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References

  • 1
    Fleming KG ( 2000) Riding the wave: structural and energetic principles of helical membrane proteins. Curr Opin Biotechnol 11: 6771.
  • 2
    Ubarretxena-Belandia I, Engelman DM ( 2001) Helical membrane proteins: diversity of functions in the context of simple architecture. Curr Opin Struct Biol 11: 370376.
  • 3
    Arkin IT ( 2002) Structural aspects of oligomerization taking place between the transmembrane alpha-helices of bitopic membrane proteins. Biochim Biophys Acta 1565: 347363.
  • 4
    Popot J-L, Engelman DM ( 2000) Helical membrane protein folding, stability and evolution. Annu Rev Biochem 69: 881922.
  • 5
    Langosch D, Lindner E, Gurezka R ( 2002) In vitro selection of self-interacting transmembrane segments—membrane proteins approached from a different perspective. IUBMB Life 54: 15.
  • 6
    Helms V ( 2002) Attraction within the membrane—forces behind transmembrane protein folding and supramolecular complex assembly. EMBO Rep 3: 11331138.
  • 7
    DeGrado WF, Gratkowski H, Lear JD ( 2003) How do helix-helix interactions help determine the folds of membrane proteins? Perspectives from the study of homo-oligomeric helical bundles. Protein Sci 12: 647665.
  • 8
    Chamberlain AK, Faham S, Yohannan S, Bowie JU ( 2003) Construction of helix-bundle membrane proteins. Adv Protein Chem 63: 1946.
  • 9
    Shai Y ( 2001) Molecular recognition within the membrane milieu: implications for the structure and function of membrane proteins. J Membr Biol 182: 91104.
  • 10
    Schneider D ( 2004) Rendezvous in a membrane: close packing, hydrogen bonding, and the formation of transmembrane helix oligomers. FEBS Lett 577: 58.
  • 11
    Seelig J ( 2004) Thermodynamics of lipid-peptide interactions. Biochim Biophys Acta 1666: 4050.
  • 12
    Rath A, Johnson RM, Deber CM ( 2007) Peptides as transmembrane segments: decrypting the determinants for helix-helix interactions in membrane proteins. Pept Sci 88: 217232.
  • 13
    MacKenzie KR, Fleming KG ( 2008) Association energetics of membrane spanning alpha-helices. Curr Opin Chem Biol 18: 18.
  • 14
    Slivka PF, Wong J, Caputo GA, Yin H ( 2008) Peptide probes for protein transmembrane domains. ACS Chem Biol 3: 402411.
  • 15
    Bowie JU ( 2005) Solving the membrane protein folding problem. Nature 438: 581589.
  • 16
    Moore DT, Berger BW, DeGrado WF ( 2008) Protein-protein interactions in the membrane: sequence, structural, and biological motifs. Structure 16: 9911001.
  • 17
    Matthews EE, Zoonens M, Engelman DM ( 2006) Dynamic helix interactions in transmembrane signaling. Cell 127: 447450.
  • 18
    MacKenzie KR ( 2006) Folding and stability of alpha-helical integral membrane proteins. Chem Rev 106: 19311977.
  • 19
    Ridder AN, Langosch D, Transmembrane domains in membrane protein folding, oligomerization, and function. In: BuchnerJ, KiefhaberT, Eds. ( 2005) Handbook of protein folding. Wiley: Weinheim, pp 876918.
  • 20
    Merzlyakov M, Chen L, Hristova K ( 2007) Studies of receptor tyrosine kinase transmembrane domain interactions: the EmEx-FRET method. J Membr Biol 215: 93103.
  • 21
    Zviling M, Kochva U, Arkin IT ( 2007) How important are transmembrane helices of bitopic membrane proteins? Biochim Biophys Acta 1768: 387392.
  • 22
    Stevens TJ, Arkin IT ( 2001) Substitution rates in alpha-helical transmembrane proteins. Protein Sci 10: 25072517.
  • 23
    Enosh A, Fleishman SJ, Ben-Tal N, Halperin D ( 2007) Prediction and simulation of motion in pairs of transmembrane alpha-helices. Bioinformatics 23: e212e218.
  • 24
    Fleishman SJ, Unger VM, Ben-Tal N ( 2006) Transmembrane protein structures without X-rays. Trends Biochem Sci 31: 106113.
  • 25
    Jones DT, Taylor WR, Thornton JM ( 1994) A mutation data matrix for transmembrane proteins. FEBS Lett 339: 269275.
  • 26
    Jones DT, Taylor WR, Thornton JM ( 1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33: 30383049.
  • 27
    Lemmon MA, Flanagan JM, Treutlein HR, Zhang J, Engelman DM ( 1992) Sequence specificity in the dimerization of transmembrane alpha-helices. Biochemistry 31: 1271912725.
  • 28
    Langosch DL, Brosig B, Kolmar H, Fritz H-J ( 1996) Dimerisation of the glycophorin A transmembrane segment in membranes probed with the ToxR transcription activator. J Mol Biol 263: 525530.
  • 29
    Langosch D, Heringa J ( 1998) Interaction of transmembrane helices by a knobs-into-holes geometry characteristic of soluble coiled coils. Proteins: Struct Funct Genet 31: 150160.
  • 30
    MacKenzie KR, Prestegard JH, Engelman DM ( 1997) A transmembrane helix dimer: structure and implications. Science 276: 131133.
  • 31
    Smith SO, Song D, Shekar S, Groesbeek M, Ziliox M, Aimoto S ( 2001) Structure of the transmembrane dimer interface of glycophorin A in membrane bilayers. Biochemistry 40: 65536558.
