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Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments

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Abstract

G-protein coupled receptors (GPCRs) are a protein family of outstanding pharmaceutical interest. GPCR homology models, based on the crystal structure of bovine rhodopsin, have been shown to be valuable tools in the drug-design process. The initial model is often refined by molecular dynamics (MD) simulations, a procedure that has been recently discussed controversially. We therefore analyzed MD simulations of bovine rhodopsin in order to identify contacts that could serve as constraints in the simulation of homology models. Additionally, the effect of an N-terminal truncation, the nature of the membrane mimic, the influence of varying protonation states of buried residues and the importance of internal water molecules was analyzed. All simulations were carried out using the program-package GROMACS. While N-terminal truncation negatively influenced the overall protein stability, a stable simulation was possible in both solvent environments. As regards the protonation state of titratable sites, the experimental data could be reproduced by the program UHBD (University of Houston Brownian Dynamics), suggesting its application for studying homology models of GPCRs. A high flexibility was observed for internal water molecules at some sites. Finally, interhelical hydrogen-bonding interactions could be derived, which can now serve as constraints in the simulations of GPCR homology models.

a Hydrogen bond pattern around residue D83/2.50 as observed in the crystal structure 1HZX. b Hydrogen bond interactions obtained after 1ns unconstrained MD-simulation of a model of bovine rhopopsin with D83 considered in its deprotonated state. c Hydrogen bond pattern observed after 5ns unconstrained MD-simulation of a model of bovine rhodopsin with D83 in its protonated state compared to the reference structure (light grey)

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Notes

  1. Numbering scheme corresponding to Baldwin et al. [5]: the most conserved residue in each transmembrane segment is assigned position 50 (Fig. 1). The first number refers to the helical segment.

Abbreviations

GPCR:

G-protein coupled receptor

DPPC:

Dipalmitoylphosphatidylcholine

POPC:

Palmitoyloleoylphosphatidylcholine

DMPC:

Dimyristoylphosphatidylcholin

RMSD:

Root-mean-square deviation (nm)

References

  1. Klabunde T, Hessler G (2002) Chem Bio Chem 3:928–944

    PubMed  CAS  Google Scholar 

  2. Rang H, Dale M, Ritter J, Moore P (2003) Pharmacology, 5th edn. Churchill Livingstone, London,

    Google Scholar 

  3. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima A, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Science 289:739–745

    Article  PubMed  CAS  Google Scholar 

  4. Caffrey M (2003) J Struct Biol 142:108–132

    Article  PubMed  CAS  Google Scholar 

  5. Baldwin J, Schertler G, Unger V (1997) J Mol Biol 272:144–164

    Article  PubMed  CAS  Google Scholar 

  6. Bissantz C, Bernard P, Hibert M, Rognan D (2003) Proteins: Struct Funct Genet 50:5–25

    Article  CAS  Google Scholar 

  7. Voigtländer U, Raasch A, Tränkle C, Buller S, Ellis J, Mohr K, Jöhren K, Höltje HD (2003) Mol Pharmacol 64:21–31

    Article  PubMed  Google Scholar 

  8. Bröer B, Gurrath M, Höltje HD (2003) J Comput Aided Mol Des 17:739–754

    Article  PubMed  Google Scholar 

  9. Anezo C, de Vries AH, Höltje HD, Tieleman DP, Marrink SJ (2003) J Phys Chem 107:9424–9433

    CAS  Google Scholar 

  10. Schuler LD, Daura X, van Gunsteren WF (2001) J Comput Chem 22:1205–1218

    Article  CAS  Google Scholar 

  11. Chandrasekhar I, Kastenholz M, Lins RD, Oostenbrink C, Schuler LD, Tieleman DP, van Gunsteren WF (2003) Eur Biophys J 32:67–77

    PubMed  CAS  Google Scholar 

  12. Berendsen HJ, van der Spoel D, van Drunen R (1995) Comput Phys Commun 91:43–56

    Article  CAS  Google Scholar 

  13. Lindahl E, Hess B, van der Spoel D (2001) J Mol Model 7:306–317

    CAS  Google Scholar 

  14. Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003) Nucleic Acids Res 31:294–297

