An analysis of oligomerization interfaces in transmembrane proteins

BMC Structural Biology

Volumn 13, Issue 1, 2013, Pages

  Duarte, Jose M ^a   Biyani, Nikhil ^a   Baskaran, Kumaran ^a   Capitani, Guido ^a  

^a PAUL SCHERRER INSTITUTE   (Switzerland)

Author keywords

Eppic; GPCR; Lipids; Membrane proteins; Protein structure; Protein protein interfaces

Indexed keywords

G PROTEIN COUPLED RECEPTOR; MEMBRANE LIPID; MEMBRANE PROTEIN; PROTEIN; SMOOTHENED PROTEIN;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; DIMERIZATION; HYDROGEN BOND; OLIGOMERIZATION; PROTEIN STRUCTURE; SOLUBILIZATION; STOICHIOMETRY; TRANSCRIPTION INITIATION;

AMINO ACID MOTIFS; ANIMALS; CRYSTALLOGRAPHY, X-RAY; HUMANS; MEMBRANE LIPIDS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, G-PROTEIN-COUPLED;

EID: 84885495867     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-13-21     Document Type: Article

References (62)

1. Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3 Å resolution. Deisenhofer J, Epp O, Miki K, Huber R, Michel H, Nature 1985 318 618 624 (Pubitemid 16172409)
2. Amino acid distributions in integral membrane protein structures. Ulmschneider MB, Sansom MS, Biochim Biophys Acta 2001 1512 1 14 (Pubitemid 32378779)
3. Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis. Adamian L, Naveed H, Liang J, Biochim Biophys Acta 1808 2011 1092 1102
4. Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. Adamian L, Liang J, J Mol Biol 2001 311 891 907 (Pubitemid 32803743)
5. Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction. Jackups R, Liang J, J Mol Biol 2005 354 979 993 (Pubitemid 41735517)
6. Protein interface classification by evolutionary analysis. Duarte JM, Srebniak A, Schärer MA, Capitani G, BMC Bioinformatics 2012 13 334
7. Lipids in membrane protein structures. Palsdottir H, Hunte C, Biochim Biophys Acta 2004 1666 2 18 (Pubitemid 39425195)
8. The role of lipids in defining membrane protein interactions: insights from mass spectrometry. Barrera NP, Zhou M, Robinson CV, Trends Cell Biol 2013 23 1 8
9. Determinants of specificity at the protein-lipid interface in membranes. Ernst AM, Contreras FX, Brügger B, Wieland F, Febs Lett 2010 584 1713 1720
10. Molecular simulations of lipid-mediated protein-protein interactions. De Meyer FJ-M, Venturoli M, Smit B, Biophys J 2008 95 1851 1865
11. Fluorescence resonance energy transfer microscopy: a mini review. Periasamy A, J Biomed Opt 2001 6 287 291 (Pubitemid 32863911)
12. Homo-FRET microscopy in living cells to measure monomer-dimer transition of GFP-tagged proteins. Gautier I, Tramier M, Durieux C, Coppey J, Pansu RB, Nicolas JC, Kemnitz K, Coppey-Moisan M, Biophys J 2001 80 3000 3008 (Pubitemid 32536682)
13. Dimerisation of the glycophorin A transmembrane segment in membranes probed with the ToxR transcription activator. Langosch D, Brosig B, Kolmar H, Fritz HJ, J Mol Biol 1996 263 525 530 (Pubitemid 26382072)
14. TOXCAT: a measure of transmembrane helix association in a biological membrane. Russ W, Engelman D, Proc Natl Acad Sci USA 1999 96 863 868 (Pubitemid 29072149)
15. Consensus motif for integrin transmembrane helix association. Berger BW, Kulp DW, Span LM, DeGrado JL, Billings PC, Senes A, Bennett JS, DeGrado WF, Proc Natl Acad Sci USA 2010 107 703 708
16. Closing in on bacteriorhodopsin: progress in understanding the molecule. Haupts U, Tittor J, Oesterhelt D, Annu Rev Bioph Biom 1999 28 367 399 (Pubitemid 29319263)
17. Lipid patches in membrane protein oligomers: crystal structure of the bacteriorhodopsin-lipid complex. Essen L-O, Siegert R, Lehmann WD, Oesterhelt D, Proc Natl Acad Sci 1998 95 11673 11678 (Pubitemid 28460473)