  • 32
    Bocharov EV, Pustovalova YE, Pavlov KV, Volynsky PE, Goncharuk MV, Ermolyuk YS, Karpunin DV, Schulga AA, Kirpichnikov MP, Efremov RG, Maslennikov IV, Arseniev AS ( 2007) Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger. J Biol Chem 282: 1625616266.
  • 33
    Zhou FX, Cocco MJ, Russ WP, Brunger AT, Engelman DM ( 2000) Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat Struct Biol 7: 154160.
  • 34
    Zhou FX, Merianos HJ, Brünger AT, Engelman DM ( 2001) Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 98: 22502255.
  • 35
    Gratkowski H, Lear JD, DeGrado WF ( 2001) Polar side chains drive the association of model transmembrane peptides. Proc Natl Acad Sci USA 98: 880885.
  • 36
    Dawson JP, Weinger JS, Engelman DM ( 2002) Motifs of serine and threonine can drive association of transmembrane helices. J Mol Biol 316: 799805.
  • 37
    Sal-Man N, Gerber D, Shai Y ( 2005) The identification of a minimal dimerization motif QXXS that enables homo- and hetero-association of transmembrane helices in vivo. J Biol Chem 280: 2744927457.
  • 38
    Kim S, Jeon TJ, Oberai A, Yang D, Schmidt JJ, Bowie JU ( 2005) Transmembrane glycine zippers: physiological and pathological roles in membrane proteins. Proc Natl Acad Sci USA 102: 1427814283.
  • 39
    Munter LM, Voigt P, Harmeier A, Kaden D, Gottschalk KE, Weise C, Pipkorn R, Schaefer M, Langosch D, Multhaup G ( 2007) GxxxG motifs within the amyloid precursor protein transmembrane sequence are critical for the etiology of Abeta42. EMBO J 26: 17021712.
  • 40
    Sulistijo ES, MacKenzie KR ( 2006) Sequence dependence of BNIP3 transmembrane domain dimerization implicates side-chain hydrogen bonding and a tandem GxxxG motif in specific helix-helix interactions. J Mol Biol 364: 974990.
  • 41
    Herrmann J, Panitz J, Unterreitmeier S, Fuchs A, Frishman D, Langosch D ( 2009) Complex patterns of histidine, hydroxylated amino acids and the GxxxG motif mediate high-affinity transmembrane domain interactions. J Mol Biol 385: 912923.
  • 42
    Unterreitmeier S, Fuchs A, Schäffler T, Heym RG, Frishman D, Langosch D ( 2007) Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs. J Mol Biol 374: 705718.
  • 43
    Ashman JB, Miller J ( 1999) A role for the transmembrane domain in the trimerization of the MHC class II-associated invariant chain. J Immunol 163: 27042712.
  • 44
    Dixon AM, Stanley BJ, Matthews EE, Dawson JP, Engelman DM ( 2006) Invariant chain transmembrane domain trimerization: a step in MHC class II assembly. Biochemistry 45: 52285234.
  • 45
    Holsinger LJ, Lamb RA ( 1991) Influenza virus M2 integral membrane protein is a homotetramer stabilized by formation of disulfide bonds. Virology 183: 3243.
  • 46
    Arkin IT, Adams PD, MacKenzie KR, Lemmon MA, Brünger AT, Engelman DM ( 1994) Structural organization of the pentameric transmembrane alpha-helices of phospholamban, a cardiac ion channel. EMBO J 13: 47574764.
  • 47
    Merzlyakov M, You M, Li E, Hristova K ( 2006) Transmembrane helix heterodimerization in lipid bilayers: probing the energetics behind autosomal dominant growth disorders. J Mol Biol 358: 17.
  • 48
    Rath A, Melnyk RA, Deber CM ( 2006) Evidence for assembly of small multidrug resistance proteins by a “two-faced” transmembrane helix. J Biol Chem 281: 1554615553.
  • 49
    Barwe SP, Kim S, Rajasekaran SA, Bowie JU, Rajasekaran AK ( 2007) Janus model of the Na,K-ATPase beta-subunit transmembrane domain: distinct faces mediate alpha/beta assembly and beta-beta homo-oligomerization. J Mol Biol 365: 706714.
  • 50
    Henzler-Wildman K, Kern D ( 2007) Dynamic personalities of proteins. Nature 450: 964972.
  • 51
    Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauß N, Choe H-W, Hofmann KP, Ernst OP ( 2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature 455: 497502.
  • 52
    Schwartz TW, Frimurer TM, Holst B, Rosenkilde MM, Elling CE ( 2006) Molecular mechanism of 7TM receptor activation—a global toggle switch model. Annu Rev Pharmacol Toxicol 46: 481519.
  • 53
    Farrens DL, Altenbach C, Yang K, Hubbell WL, Khorana HG ( 1996) Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274: 768770.
  • 54
    Cordes FS, Bright JN, Sansom MSP ( 2002) Proline-induced distortions of transmembrane helices. J Mol Biol 323: 951960.
  • 55
    Mukherjee P, Kass I, Arkin I, Zanni MT ( 2006) Picosecond dynamics of a membrane protein revealed by 2D IR. Proc Natl Acad Sci USA 103: 35283533.
  • 56
    Stelzer W, Poschner BC, Stalz H, Heck AJ, Langosch D ( 2008) Sequence-specific conformational flexibility of SNARE transmembrane helices probed by hydrogen/deuterium exchange. Biophys J 95: 13261330.
  • 57
    Poschner BC, Quint S, Hofmann M, Langosch D ( 2009) Sequence-specific conformational dynamics of model transmembrane domains determines their membrane fusogenic function. J Mol Biol 386: 733741.
