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. 1998 Aug;75(2):601–611. doi: 10.1016/S0006-3495(98)77551-4

A proposed structure for transmembrane segment 7 of G protein-coupled receptors incorporating an asn-Pro/Asp-Pro motif.

K Konvicka 1, F Guarnieri 1, J A Ballesteros 1, H Weinstein 1
PMCID: PMC1299736  PMID: 9675163

Abstract

Transmembrane segment (TMS) 7 has been shown to play an important role in the signal transduction function of G-protein-coupled receptors (GPCRs). Although transmembrane segments are most likely to adopt a helical structure, results from a variety of experimental studies involving TMS 7 are inconsistent with it being an ideal alpha-helix. Using results from a search of the structure database and extensive simulated annealing Monte Carlo runs with the new Conformational Memories method, we have identified the conserved (N/D)PxxY region of TMS 7 as the major determinant for deviation of TMS 7 from ideal helicity. The perturbation consists of an Asx turn and a flexible "hinge" region. The Conformational Memories procedure yielded a model structure of TMS 7 which, unlike an ideal alpha-helix, is capable of accommodating all of the experimentally derived geometrical criteria for the interactions of TMS 7 in the transmembrane bundle of GPCRs. In the context of the entire structure of a transmembrane bundle model for the 5HT2a receptor, the specific perturbation of TMS 7 by the NP sequence suggests a structural hypothesis for the pattern of amino acid conservation observed in TMS 1, 2, and 7 of GPCRs. The structure resulting from the incorporation of the (N/D)P motif satisfies fully the H-bonding capabilities of the 100% conserved polar residues in these TMSs, in agreement with results from mutagenesis experiments. The flexibility introduced by the specific structural perturbation produced by the (NP/DP) motif in TMS 7 is proposed to have a significant role in receptor activation.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altenbach C., Yang K., Farrens D. L., Farahbakhsh Z. T., Khorana H. G., Hubbell W. L. Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study. Biochemistry. 1996 Sep 24;35(38):12470–12478. doi: 10.1021/bi960849l. [DOI] [PubMed] [Google Scholar]
  2. Baldwin J. M., Schertler G. F., Unger V. M. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol. 1997 Sep 12;272(1):144–164. doi: 10.1006/jmbi.1997.1240. [DOI] [PubMed] [Google Scholar]
  3. Baldwin J. M. Structure and function of receptors coupled to G proteins. Curr Opin Cell Biol. 1994 Apr;6(2):180–190. doi: 10.1016/0955-0674(94)90134-1. [DOI] [PubMed] [Google Scholar]
  4. Baldwin J. M. The probable arrangement of the helices in G protein-coupled receptors. EMBO J. 1993 Apr;12(4):1693–1703. doi: 10.1002/j.1460-2075.1993.tb05814.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Ballesteros J. A., Weinstein H. The role of Pro/Hyp-kinks in determining the transmembrane helix length and gating mechanism of a [Leu]zervamicin channel. Biophys J. 1992 Apr;62(1):110–111. doi: 10.1016/S0006-3495(92)81795-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Ballesteros J., Kitanovic S., Guarnieri F., Davies P., Fromme B. J., Konvicka K., Chi L., Millar R. P., Davidson J. S., Weinstein H. Functional microdomains in G-protein-coupled receptors. The conserved arginine-cage motif in the gonadotropin-releasing hormone receptor. J Biol Chem. 1998 Apr 24;273(17):10445–10453. doi: 10.1074/jbc.273.17.10445. [DOI] [PubMed] [Google Scholar]
  7. Berlose J. P., Convert O., Brunissen A., Chassaing G., Lavielle S. Three-dimensional structure of the highly conserved seventh transmembrane domain of G-protein-coupled receptors. Eur J Biochem. 1994 Nov 1;225(3):827–843. doi: 10.1111/j.1432-1033.1994.0827b.x. [DOI] [PubMed] [Google Scholar]