18. Structure of bacteriorhodopsin at 1.55 A resolution. Luecke H, Schobert B, Richter HT, Cartailler JP, Lanyi JK, J Mol Biol 1999 291 899 911
19. Structure and thermal stability of monomeric bacteriorhodopsin in mixed phospholipid/detergent micelles. Brouillette CG, McMichens RB, Stern LJ, Khorana HG, Proteins 1989 5 38 46 (Pubitemid 19128899)
20. Monomeric and aggregated bacteriorhodopsin: single-turnover proton transport stoichiometry and photochemistry. Grzesiek S, Dencher NA, Proc Natl Acad Sci USA 1988 85 9509 9513
21. Bicelle crystallization: a new method for crystallizing membrane proteins yields a monomeric bacteriorhodopsin structure. Faham S, Bowie JU, J Mol Biol 2002 316 1 6 (Pubitemid 34729261)
22. How and why do GPCRs dimerize? Gurevich VV, Gurevich EV, Trends Pharmacol Sci 2008 29 234 240
23. Monomeric G-protein-coupled receptor as a functional unit. Chabre M, Le Maire M, Biochemistry 2005 44 9395 9403 (Pubitemid 40962038)
24. Oligomerization of G protein-coupled receptors: past, present, and future. Park PS-H, Filipek S, Wells JW, Palczewski K, Biochemistry 2004 43 15643 15656 (Pubitemid 39665065)
25. Structure of the human κ-opioid receptor in complex with JDTic. Wu H, Wacker D, Mileni M, Katritch V, Han GW, Vardy E, Liu W, Thompson AA, Huang X-P, Carroll FI, Mascarella SW, Westkaemper RB, Mosier PD, Roth BL, Cherezov V, Stevens RC, Nature 2012 485 327 332
26. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K, Proc Natl Acad Sci USA 2006 103 16123 16128 (Pubitemid 44715162)
27. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Wu B, Chien EYT, 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, Science 2010 330 1066 1071
28. Crystal structure of oligomeric β(1)-adrenergic G protein-coupled receptors in ligand-free basal state. Huang J, Chen S, Zhang JJ, Huang X-Y, Nat Struct Mol Biol 2013 20 419 425
29. The yeast mitochondrial ADP/ATP carrier functions as a monomer in mitochondrial membranes. Bamber L, Harding M, Monné M, Slotboom D-J, Kunji ERS, Proc Natl Acad Sci U S A 2007 104 10830 10834 (Pubitemid 47175186)
30. Yeast mitochondrial ADP/ATP carriers are monomeric in detergents. Bamber L, Harding M, Butler PJG, Kunji ERS, Proc Natl Acad Sci USA 2006 103 16224 16229 (Pubitemid 44715178)
31. Structural basis for lipid-mediated interactions between mitochondrial ADP/ATP carrier monomers. Nury H, Dahout-Gonzalez C, Trézéguet V, Lauquin G, Brandolin G, Pebay-Peyroula E, Febs Lett 2005 579 6031 6036 (Pubitemid 41546242)
32. CRK: an evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts. Schärer MA, Grütter MG, Capitani G, Proteins 2010 78 2707 2713
33. Automatic inference of protein quaternary structure from crystals. Ponstingl H, Kabir T, Thornton JM, J Appl Crystallogr 2003 36 1116 1122
34. Dissecting subunit interfaces in homodimeric proteins. Bahadur RP, Chakrabarti P, Rodier F, Janin J, Proteins 2003 53 708 719 (Pubitemid 37352183)
35. Shape complementarity at protein/protein interfaces. Lawrence MC, Colman PM, J Mol Biol 1993 234 946 950 (Pubitemid 24027225)
36. Internal packing of helical membrane proteins. Eilers M, Shekar SC, Shieh T, Smith SO, Fleming PJ, Proc Natl Acad Sci USA 2000 97 5796 5801 (Pubitemid 30367478)
37. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Eilers M, Patel AB, Liu W, Smith SO, Biophys J 2002 82 2720 2736 (Pubitemid 34441309)
38. The Calpha - H.O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Senes A, Ubarretxena-Belandia I, Engelman DM, Proc Natl Acad Sci USA 2001 98 9056 9061 (Pubitemid 32743868)
39. Stoichiometry of lipid-protein interaction and integral membrane protein structure. Marsh D, Eur Biophys J 1997 26 203 208 (Pubitemid 27405100)
40. Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern. Huang L-S, Cobessi D, Tung EY, Berry EA, J Mol Biol 2005 351 573 597 (Pubitemid 41021942)
41. Molecular weight and hydrodynamic parameters of the adenosine 5'-diphosphate-adenosine 5'-triphosphate carrier in Triton X-100. Hackenberg H, Klingenberg M, Biochemistry 1980 19 548 555
42. Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trézéguet V, Lauquin GJ-M, Brandolin G, Nature 2003 426 39 44 (Pubitemid 37432535)
43. Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. Schobert B, Cupp-Vickery J, Hornak V, Smith S, Lanyi J, J Mol Biol 2002 321 715 726 (Pubitemid 36124806)
44. Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures. Pozharski E, Weichenberger CX, Rupp B, Acta Crystallogr D 2013 69 150 167
45. Crystallizing membrane proteins in lipidic mesophases. A host lipid screen. Li D, Lee J, Caffrey M, Cryst Growth Des 2011 11 530 537
46. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Kuhn P, Weis WI, Kobilka BK, Stevens RC, Science (New York, N.Y.) 2007 318 1258 1265 (Pubitemid 350172884)
47. GPCR monomers and oligomers: it takes all kinds. Gurevich VV, Gurevich EV, Trends Neurosci 2008 31 74 81
48. Structure and ligand recognition of class C GPCRs. Chun L, Zhang W, Liu J, Acta Pharm Sinic 2012 33 312 323
49. Ligand-independent dimerization of CXCR4, a principal HIV-1 coreceptor. Babcock GJ, Farzan M, Sodroski J, J Biol Chem 2003 278 3378 3385 (Pubitemid 36801253)
50. Bioluminescence resonance energy transfer reveals ligand-induced conformational changes in CXCR4 homo- and heterodimers. Percherancier Y, Berchiche YA, Slight I, Volkmer-Engert R, Tamamura H, Fujii N, Bouvier M, Heveker N, J Biol Chem 2005 280 9895 9903 (Pubitemid 40395837)
51. Protein-protein interaction at crystal contacts. Janin J, Rodier F, Proteins 1995 23 580 587 (Pubitemid 26009521)
52. PQS: a protein quaternary structure file server. Henrick K, Thornton JM, Trends Biochem Sci 1998 23 358 361 (Pubitemid 28461869)
53. Conservation helps to identify biologically relevant crystal contacts. Valdar WS, Thornton JM, J Mol Biol 2001 313 399 416 (Pubitemid 33587196)
54. Inference of macromolecular assemblies from crystalline state. Krissinel E, Henrick K, J Mol Biol 2007 372 774 797 (Pubitemid 47321791)
55. Structure of the human smoothened receptor bound to an antitumour agent. Wang C, Wu H, Katritch V, Han GW, Huang X-P, Liu W, Siu FY, Roth BL, Cherezov V, Stevens RC, Nature 2013 497 338 343
56. Hedgehog regulates smoothened activity by inducing a conformational switch. Zhao Y, Tong C, Jiang J, Nature 2007 450 252 258 (Pubitemid 350100532)
57. Crystal structure of the β2 adrenergic receptor-Gs protein complex. Rasmussen SGF, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah STA, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK, Nature 2011 477 549 555
58. OPM: orientations of proteins in membranes database. Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI, Bioinformatics 2006 22 623 625 (Pubitemid 43372827)
59. Transmembrane proteins in the protein data bank: identification and classification. Tusnády GE, Dosztányi Z, Simon I, Bioinformatics 2004 20 2964 2972 (Pubitemid 39619188)
60. Bootstrap methods: another look at the jackknife. Efron B, The annals of Statistics 1979 7 1 26
61. R Development Core Team, R: A Language and Environment for Statistical Computing Vienna Austria: R Foundation for Statistical Computing 2010
62. The uppsala electron-density server. Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wählby A, Jones TA, Acta Crystallogr D 2004 60 2240 2249 (Pubitemid 41742776)