  • 58
    MacKenzie KR, Prestegard JH, Engelman DM ( 1996) Leucine side-chain rotamers in a glycophorin A transmembrane peptide as revealed by three-bond carbon-carbon couplings and 13C chemical shifts. J Biomol NMR 7: 256260.
  • 59
    Bowie JU ( 1997) Helix packing in membrane proteins. J Mol Biol 272: 780789.
  • 60
    Walters RFS, deGrado WF ( 2006) Helix-packing motifs in membrane proteins. Proc Natl Acad Sci USA 103: 1365813663.
  • 61
    Oberai A, Ihm Y, Kim S, Bowie JU ( 2006) A limited universe of membrane protein families and folds. Protein Sci 15: 17231734.
  • 62
    Lehnert U, Xia Y, Royce TE, Goh CS, Liu Y, Senes A, Yu HY, Zhang ZL, Engelman DM, Gerstein M ( 2004) Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. Q Rev Biophys 37: 121146.
  • 63
    Call ME, Schnell JR, Xu CQ, Lutz RA, Chou JJ, Wucherpfennig KW ( 2006) The structure of the zeta zeta transmembrane dimer reveals features essential for its assembly with the T cell receptor. Cell 127: 355368.
  • 64
    Bocharov EV, Mineev KS, Volynsky PE, Ermolyuk YS, Tkach EN, Sobol AG, Chupin VV, Kirpichnikov MP, Efremov RG, Arseniev AS ( 2008) Spatial structure of the dimeric transmembrane domain of the growth factor receptor ErbB2 presumably corresponding to the receptor active state. J Biol Chem 283: 69506956.
  • 65
    Schnell JR, Chou JJ ( 2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451: 591595.
  • 66
    Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF ( 2008) Structural basis for the function and inhibition of an influenza virus proton channel. Nature 451: 596599.
  • 67
    Ruan W, Lindner E, Langosch D ( 2004) The interface of a membrane-spanning leucine zipper mapped by asparagine-scanning mutagenesis. Protein Sci 13: 555559.
  • 68
    Ruan W, Becker V, Klingmüller U, Langosch D ( 2004) The interface between the self-assembling erythropoietin receptor transmembrane segments corresponds to a heptad repeat pattern. J Biol Chem 279: 32733279.
  • 69
    Laage R, Langosch D ( 1997) Dimerization of the synaptic vesicle protein synaptobrevin/VAMP II depends on specific residues within the transmembrane segment. Eur J Biochem 249: 540546.
  • 70
    Dews IC, MacKenzie KR ( 2007) Transmembrane domains of the syndecan family of growth factor coreceptors display a hierarchy of homotypic and heterotypic interactions. Proc Natl Acad Sci USA 104: 2078220787.
  • 71
    Li R, Gorelik R, Nanda V, Law PB, Lear JD, DeGrado WF, Bennett JS ( 2004) Dimerization of the transmembrane domain of integrin αIIb subunit in cell membranes. J Biol Chem 279: 2666626673.
  • 72
    Silverman BD ( 2003) Hydrophobicity of transmembrane proteins: spatially profiling the distribution. Protein Sci 12: 586599.
  • 73
    Joh NH, Min A, Faham S, Whitelegge JP, Yang D, Woods VL, Bowie JU ( 2008) Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins. Nature 453: 12661270.
  • 74
    Choma C, Gratkowski H, Lear JD, DeGrado WF ( 2000) Asparagine-mediated self-association of a model transmembrane helix. Nat Struct Biol 7: 161166.
  • 75
    North B, Cristian L, Stowell XF, Lear JD, Saven JG, deGrado WF ( 2006) Characterization of a membrane protein folding motif the Ser zipper, using designed peptides. J Mol Biol 359: 930939.
  • 76
    Adamian L, Liang J ( 2006) Prediction of transmembrane helix orientation in polytopic membrane proteins. BMC Struct Biol 6: 1320.
  • 77
    Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N ( 2004) An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J 87: 34483459.
  • 78
    Senes A, Ubarretxena-Belandia I, Engelman DM ( 2001) The Calpha —H···O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci USA 98: 90569061.
  • 79
    Yohannan S, Faham S, Yang D, Grosfeld D, Chamberlain AK, Bowie JU ( 2004) A C alpha-H···O hydrogen bond in a membrane protein is not stabilizing. J Am Chem Soc 126: 22842285.
  • 80
    Arbely E, Arkin IT ( 2004) Experimental measurement of the strength of alpha Ca[BOND]H···O bond in a lipid bilayer. J Am Chem Soc 126: 53625363.
  • 81
    Rosenbaum DM, Cherezov V, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Yao XJ, Weis WI, Stevens RC, Kobilka BK ( 2007) GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function. Science 318: 12661273.
  • 82
    Mottamal M, Lazaridis T ( 2005) The contribution of C alpha-H···O hydrogen bonds to membrane protein stability depends on the position of the amide. Biochemistry 44: 16071613.
  • 83
    Forrest LR, Tang CL, Honig B ( 2006) On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys J 91: 508517.
  • 84
    Adams PD, Arkin IT, Engelman DM, Brunger AT ( 1995) Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban. Nat Struct Biol 2: 154162.
  • 85
    Treutlein HR, Lemmon MA, Engelman DM, Brünger AT ( 1992) The glycophorin A transmembrane domain dimer: sequence-specific propensity for a right-handed supercoil of helices. Biochemistry 31: 1272612733.
  • 86
    Gottschalk KE, Kessler H ( 2004) A computational model of transmembrane integrin clustering. Structure 12: 11091116.