  8. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  9. Birnbaumer L., Abramowitz J., Brown A. M. Receptor-effector coupling by G proteins. Biochim Biophys Acta. 1990 May 7;1031(2):163–224. doi: 10.1016/0304-4157(90)90007-y. [DOI] [PubMed] [Google Scholar]
  10. Clapham D. E. The G-protein nanomachine. Nature. 1996 Jan 25;379(6563):297–299. doi: 10.1038/379297a0. [DOI] [PubMed] [Google Scholar]
  11. Colson A. O., Perlman J. H., Smolyar A., Gershengorn M. C., Osman R. Static and dynamic roles of extracellular loops in G-protein-coupled receptors: a mechanism for sequential binding of thyrotropin-releasing hormone to its receptor. Biophys J. 1998 Mar;74(3):1087–1100. doi: 10.1016/S0006-3495(98)77827-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dohlman H. G., Thorner J., Caron M. G., Lefkowitz R. J. Model systems for the study of seven-transmembrane-segment receptors. Annu Rev Biochem. 1991;60:653–688. doi: 10.1146/annurev.bi.60.070191.003253. [DOI] [PubMed] [Google Scholar]
  13. Donnelly D., Overington J. P., Ruffle S. V., Nugent J. H., Blundell T. L. Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci. 1993 Jan;2(1):55–70. doi: 10.1002/pro.5560020106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Elling C. E., Nielsen S. M., Schwartz T. W. Conversion of antagonist-binding site to metal-ion site in the tachykinin NK-1 receptor. Nature. 1995 Mar 2;374(6517):74–77. doi: 10.1038/374074a0. [DOI] [PubMed] [Google Scholar]
  15. Elling C. E., Schwartz T. W. Connectivity and orientation of the seven helical bundle in the tachykinin NK-1 receptor probed by zinc site engineering. EMBO J. 1996 Nov 15;15(22):6213–6219. [PMC free article] [PubMed] [Google Scholar]
  16. Farahbakhsh Z. T., Ridge K. D., Khorana H. G., Hubbell W. L. Mapping light-dependent structural changes in the cytoplasmic loop connecting helices C and D in rhodopsin: a site-directed spin labeling study. Biochemistry. 1995 Jul 11;34(27):8812–8819. doi: 10.1021/bi00027a033. [DOI] [PubMed] [Google Scholar]
  17. Farrens D. L., Altenbach C., Yang K., Hubbell W. L., Khorana H. G. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science. 1996 Nov 1;274(5288):768–770. doi: 10.1126/science.274.5288.768. [DOI] [PubMed] [Google Scholar]
  18. Findlay J. B., Donnelly D., Bhogal N., Hurrell C., Attwood T. K. Structure of G-protein-linked receptors. Biochem Soc Trans. 1993 Nov;21(4):869–873. doi: 10.1042/bst0210869. [DOI] [PubMed] [Google Scholar]
  19. Fu D., Ballesteros J. A., Weinstein H., Chen J., Javitch J. A. Residues in the seventh membrane-spanning segment of the dopamine D2 receptor accessible in the binding-site crevice. Biochemistry. 1996 Sep 3;35(35):11278–11285. doi: 10.1021/bi960928x. [DOI] [PubMed] [Google Scholar]
  20. Gether U., Lin S., Ghanouni P., Ballesteros J. A., Weinstein H., Kobilka B. K. Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor. EMBO J. 1997 Nov 17;16(22):6737–6747. doi: 10.1093/emboj/16.22.6737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Gether U., Lin S., Kobilka B. K. Fluorescent labeling of purified beta 2 adrenergic receptor. Evidence for ligand-specific conformational changes. J Biol Chem. 1995 Nov 24;270(47):28268–28275. doi: 10.1074/jbc.270.47.28268. [DOI] [PubMed] [Google Scholar]
  22. Gudermann T., Schöneberg T., Schultz G. Functional and structural complexity of signal transduction via G-protein-coupled receptors. Annu Rev Neurosci. 1997;20:399–427. doi: 10.1146/annurev.neuro.20.1.399. [DOI] [PubMed] [Google Scholar]
  23. Javitch J. A., Fu D., Chen J. Residues in the fifth membrane-spanning segment of the dopamine D2 receptor exposed in the binding-site crevice. Biochemistry. 1995 Dec 19;34(50):16433–16439. doi: 10.1021/bi00050a026. [DOI] [PubMed] [Google Scholar]
