Internally bridging water molecule in transmembrane α-helical kink

Current Opinion in Structural Biology

Volumn 20, Issue 4, 2010, Pages 456-463

  Miyano, Masashi ^a   Ago, Hideo ^a   Saino, Hiromichi ^a   Hori, Tetsuya ^a   Ida, Koh ^a  

^a Harima Institute ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE (POTASSIUM SODIUM); G PROTEIN COUPLED RECEPTOR; LEUKOTRIENE C4 SYNTHASE; MEMBRANE PROTEIN; POTASSIUM CHANNEL; RHODOPSIN; SODIUM CHANNEL; WATER;

ALPHA HELIX; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; HUMAN; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REGULATORY MECHANISM; REVIEW; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; CELL MEMBRANE; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; WATER;

EID: 77955984919     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2010.05.008     Document Type: Review

References (46)

1. McLuskey K., Roszak A.W., Zhu Y., Isaacs N.W. Crystal structures of all-alpha type membrane proteins. Eur Biophys J 2010, 39:723-755.
2. White S. Membrane Proteins of Known 3D Structure 2010, http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html.
3. Topiol S., Sabio M. X-ray structure breakthroughs in the GPCR transmembrane region. Biochem Pharmacol 2009, 78:11-20.
4. Jaakola V.P., Griffith M.T., Hanson M.A., Cherezov V., Chien E.Y., Lane J.R., Ijzerman A.P., Stevens R.C. The 2.6Å crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 2008, 322:1211-1217.
5. Warne A., Serrano-Vega M.J., Baker J.G., Moukhametzianov R., Edwards P.C., Henderson R., Leslie A.G.W., Tate C.G., Schertler G.F.X. Structure of the β1-adrenergic G protein-coupled receptor. Nature 2008, 454:486-491.
6. Cherezov V., Rosenbaum D.M., Hanson M.A., Rasmussen S.G., Thian F.S., Kobilka T.S., Choi H.J., Kuhn P., Weis W.I., Kobilka B.K., Stevens R.C. High-resolution crystal structure of an engineered human β2-adrenergic G protein-coupled receptor. Science 2007, 318:1258-1265.
7. Rosenbaum D.M., Cherezov V., Hanson M.A., Rasmussen S.G., Thian F.S., Kobilka T.S., Choi H.J., Yao X.J., Weis W.I., Stevens R.C., Kobilka B.K. GPCR engineering yields high-resolution structural insights into β2-adrenergic receptor function. Science 2007, 318:1266-1273.
8. Rasmussen S.G., Choi H.J., Rosenbaum D.M., Kobilka T.S., Thian F.S., Edwards P.C., Burghammer M., Ratnala V.R., Sanishvili R., Fischetti R.F., et al. Crystal structure of the human β2 adrenergic G-protein-coupled receptor. Nature 2007, 450:383-387.
9. Scheerer P., Park J.H., Hildebrand P.W., Kim Y.J., Krauss N., Choe H.-W., Hofmann K.P., Ernst O.P. Crystal structure of opsin in its G-protein-interacting conformation. Nature 2008, 455:497-502.
10. Park J.H., Scheerer P., Hofmann K.P., Choe H.-W., Ernst O.P. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 2008, 454:183-187.
11. Murakami M., Kouyama T. Crystal structure of squid rhodopsin. Nature 2008, 453:363-367.
12. Shimamura T., Hiraki K., Takahashi N., Hori T., Ago H., Masuda K., Takio K., Ishiguro M., Miyano M. Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region. J Biol Chem 2008, 283:17753-17756.
13. Okada T., Sugihara M., Bondar A.N., Elstner M., Entel P., Buss V. The retinal conformation and its environment in rhodopsin in light of a new 2.2Å crystal structure. J Mol Biol 2004, 342:571-583.
14. Li J., Edwards P., Burghammer M., Villa C. Schertler GFX: structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol 2004, 343:1409.
15. Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E., et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 2000, 289:739-745.
16. 2. Proc Natl Acad Sci USA 2008, 105:11110-11111.
17. Ago H., Kanaoka Y., Irikura D., Lam B.K., Shimamura T., Austen K.F., Miyano M. Crystal structure of a human membrane protein involved in cysteinyl leukotriene biosynthesis. Nature 2007, 448:609-612.
18. 4 synthase. Nature 2007, 448:613-616.
19. Ferguson A.D., McKeever B.M., Xu S., Wisniewski D., Miller D.K., Yamin T.T., Spencer R.H., Chu L., Ujjainwalla F., Cunningham B.R., et al. Crystal structure of inhibitor-bound human 5-lipoxygenase-activating protein. Science 2007, 317:510-512.