  • 87
    Freeman-Cook LL, Edwards AP, Dixon AM, Yates KE, Ely L, Engelman DM, Dimaio D ( 2005) Specific locations of hydrophilic amino acids in constructed transmembrane ligands of the platelet-derived growth factor beta receptor. J Mol Biol 345: 907921.
  • 88
    Kroch AE, Fleming KG ( 2006) Alternate interfaces may mediate homomeric and heteromeric assembly in the transmembrane domains of SNARE proteins. J Mol Biol 357: 184194.
  • 89
    Lin X, Tan SM, Law SKA, Torres J ( 2006) Unambiguous prediction of human integrin transmembrane heterodimer interactions using only homologous sequences. Proteins: Struct Funct Bioinformatics 65: 274279.
  • 90
    Cheung JC, Deber CM ( 2008) Misfolding of the cystic fibrosis transmembrane conductance regulator and disease. Biochemistry 47: 14651473.
  • 91
    Briggs JAG, Torres J, Arkin IT ( 2001) A new method to model membrane protein structure based on silent amino acid substitutions. Proteins: Struct Funct Genet 44: 370375.
  • 92
    Beevers AJ, Kukol A ( 2006) Systematic molecular dynamics searching in a lipid bilayer: application to the glycophorin A and oncogenic ErbB-2 transmembrane domains. J Mol Graph Model 25: 226233.
  • 93
    Kruger J, Fischer WB ( 2008) Exploring the conformational space of Vpu from HIV-1: a versatile adaptable protein. J Comput Chem 29: 24162424.
  • 94
    Lemmon MA, Flanagan JM, Hunt JF, Adair BD, Bormann B-J, Dempsey CE, Engelman DM ( 1992) Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices. J Biol Chem 267: 76837689.
  • 95
    Lemmon MA, Treutlein HR, Adams PD, Brünger AT, Engelman D ( 1994) A dimerization motif for transmembrane alpha-helices. Nat Struct Biol 1: 157163.
  • 96
    Russ WP, Engelman DM ( 1999) TOXCAT: a measure of transmembrane helix association in a biological membrane. Proc Natl Acad Sci USA 96: 863868.
  • 97
    Fisher LE, Engelman DM, Sturgis JN ( 1999) Detergents modulate dimerization but not helicity, of the glycophorin A transmembrane domain. J Mol Biol 293: 639651.
  • 98
    Adams PD, Engelman DM, Brünger AT ( 1996) Improved prediction for the structure of the dimeric transmembrane domain of glycophorin A obtained through global searching. Proteins 26: 257261.
  • 99
    Fleming KG, Ackerman AL, Engelman DM ( 1997) The effect of point mutations on the free energy of transmembrane alpha helix dimerization. J Mol Biol 272: 266275.
  • 100
    Brosig B, Langosch D ( 1998) The dimerization motif of the glycophorin A transmembrane segment in membranes: importance of glycine residues. Protein Sci 7: 10521056.
  • 101
    Fleming KG, Engelman DM ( 2001) Specificity in transmembrane helix-helix interactions can define a hierarchy of stability for sequence variants. Proc Natl Acad Sci USA 98: 1434014344.
  • 102
    Doura AK, Fleming KG ( 2004) Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer. J Mol Biol 343: 14871497.
  • 103
    Doura AK, Kobus FJ, Dubrovsky L, Hibbard E, Fleming KG ( 2004) Sequence context modulates the stability of a GxxxG-mediated transmembrane helix-helix dimer. J Mol Biol 341: 991998.
  • 104
    MacKenzie KR, Engelman DM ( 1998) Structure-based prediction of the stability of transmembrane helix-helix interactions: the sequence dependence of glycophorin A dimerization. Proc Natl Acad Sci USA 95: 35833590.
  • 105
    Russ WP, Engelman DM ( 2000) The GxxxG motif: a framework for transmembrane helix-helix association. J Mol Biol 296: 911919.
  • 106
    Senes A, Ubarretxena-Belandia I, Engelman DM ( 2001) The Ca[BOND]H···O hydrogen bond: a determinant of stability and specificity in transmembrane helix interactions. Proc Natl Acad Sci 98: 90569061.
  • 107
    Asundi VK, Carey DJ ( 1995) Self-association of N-syndecan (syndecan-3) core protein is mediated by a novel structural motif in the transmembrane domain and ectodomain flanking region. J Biol Chem 270: 2640426410.
  • 108
    Sulistijo ES, Jaszewski TM, MacKenzie KR ( 2003) Sequence-specific dimerization of the transmembrane domain of the “BH3-only” protein BNIP3 in membranes and detergent. J Biol Chem 278: 5195051956.
  • 109
    Chin CN, Sachs JN, Engelman DM ( 2005) Transmembrane homodimerization of receptor-like protein tyrosine phosphatases. FEBS Lett 579: 38553858.
  • 110
    Miyauchi K, Komano J, Yokomaku Y, Sugiura W, Yamamoto N, Matsuda Z ( 2005) Role of the specific amino acid sequence of the membrane-spanning domain of human immunodeficiency virus type 1 in membrane fusion. J Virol 79: 47204729.
  • 111
    Mendrola JM, Berger MB, King MC, Lemmon MA ( 2002) The single transmembrane domains of ErbB receptors self-associate in cell membranes. J Biol Chem 277: 47044712.
  • 112
    Schneider D, Engelman DM ( 2004) Involvement of transmembrane domain interactions in signal transduction by alpha/beta integrins. J Biol Chem 279: 98409846.