  24. Javitch J. A., Li X., Kaback J., Karlin A. A cysteine residue in the third membrane-spanning segment of the human D2 dopamine receptor is exposed in the binding-site crevice. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10355–10359. doi: 10.1073/pnas.91.22.10355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Laakkonen L. J., Guarnieri F., Perlman J. H., Gershengorn M. C., Osman R. A refined model of the thyrotropin-releasing hormone (TRH) receptor binding pocket. Novel mixed mode Monte Carlo/stochastic dynamics simulations of the complex between TRH and TRH receptor. Biochemistry. 1996 Jun 18;35(24):7651–7663. doi: 10.1021/bi952203j. [DOI] [PubMed] [Google Scholar]
  26. Liu J., Schöneberg T., van Rhee M., Wess J. Mutational analysis of the relative orientation of transmembrane helices I and VII in G protein-coupled receptors. J Biol Chem. 1995 Aug 18;270(33):19532–19539. doi: 10.1074/jbc.270.33.19532. [DOI] [PubMed] [Google Scholar]
  27. Luo X., Zhang D., Weinstein H. Ligand-induced domain motion in the activation mechanism of a G-protein-coupled receptor. Protein Eng. 1994 Dec;7(12):1441–1448. doi: 10.1093/protein/7.12.1441. [DOI] [PubMed] [Google Scholar]
  28. MaloneyHuss K., Lybrand T. P. Three-dimensional structure for the beta 2 adrenergic receptor protein based on computer modeling studies. J Mol Biol. 1992 Jun 5;225(3):859–871. doi: 10.1016/0022-2836(92)90406-a. [DOI] [PubMed] [Google Scholar]
  29. McDonald I. K., Thornton J. M. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 1994 May 20;238(5):777–793. doi: 10.1006/jmbi.1994.1334. [DOI] [PubMed] [Google Scholar]
  30. Mizobe T., Maze M., Lam V., Suryanarayana S., Kobilka B. K. Arrangement of transmembrane domains in adrenergic receptors. Similarity to bacteriorhodopsin. J Biol Chem. 1996 Feb 2;271(5):2387–2389. doi: 10.1074/jbc.271.5.2387. [DOI] [PubMed] [Google Scholar]
  31. Oprian D. D. The ligand-binding domain of rhodopsin and other G protein-linked receptors. J Bioenerg Biomembr. 1992 Apr;24(2):211–217. doi: 10.1007/BF00762679. [DOI] [PubMed] [Google Scholar]
  32. Perlman J. H., Colson A. O., Wang W., Bence K., Osman R., Gershengorn M. C. Interactions between conserved residues in transmembrane helices 1, 2, and 7 of the thyrotropin-releasing hormone receptor. J Biol Chem. 1997 May 2;272(18):11937–11942. doi: 10.1074/jbc.272.18.11937. [DOI] [PubMed] [Google Scholar]
  33. Pogozheva I. D., Lomize A. L., Mosberg H. I. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J. 1997 May;72(5):1963–1985. doi: 10.1016/S0006-3495(97)78842-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Rao V. R., Cohen G. B., Oprian D. D. Rhodopsin mutation G90D and a molecular mechanism for congenital night blindness. Nature. 1994 Feb 17;367(6464):639–642. doi: 10.1038/367639a0. [DOI] [PubMed] [Google Scholar]
  35. Resek J. F., Farahbakhsh Z. T., Hubbell W. L., Khorana H. G. Formation of the meta II photointermediate is accompanied by conformational changes in the cytoplasmic surface of rhodopsin. Biochemistry. 1993 Nov 16;32(45):12025–12032. doi: 10.1021/bi00096a012. [DOI] [PubMed] [Google Scholar]
  36. Richardson J. S., Richardson D. C. Amino acid preferences for specific locations at the ends of alpha helices. Science. 1988 Jun 17;240(4859):1648–1652. doi: 10.1126/science.3381086. [DOI] [PubMed] [Google Scholar]
  37. Sankararamakrishnan R., Vishveshwara S. Geometry of proline-containing alpha-helices in proteins. Int J Pept Protein Res. 1992 Apr;39(4):356–363. doi: 10.1111/j.1399-3011.1992.tb01595.x. [DOI] [PubMed] [Google Scholar]
  38. Schertler G. F., Hargrave P. A. Projection structure of frog rhodopsin in two crystal forms. Proc Natl Acad Sci U S A. 1995 Dec 5;92(25):11578–11582. doi: 10.1073/pnas.92.25.11578. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Schwartz T. W. Locating ligand-binding sites in 7TM receptors by protein engineering. Curr Opin Biotechnol. 1994 Aug;5(4):434–444. doi: 10.1016/0958-1669(94)90054-x. [DOI] [PubMed] [Google Scholar]
