) Systematic analysis of the entire second extracellular loop of the V(1a) vasopressin receptor: key residues, conserved throughout a G-protein-coupled receptor family, identified. J Biol Chem 282:17405–17412CrossRefGoogle Scholar
  63. 63.
    Dunham TD, Farrens DL (1999) Conformational changes in rhodopsin. Movement of helix f detected by site-specific chemical labeling and fluorescence spectroscopy. J Biol Chem 274:1683–1690CrossRefGoogle Scholar
  64. 64.
    Knierim B, Hofmann KP, Ernst OP, Hubbell WL (2007) Sequence of late molecular events in the activation of rhodopsin. Proc Natl Acad Sci USA 104:20290–20295CrossRefGoogle Scholar
  65. 65.
    Kobilka BK (2007) G protein coupled receptor structure and activation. Biochim Biophys Acta 1768:794–807CrossRefGoogle Scholar
  66. 66.
    Kobilka BK (2002) Agonist-induced conformational changes in the beta2 adrenergic receptor. J Pept Res 60:317–321CrossRefGoogle Scholar
  67. 67.
    Shi L, Liapakis G, Xu R, Guarnieri F, Ballesteros JA et al (2002) Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch. J Biol Chem 277:40989–40996CrossRefGoogle Scholar
  68. 68.
    Bhattacharya S, Hall SE, Li H, Vaidehi N (2008) Ligand-stabilized conformational states of human β2 adrenergic receptor: insight into G-protein-coupled receptor activation. Bio Phys J 94:2027–2042Google Scholar
  69. 69.
    Bhattacharya S, Hall SE, Vaidehi N (2008) Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors. J Mol Biol 382:539–555CrossRefGoogle Scholar
  70. 70.
    Farahbakhsh ZT, Hideg K, Hubbell WL (1993) Photoactivated conformational-changes in rhodopsin—a time-resolved spin-label study. Science 262:1416–1419CrossRefGoogle Scholar
  71. 71.
    Hubbell WL, Cafiso D, Altenbach C (2000) Identifying conformational changes with site-directed spin labeling. Nature Struct Biol 7:735–739CrossRefGoogle Scholar
  72. 72.
    Langen R, Cai K, Altenbach C, Khorana HG, Hubbell WL (1999) Structural features of the C-terminal domain of bovine rhodopsin: a site directed spin-labeling study. Biochemistry 38:7918–7924CrossRefGoogle Scholar
  73. 73.
    Farrens D, Altenbach C, Yang K, Hubbell WL, Khorana HG (1996) Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274:768–770CrossRefGoogle Scholar
  74. 74.
    Crozier PS, Stevens MJ, Forrest LR, Woolf TB (2003) Molecular dynamics simulations of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. J Mol Biol 333:493–514CrossRefGoogle Scholar
  75. 75.
    Vogel R, Mahalingam M, Lüdeke S, Huber T, Siebert F et al (2008) Functional role of the “Ionic Lock”—an interhelical hydrogen-bond network in family a heptahelical receptors. J Mol Biol 380:648–655CrossRefGoogle Scholar
  76. 76.
    Ballesteros JA, Jensen AD, Liapakis G, Rasmussen SGF, Shi L et al (2001) Activation of the β2-adrenergic receptor involves disruption of an ionic lock between cytoplasmic ends of transmembrane segments 3 and 6. J Biol Chem 276:29171–29177CrossRefGoogle Scholar
  77. 77.
    Dror RO, Arlow DH, Borhani DW, Jensen MØ, Piana S et al (2009) Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 106:4689–4694CrossRefGoogle Scholar
  78. 78.
    Romo TD, Grossfield A, Pitman MC (2010) Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics. Biophys J 98:76–84CrossRefGoogle Scholar
  79. 79.
    Sgourakis NG, Garcia AE (2010) The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J Mol Biol 398:161–173CrossRefGoogle Scholar
  80. 80.
    Fanelli F, De Benedetti PG (2006) Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. J Comput Aided Mol Des 20:449–461CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Anirban Ghosh
    • 1
  • Uddhavesh Sonavane
    • 1
  • Sai Krishna Andhirka
    • 2
  • Gopala Krishna Aradhyam
    • 2
  • Rajendra Joshi
    • 1
  1. 1.Bioinformatics GroupCentre for Development of Advanced Computing (C-DAC)PuneIndia
  2. 2.Department of BiotechnologyIndian Institute of Technology MadrasChennaiIndia

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