  • 113
    Gottschalk KE, Adams PD, Brunger AT, Kessler H ( 2002) Transmembrane signal transduction of the alpha(IIb)beta(3) integrin. Protein Sci 11: 18001812.
  • 114
    Wegener KL, Campbell ID ( 2008) Transmembrane and cytoplasmic domains in integrin activation and protein-protein interactions (Review). Mol Membr Biol 25: 376387.
  • 115
    Lin X, Tan SM, Law SKA, Torres J ( 2006) Two types of transmembrane homomeric interactions in the integrin receptor family are evolutionarily conserved. Proteins: Struct Funct Bioinformatics 63: 1623.
  • 116
    Gorman PM, Kim S, Guo M, Melnyk RA, McLaurin J, Fraser PE, Bowie JU, Chakrabartty A ( 2008) Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants. BMC Neurosci 9: 17.
  • 117
    Javadpour MM, Eilers M, Groesbeek M, Smith SO ( 1999) Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J 77: 16091618.
  • 118
    Eilers M, Shekar SC, Shieh T, Smith SO, Fleming PJ ( 2000) Internal packing of helical membrane proteins. Proc Natl Acad Sci USA 97: 57965801.
  • 119
    Adamian L, Liang J ( 2001) Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins. J Mol Biol 311: 891907.
  • 120
    Wigley WC, Corboy MJ, Cutler TD, Thibodeau PH, Oldan J, Lee MG, Rizo J, Hunt JF, Thomas PJ ( 2002) A protein sequence that can encode native structure by disfavoring alternate conformations. Nat Struct Biol 9: 381388.
  • 121
    Lear JD, Gratkowski H, Adamian L, Liang J, DeGrado WF ( 2003) Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles. Biochemistry 42: 64006407.
  • 122
    Roy R, Peplowska K, Rohde J, Ungermann C, Langosch D ( 2006) Role of the Vam3p transmembrane segment in homodimerization and SNARE complex formation. Biochemistry 45: 76547660.
  • 123
    Roy R, Laage R, Langosch D ( 2004) Synaptobrevin transmembrane domain dimerization—revisited. Biochemistry 43: 49644970.
  • 124
    Laage R, Rohde J, Brosig B, Langosch D ( 2000) A conserved membrane-spanning amino acid motif drives homomeric and supports heteromeric assembly of presynaptic SNARE proteins. J Biol Chem 275: 1748117487.
  • 125
    Huber O, Kemmler R, Langosch D ( 1999) Mutations affecting transmembrane segment interaction impair adhesiveness of E-cadherin. J Cell Sci 112: 44154423.
  • 126
    Kubatzky KF, Ruan W, Gurezka R, Cohen J, Ketteler R, Watowich SS, Neumann D, Langosch D, Klingmüller U ( 2001) Self-assembly of the transmembrane domain is a crucial mediator for signalling through the erythropoietin receptor. Curr Biol 11: 110115.
  • 127
    Constantinescu SN, Keren T, Socolovsky M, Nam HS, Henis YI, Lodish HF ( 2001) Ligand-independent oligomerization of cell-surface erythropoietin receptor is mediated by the transmembrane domain. Proc Natl Acad Sci USA 98: 43794384.
  • 128
    Ebie AZ, Fleming KG ( 2007) Dimerization of the erythropoietin receptor transmembrane domain in micelles. J Mol Biol 366: 517524.
  • 129
    Volkmer T, Becker C, Prodöhl A, Finger C, Schneider D ( 2006) Assembly of a transmembrane b-type cytochrome is mainly driven by transmembrane helix interactions. Biochim Biophys Acta 1758: 18151822.
  • 130
    Gurezka R, Langosch D ( 2001) In vitro selection of membrane-spanning leucine zipper protein-protein interaction motifs using POSSYCCAT. J Biol Chem 276: 4558045587.
  • 131
    Lindner E, Langosch D ( 2006) A ToxR-based dominant-negative system to investigate heterotypic transmembrane domain interactions. Proteins: Struct Funct Bioinformatics 65: 803807.
  • 132
    Yin H, Slusky JS, Berger BW, Walters RS, Vilaire G, Litvinov RI, Lear JD, Caputo GA, Bennett JS, DeGrado WF ( 2007) Computational design of peptides that target transmembrane helices. Science 315: 18171822.
  • 133
    Arkin IT, Brünger AT ( 1998) Statistical analysis of predicted transmembrane alpha-helices. Biochim Biophys Acta 1429: 113128.
  • 134
    Senes A, Gerstein M, Engelman DM ( 2000) Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with β-branched residues at neighboring positions. J Mol Biol 296: 921936.
  • 135
    Weigang LMM, Langosch D, Letzel L ( 2008) Gas-phase behavior of noncovalent transmembrane segment complexes. Rapid Commun Mass Spectrom 22: 40894097.
  • 136
    Brandl M, Weiss MS, Jabs A, Sühnel J, Hilgenfeld R ( 2001) C[BOND]H···π-interactions in proteins. J Mol Biol 307: 357377.
  • 137
    Ridder A, Skupjen P, Unterreitmeier S, Langosch D ( 2005) Tryptophan supports interaction of transmembrane helices. J Mol Biol 354: 894902.
  • 138
    Sal-Man N, Gerber D, Bloch I, Shai Y ( 2007) Specificity in transmembrane helix-helix interactions mediated by aromatic residues. J Biol Chem 282: 1975319761.
  • 139
    Johnson RM, Hecht K, Deber CM ( 2007) Aromatic and cation-pi interactions enhance helix-helix association in a membrane environment. Biochemistry 46: 92089214.