    Article  PubMed  CAS  Google Scholar 

  15. Piascik MT, Perez DM (2001) J Pharmacol Exp Ther 298:403–410

    PubMed  CAS  Google Scholar 

  16. Zhao MM, Hwa J, Perez DM (1996) Mol Pharm 50:1118–1126

    CAS  Google Scholar 

  17. Wurch T, Pauwels PJ (2000) J Neurochem 75:1180–1189

    Article  PubMed  CAS  Google Scholar 

  18. Mehler EL, Periole X, Hassan SA, Weinstein H (2002) J Comput Aided Mol Des 16:841–853

    Article  PubMed  CAS  Google Scholar 

  19. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) J Mol Biol 342:571–583

    Article  PubMed  CAS  Google Scholar 

  20. Wymore T, Wong T (1999) Biophys J 76:1199–1212

    PubMed  CAS  Google Scholar 

  21. Tieleman DP, Berendsen HJ, Sansom MS (2001) Biophys J 80:331–346

    Article  PubMed  CAS  Google Scholar 

  22. Trent JO, Wang ZX, Murray JL, Shao W, Tamamura H, Fujll N, Peiper SC (2003) J Biol Chem 278:47136–47144

    Article  PubMed  CAS  Google Scholar 

  23. Crozier PS, Stevens MJ, Forrest LR, Woolf TB (2003) J Mol Biol 333:493–514

    Article  PubMed  CAS  Google Scholar 

  24. Huber T, Botelho AV, Beyer K, Brown MF (2004) Biophys J 86(4):2078–2100

    PubMed  CAS  Google Scholar 

  25. Flohil JA, Vriend G, Berendsen HJC (2002) Proteins: Struct Funct Genet 48:593–604

    Article  CAS  Google Scholar 

  26. Fan H, Mark AE (2004) Protein Sci 13:211–220

    Article  PubMed  CAS  Google Scholar 

  27. Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE (2001) Biochemistry 40:7761–7772

    Article  PubMed  CAS  Google Scholar 

  28. INSIGHT II (2000) FDISCOVER/HOMOLOGY, Biosym/MSI, San Diego, USA

  29. Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y (2002) PNAS 99:5982–5987

    Article  PubMed  CAS  Google Scholar 

  30. Essman U, Perela L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577–8592

    Article  Google Scholar 

  31. Ibragimova GT, Wade RC (1998) Biophys J 74:2906–2911

    PubMed  CAS  Google Scholar 

  32. Tieleman DP, Berendsen HJ (1996) J Chem Phys 105:4871–4880

    Article  CAS  Google Scholar 

  33. Department of Biological Sciences, Calgary/Canada, http://moose.bio.ucalgary.ca

  34. Faraldo-Gómez JD, Smith GR, Sansom MS (2002) Eur Biophys J 31:217–227

    Article  PubMed  CAS  Google Scholar 

  35. Briggs JM, Madura JD, Davis ME, Gilson MK, Antosiewicz J, Luty BA, Wade RC, Bagheri B, Ilin A, Tan RC, McCammon JA (1989) UHBD (University of Houston Brownian Dynamics) Release 5.1

  36. Schutz CN, Warshel A (2001) Proteins: Struct Funct Genet 44:400–417

    Article  CAS  Google Scholar 

  37. Shapiro DA, Kristiansen K, Kroeze WK, Roth BL (2000) Mol Pharm 58:877–886

    CAS  Google Scholar 

  38. Shi L, Simpson MM, Ballesteros JA, Javitch JA (2001) Biochemistry 40/41:12339–12348

    Article  PubMed  CAS  Google Scholar 

  39. Rarey M, Kramer B, Lengauer T (1999) Proteins: Struct Funct Genet 34:17–28

    Article  CAS  Google Scholar 

  40. von Itzstein M, Wu WY, Kok GB, Pegg MS, Dyason JC, Jin B, van Phan T, Smythe ML, White HF, Oliver SW (1993) Nature 363:418–423

    Article  PubMed  Google Scholar 

  41. Canutescu AA, Shelenkov AA, Dunbrack RL (2003) Protein Sci 12:2001–2014

    Article  PubMed  CAS  Google Scholar 

  42. Braganza LF, Worcester DL (1986) Biochemistry 25:2591–2596

    Article  PubMed  CAS  Google Scholar 

  43. Egberts E, Marrink SJ, Berendsen HJ (1994) Eur Phys J 22:423–436

    CAS  Google Scholar 

  44. Fahmy K, Jager F, Beck M, Zvyaga TA, Sakamar TP, Siebertm F (1993) PNAS 90:10206–10210

    Article  PubMed  CAS  Google Scholar 

  45. Yan EC, Kazmi MA, Ganim Y, Hou JM, Pan D, Chang BS, Sakmar TP, Mathies RA (2003) PNAS 100:9262–9267

    Article  PubMed  CAS  Google Scholar 

  46. Neve KA, Cumbay MG, Thompson KR, Yang R, Buck DC, Watts VJ, Durand CJ, Teeter MM (2001) Mol Pharm 60:373–381

    CAS  Google Scholar 

  47. Khare D, Alexander P, Antosiewicz J, Bryan P, Gilson M, Orban J (1997) Biochemistry 36:3580–3589

    Article  PubMed  CAS  Google Scholar 

  48. Noble MA, Gul S, Verma CS, Brocklehurst K (2000) Biochem J 351:723–733

    Article  PubMed  CAS  Google Scholar 

  49. Koehl P, Levitt M (1999) Nat Struct Biol 6:108–111

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

HDH acknowledges financial support from the HPC-Europa transnational access program. We wish to thank Peter Tieleman for making available the DPPC/SOL box to the scientific community via Ref. [33].

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Correspondence to Wolfgang Sippl.

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Schlegel, B., Sippl, W. & Höltje, HD. Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments. J Mol Model 12, 49–64 (2005). https://doi.org/10.1007/s00894-005-0004-z

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