20. Holm P.J., Bhakat P., Jegerschöld C., Gyobu N., Mitsuoka K., Fujiyoshi Y., Morgenstern R., Hebert H. Structural basis for detoxification and oxidative stress protection in membranes. J Mol Biol 2006, 360:934-945.
21. Serrano-Vega M.J., Magnani F., Shibata Y., Tate C.G. Conformational thermostabilization of the β1-adrenergic receptor in a detergent-resistant form. Proc Natl Acad Sci USA 2008, 105:877-882.
22. Li L., Mustafi D., Fu Q., Tereshko V., Chen D.L., Tice J.D., Ismagilov R.F. Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins. Proc Natl Acad Sci USA 2006, 103:19243-19248.
23. Caffrey M. Crystallizing membrane proteins for structure determination: use of lipidic mesophases. Annu Rev Biophys 2009, 38:29-51.
24. Nollert P. Membrane protein crystallization in amphiphile phases: practical and theoretical considerations. Prog Biophys Mol Biol 2005, 88:339-357.
25. Flot D., Mairs T., Giraud T., Guijarro M., Lesourd M., Rey V., van Brussel D., Morawe C., Borel C., Hignette O., et al. The ID23-2 structural biology microfocus beamline at the ESRF. J Synchrotron Radiat 2010, 17:107-118.
26. Fischer G., Kosinska-Eriksson U., Aponte-Santamaría C., Palmgren M., Geijer C., Hedfalk K., Hohmann S., de Groot B.L., Neutze R., Lindkvist-Petersson K. Crystal structure of a yeast aquaporin at 1.15Å reveals a novel gating mechanism. PLoS Biol 2009, 7:e1000130.
27. Okada T., Fujiyoshi Y., Silow M., Navarro J., Landau E.M., Shichida Y. Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc Natl Acad Sci USA 2002, 99:5982-5987.
28. Riek R.P., Rigoutsos I., Novotny J., Graham R.M. Non-alpha-helical elements modulate polytopic membrane protein architecture. J Mol Biol 2001, 306:349-362.
29. Miyano M., Kumasaka T., Hori T., Yamamoto M. Atomic structure of bovine rhodopsin, a seven transmembrane receptor: toward the elucidation of GPCR's molecular mechanism. Tanpakushitsu Kakusan Koso 2001, 46:687-697.
30. Muñoz V., Serrano L. Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales. Proteins 1994, 20:301-311.
31. Blaber M., Zhang X.J., Matthews B.W. Structural basis of amino acid alpha helix propensity. Science 1993, 260:1637-1640.
32. Cordes F.S., Bright J.N., Sansom M.S. Proline-induced distortions of transmembrane helices. J Mol Biol 2002, 323:951-960.
33. Sankararamakrishnan R., Vishveshwara S. Geometry of proline-containing α-helices in proteins. Int J Pept Protein Res 1992, 39:356-363.
34. Yohannan S., Faham S., Yang D., Whitelegge J.P., Bowie J.U. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc Natl Acad Sci USA 2004, 101:959-963.
35. Ludtke S.J., Serysheva I.I., Hamilton S.L., Chiu W. The pore structure of the closed RyR1 channel. Structure 2005, 13:1203-1211.
36. Rosenhouse-Dantsker A., Logothetis D.E. New roles for a key glycine and its neighboring residue in potassium channel gating. Biophys J 2006, 91:2860-2873.
37. Li S.C., Deber C.M. Glycine and β-branched residues support and modulate peptide helicity in membrane environments. FEBS Lett 1992, 311:217-220.
38. Deupi X., Olivella M., Govaerts C., Ballesteros J.A., Campillo M., Pardo L. Ser and Thr residues modulate the conformation of pro-kinked transmembrane alpha-helices. Biophys J 2004, 86:105-115.
39. Pardo L., Deupi X., Dölker N., López-Rodríguez M.L., Campillo M. The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors. Chembiochem 2007, 8:19-24.
40. Alam A., Jiang Y. High-resolution structure of the open NaK channel. Nat Struct Mol Biol 2009, 16:30-34.
41. +-conducting channel. Nature 2006, 440:570-574.
42. + channel by pivoted bending of a transmembrane segment. Mol Cell 2002, 10:469-481.
43. Zhou H.X., McCammon J.A. The gates of ion channels and enzymes. Trends Biochem Sci 2010, 35:179-185.
44. Aurora R., Rose G.D. Helix capping. Protein Sci 1998, 7:21-38.
45. Serrano L., Fersht A.R. Capping and α-helix stability. Nature 1989, 342:296-299.
46. Sengupta D., Behera R.N., Smith J.C., Ullmann G.M. The α helix dipole: screened out?. Structure 2005, 13:849-855.