  • 140
    Hong HD, Park S, Jimenez RHF, Rinehart D, Tamm LK ( 2007) Role of aromatic side chains in the folding and thermodynamic stability of integral membrane proteins. J Am Chem Soc 129: 83208327.
  • 141
    Melnyk RA, Deber CM ( 2005) Ala and Ser substitutions in the Gly-xxx-Gly motif: relative affinities of the glycophorin A and M13 coat protein transmembrane segment dimers. Biophys J 88: 49A.
  • 142
    Melnyk RA, Kim S, Curran AR, Engelman DM, Bowie JU, Deber CM ( 2004) The affinity of GXXXG motifs in transmembrane helix-helix interactions is modulated by long-range communication. J Biol Chem 279: 1659116597.
  • 143
    Zhang YP, Lewis RN, Hodges RS, McElhaney RN ( 2001) Peptide models of the helical hydrophobic transmembrane segments of membrane proteins: interactions of acetyl-K2-(LA)12-K2-amide with phosphatidylethanolamine bilayer membranes. Biochemistry 40: 474482.
  • 144
    Dawson JP, Melnyk RA, Deber CM, Engelman DM ( 2003) Sequence context strongly modulates association of polar residues in transmembrane helices. J Mol Biol 331: 255262.
  • 145
    Weiner DB, Liu J, Cohen JA, Williams WV, Greene MI ( 1989) A point mutation in the neu oncogene mimics ligand induction of receptor aggregation. Nature 339: 230231.
  • 146
    Smith SO, Smith CS, Bormann BJ ( 1996) Strong hydrogen bonding interactions involving a buried glutamic acid in the transmembrane sequence of the neu/erbB-2 receptor. Nat Struct Biol 3: 252258.
  • 147
    Onishi M, Mui ALF, Morikawa Y, Cho L, Kinoshita S, Nolan GP, Gorman DM, Miyajima A, Kitamura T ( 1996) Identification of an oncogenic form of the thrombopoietin receptor MPL using retrovirus-mediated gene transfer. Blood 88: 13991406.
  • 148
    Forbes LV, Gale RE, Pizzey A, Pouwels K, Nathwani A, Linch DC ( 2002) An activating mutation in the transmembrane domain of the granulocyte colony-stimulating factor receptor in patients with acute myeloid leukemia. Oncogene 21: 59815989.
  • 149
    Li E, Hristova K ( 2006) Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies. Biochemistry 45: 62416251.
  • 150
    You M, Li E, Hristova K ( 2006) The achondroplasia mutation does not alter the dimerization energetics of the fibroblast growth factor receptor 3 transmembrane domain. Biochemistry 45: 55515556.
  • 151
    Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Trong LT, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M ( 2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289: 739744.
  • 152
    Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP ( 2008) Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454: 183187.
  • 153
    Wang W, Black SS, Edwards MD, Miller S, Morrison EL, Bartlett W, Dong C, Naismith JH, Booth IR ( 2008) The structure of an open form of an E. coli mechanosensitive channel at 3.45 A resolution. Science 321: 11791183.
  • 154
    Luo BH, Springer TA ( 2006) Integrin structures and conformational signaling. Curr Opin Cell Biol 18: 579586.
  • 155
    Gottschalk K-E, Kessler H ( 2002) The structures of integrins and integrin-ligand complexes: implications for drug design and signal transduction. Angew Chem Int Ed Engl 41: 37673774.
  • 156
    Gottschalk KE, Kessler H ( 2004) Evidence for hetero-association of transmembrane helices of integrins. FEBS Lett 557: 253258.
  • 157
    Lau TL, Kim C, Ginsberg MH, Ulmer TS ( 2009) The structure of the integrin alphaIIbbeta3 transmembrane complex explains integrin transmembrane signalling. EMBO J 28: 13511361.
  • 158
    Li R, Bennett JS, DeGrado WF ( 2004) Structural basis for integrin alpha IIb beta 3 clustering. Biochem Soc Trans 32: 412415.
  • 159
    Caputo GA, Litvinov RI, Li W, Bennett JS, DeGrado WF, Yin H ( 2008) Computationally designed peptide inhibitors of protein-protein interactions in membranes. Biochemistry 47: 86008606.
  • 160
    Seubert N, Royer Y, Staerk J, Kubatzky KF, Moucadel V, Krishnakumar S, Smith SO, Constantinescu SN ( 2003) Active and inactive orientations of the transmembrane and cytosolic domains of the erythropoietin receptor dimer. Mol Cell 12: 12391250.
  • 161
    Moriki T, Maruyama H, Maruyama IN ( 2001) Activation of preformed EGF receptor dimers by ligand-induced rotation of the transmembrane domain. J Mol Biol 311: 10111026.
  • 162
    Brown RJ, Adams JJ, Pelekanos RA, Wan Y, McKinstry WJ, Palethorpe K, Seeber RM, Monks TA, Eidne KA, Parker MW, Waters MJ ( 2005) Model for growth hormone receptor activation based on subunit rotation within a receptor dimer. Nat Struct Mol Biol 12: 814821.
  • 163
    Nakamura T, Miyakawa Y, Miyamura A, Yamane A, Suzuki H, Ito M, Ohnishi Y, Ishiwata N, Ikeda Y, Tsuruzoe N ( 2006) A novel nonpeptidyl human c-Mpl activator stimulates human megakaryopoiesis and thrombopoiesis. Blood 107: 43004307.
  • 164
    Kim MJ, Park SH, Opella SJ, Marsilje TH, Michellys PY, Seidel HM, Tian SS ( 2007) NMR structural studies of interactions of a small, nonpeptidyl Tpo mimic with the thrombopoietin receptor extracellular juxtamembrane and transmembrane domains. J Biol Chem 282: 1425314261.