  40. Sealfon S. C., Chi L., Ebersole B. J., Rodic V., Zhang D., Ballesteros J. A., Weinstein H. Related contribution of specific helix 2 and 7 residues to conformational activation of the serotonin 5-HT2A receptor. J Biol Chem. 1995 Jul 14;270(28):16683–16688. doi: 10.1074/jbc.270.28.16683. [DOI] [PubMed] [Google Scholar]
  41. Sheikh S. P., Zvyaga T. A., Lichtarge O., Sakmar T. P., Bourne H. R. Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F. Nature. 1996 Sep 26;383(6598):347–350. doi: 10.1038/383347a0. [DOI] [PubMed] [Google Scholar]
  42. Strahs D., Weinstein H. Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors. Protein Eng. 1997 Sep;10(9):1019–1038. doi: 10.1093/protein/10.9.1019. [DOI] [PubMed] [Google Scholar]
  43. Trumpp-Kallmeyer S., Hoflack J., Bruinvels A., Hibert M. Modeling of G-protein-coupled receptors: application to dopamine, adrenaline, serotonin, acetylcholine, and mammalian opsin receptors. J Med Chem. 1992 Sep 18;35(19):3448–3462. doi: 10.1021/jm00097a002. [DOI] [PubMed] [Google Scholar]
  44. Turcatti G., Nemeth K., Edgerton M. D., Meseth U., Talabot F., Peitsch M., Knowles J., Vogel H., Chollet A. Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites. J Biol Chem. 1996 Aug 16;271(33):19991–19998. doi: 10.1074/jbc.271.33.19991. [DOI] [PubMed] [Google Scholar]
  45. Unger V. M., Hargrave P. A., Baldwin J. M., Schertler G. F. Arrangement of rhodopsin transmembrane alpha-helices. Nature. 1997 Sep 11;389(6647):203–206. doi: 10.1038/38316. [DOI] [PubMed] [Google Scholar]
  46. Wess J., Nanavati S., Vogel Z., Maggio R. Functional role of proline and tryptophan residues highly conserved among G protein-coupled receptors studied by mutational analysis of the m3 muscarinic receptor. EMBO J. 1993 Jan;12(1):331–338. doi: 10.1002/j.1460-2075.1993.tb05661.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wong S. K., Slaughter C., Ruoho A. E., Ross E. M. The catecholamine binding site of the beta-adrenergic receptor is formed by juxtaposed membrane-spanning domains. J Biol Chem. 1988 Jun 15;263(17):7925–7928. [PubMed] [Google Scholar]
  48. Yang K., Farrens D. L., Hubbell W. L., Khorana H. G. Structure and function in rhodopsin. Single cysteine substitution mutants in the cytoplasmic interhelical E-F loop region show position-specific effects in transducin activation. Biochemistry. 1996 Sep 24;35(38):12464–12469. doi: 10.1021/bi960848t. [DOI] [PubMed] [Google Scholar]
  49. Yu H., Kono M., McKee T. D., Oprian D. D. A general method for mapping tertiary contacts between amino acid residues in membrane-embedded proteins. Biochemistry. 1995 Nov 21;34(46):14963–14969. doi: 10.1021/bi00046a002. [DOI] [PubMed] [Google Scholar]
  50. Zhang D., Weinstein H. Polarity conserved positions in transmembrane domains of G-protein coupled receptors and bacteriorhodopsin. FEBS Lett. 1994 Jan 10;337(2):207–212. doi: 10.1016/0014-5793(94)80274-2. [DOI] [PubMed] [Google Scholar]
  51. Zhang D., Weinstein H. Signal transduction by a 5-HT2 receptor: a mechanistic hypothesis from molecular dynamics simulations of the three-dimensional model of the receptor complexed to ligands. J Med Chem. 1993 Apr 2;36(7):934–938. doi: 10.1021/jm00059a021. [DOI] [PubMed] [Google Scholar]
  52. Zhou W., Flanagan C., Ballesteros J. A., Konvicka K., Davidson J. S., Weinstein H., Millar R. P., Sealfon S. C. A reciprocal mutation supports helix 2 and helix 7 proximity in the gonadotropin-releasing hormone receptor. Mol Pharmacol. 1994 Feb;45(2):165–170. [PubMed] [Google Scholar]

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