  • 165
    Fleishman SJ, Schlessinger J, Ben-Tal N ( 2002) A putative molecular-activation switch in the transmembrane domain of erbB2. Proc Natl Acad Sci USA 99: 1593715940.
  • 166
    Holsinger LJ, Nichani D, Pinto LH, Lamb RA ( 1994) Influenza-a virus M(2) ion-channel protein—a structure-function analysis. J Virol 68: 15511563.
  • 167
    Pinto LH, Dieckmann GR, Gandhi CS, Papworth CG, Braman J, Shaughnessy MA, Lear JD, Lamb RA, DeGrado WF ( 1997) A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity. Proc Natl Acad Sci USA 94: 1130111306.
  • 168
    Bauer CM, Pinto LH, Cross TA, Lamb RA ( 1999) The influenza virus M2 ion channel protein: probing the structure of the transmembrane domain in intact cells by using engineered disulfide cross-linking. Virology 254: 196209.
  • 169
    Dieckmann GR, DeGrado WF ( 1997) Modeling transmembrane helical oligomers. Curr Opin Struct Biol 7: 486494.
  • 170
    Khurana E, Dal Peraro M, DeVane R, Vemparala S, DeGrado WF, Klein ML ( 2009) Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proc Natl Acad Sci USA 106: 10691074.
  • 171
    Manor J, Mukherjee P, Lin Y, Leononv H, Skinner JL, Zanni MT, Arkin IT ( 2009) Gating mechanism of the influenza A M2 channel revealed by 1 and 2D-IR spectroscopies. Structure 17: 247254.
  • 172
    Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX ( 2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454: 486491.
  • 173
    Rasmussen SGF, Choi H-J, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VRP, Sanishvili R, Fischetti RF, Schertler GFX, Weis WI, Kobilka BK ( 2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450: 383388.
  • 174
    Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Kuhn P, Weis WI, Kobilka BK, Stevens RC ( 2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318: 12581265.
  • 175
    Gether U, Lin S, Ghanouni P, Ballesteros JA, Weinstein H, Kobilka BK ( 1997) Agonists induce conformational changes in transmembrane domains III and VI of the β2 adrenoreceptor. EMBO J 16: 67376747.
  • 176
    Miura S, Zhang JL, Boros J, Karnik SS ( 2003) TM2-TM7 interaction in coupling movement of transmembrane helices to activation of the angiotensin II type-1 receptor. J Biol Chem 278: 37203725.
  • 177
    Vásquez V, Sotomayor M, Cordero-Morales J, Schulten K, Perozo E ( 2008) A structural mechanism for MscS gating in lipid bilayers. Science 321: 12101214.
  • 178
    Klingenberg M ( 2005) Ligand-protein interaction in biomembrane carriers. The induced transition fit of transport catalysis. Biochemistry 44: 85638570.
  • 179
    Faham S, Watanabe A, Besserer GM, Cascio D, Specht A, Hirayama BA, Wright EM, Abramson J ( 2008) The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport. Science 321: 810814.
  • 180
    Long SB, Tao X, Campbell EB, MacKinnon R ( 2007) Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature 450: 376383.
  • 181
    Bocquet N, Nury H, Baaden M, Poupon LC, Changeux J-P, Delarue M, Corringer P-J ( 2009) X-ray structure of a pentameric ligand, gated ion channel in an apparently open conformation. Nature 457: 111114.
  • 182
    Pebay-Peyroula E, Rosenbusch JP ( 2001) High-resolution structures and dynamics of membrane protein–lipid complexes: a critique. Curr Opin Struct Biol 11: 427432.
  • 183
    Fyfe PK, McAuley KE, Roszak AW, Isaacs NW, Cogdell RJ, Jones MR ( 2001) Probing the interface between membrane proteins and membrane lipids by X-ray crystallography. Trends Biochem Sci 26: 106112.
  • 184
    Lee AG ( 2003) Lipid-protein interactions in biological membranes: a structural perspective. Biochim Biophys Acta 1612: 140.
  • 185
    Nyholm TKM, Ozdirekcan S, Killian JA ( 2007) How protein transmembrane segments sense the lipid environment. Biochemistry 46: 14571465.
  • 186
    Killian JA, Nyholm TKM ( 2006) Peptides in lipid bilayers: the power of simple models. Curr Opin Struct Biol 16: 473479.
  • 187
    Veglia G, Zeri AC, Ma C, Opella SJ ( 2002) Deuterium/hydrogen exchange factors measured by solution nuclear magnetic resonance spectroscopy as indicators of the structure and topology of membrane proteins. Biophys J 82: 21762183.
  • 188
    Arkin IT, Russ WP, Lebendiker M, Schuldiner S ( 1996) Determining the secondary structure and orientation of EmrE, a multi-drug transporter, indicates a transmembrane four-helix bundle. Biochemistry 35: 72337238.
  • 189
    Kukol A, Arkin IT ( 1999) vpu transmembrane peptide structure obtained by site-specific Fourier transform infrared dichroism and global molecular dynamics searching. Biophys J 77: 15941601.
  • 190
    Sharpe S, Yau WM, Tycko R ( 2006) Structure and dynamics of the HIV-1 Vpu transmembrane domain revealed by solid-state NMR with magic-angle spinning. Biochemistry 45: 918933.
  • 191
    Beevers AJ, Kukol A ( 2006) Secondary structure, orientation, and oligomerization of phospholemman, a cardiac transmembrane protein. Protein Sci 15: 11271132.
  • 192
    le Coutre J, Kaback HR, Patel CKN, Heginbotham L, Miller C ( 1998) Fourier transform infrared spectroscopy reveals a rigid alpha-helical assembly for the tetrameric Streptomyces lividans K+ channel. Proc Natl Acad Sci USA 95: 61146117.
  • 193
    Demmers JA, Haverkamp J, Heck AJ, Koeppe REII, Killian JA ( 2000) Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers. Proc Natl Acad Sci USA 97: 31893194.
  • 194
    Demmers JA, van Duijn E, Haverkamp J, Greathouse DV, Koeppe RE,II, Heck AJ, Killian JA ( 2001) Interfacial positioning and stability of transmembrane peptides in lipid bilayers studied by combining hydrogen/deuterium exchange and mass spectrometry. J Biol Chem 276: 3450134508.
  • 195
    Tatulian SA, Tamm LK ( 2000) Secondary structure, orientation, oligomerization, and lipid interactions of the transmembrane domain of influenza hemagglutinin. Biochemistry 39: 496507.
  • 196
    Abramson J, Kaback HR, Iwata S ( 2004) Structural comparison of lactose permease and the glycerol-3-phosphate antiporter: members of the major facilitator superfamily. Curr Opin Struct Biol 14: 413419.
  • 197
    Hansen RK, Broadhurst RW, Skelton PC, Arkin IT ( 2002) Hydrogen/deuterium exchange of hydrophobic peptides in model membranes by electrospray ionization mass spectrometry. J Am Soc Mass Spectrom 13: 13761387.
  • 198
    Tian CL, Gao PF, Pinto LH, Lamb RA, Cross TA ( 2003) Initial structural and dynamic characterization of the M2 protein transmembrane and amphipathic helices in lipid bilayers. Protein Sci 12: 25972605.
  • 199
    Mukherjee P, Kass I, Arkin IT, Zanni MT ( 2006) Structural disorder of the CD3 xi transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations. J Phys Chem B 110: 2474024749.
  • 200
    Fersht A ( 2006) Structure and mechanism in protein science. New York: Freeman.
  • 201
    Doig AJ, Errington N, Iqbalsyah TM, Stability and design of alpha-helices. In: BuchnerK, Ed. ( 2005) Handbook of protein folding. Wiley: Weinheim, pp 247313.
  • 202
    Blaber M, Zhang X, Matthews BW ( 1993) Structural basis for amino acid alpha helix propensity. Science 260: 16371640.
  • 203
    Blaber M, Zhang XJ, Lindstrom JD, Pepiot SD, Baase WA, Matthews BW ( 1994) Determination of alpha-helix propensity within the context of a folded protein—sites 44 and 131 in bacteriophage T4 lysozyme. J Mol Biol 235: 600624.
  • 204
    Creamer TP, Rose GD ( 1992) Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. Proc Natl Acad Sci USA 89: 59375941.
  • 205
    Chellgren BW, Creamer TP ( 2006) Side-chain entropy effects on protein secondary structure formation. Proteins: Struct Funct Bioinformatics 62: 411420.
  • 206
    Li SC, Deber CM ( 1992) Glycine and beta-branched residues support and modulate peptide helicity in membrane environments. FEBS Lett 311: 217220.
  • 207
    Li SC, Deber CM ( 1994) A measure of helical propensity for amino acids in membrane environments. Nat Struct Biol 1: 368373.
  • 208
    Langosch D, Crane JM, Brosig B, Hellwig A, Tamm LK, Reed J ( 2001) Peptide mimics of SNARE transmembrane segments drive membrane fusion depending on their conformational plasticity. J Mol Biol 311: 709721.
  • 209
    Cleverley DZ, Lenard J ( 1998) The transmembrane domain in viral fusion: essential role for a conserved glycine residue in vesicular stomatitis virus G protein. Proc Natl Acad Sci USA 95: 34253430.
  • 210
    Odell D, Wanas E, Yan J, Ghosh HP ( 1997) Influence of membrane anchoring and cytoplasmic domains on the fusogenic activity of vesicular stomatitis virus glycoprotein G. J Virol 71: 79968000.
  • 211
    Armstrong RT, Kushnir AS, White JM ( 2000) The transmembrane domain of influenza hemagglutinin exhibits a stringent length requirement to support the hemifusion to fusion transition. J Cell Biol 151: 425437.
  • 212
    Giraudo CG, Hu C, You DQ, Slovic AM, Mosharov EV, Sulzer D, Melia TJ, Rothman JE ( 2005) SNAREs can promote complete fusion and hemifusion as alternative outcomes. J Cell Biol 170: 249260.
  • 213
    Langosch D, Hofmann MW, Ungermann C ( 2007) The role of transmembrane domains in membrane fusion. Cell Mol Life Sci 64: 850864.
  • 214
    Hofmann MW, Peplowska K, Rohde J, Poschner B, Ungermann C, Langosch D ( 2006) Self-interaction of a SNARE transmembrane domain promotes the hemifusion-to-fusion transition in lipid mixing. J Mol Biol 364: 10481060.
  • 215
    Weber T, Zemelman BV, McNew JA, Westermann B, Gmachl M, Parlati F, Söllner TH, Rothman JE ( 1998) SNAREpins: minimal machinery for membrane fusion. Cell 92: 759772.
  • 216
    Schuette CG, Hatsuzawa K, Margittai M, Stein A, Riedel D, Küster P, König M, Seidel C, Jahn R ( 2004) Determinants of liposome fusion mediated by synaptic SNARE proteins. Proc Natl Acad Sci USA 101: 28582863.
  • 217
    Hofmann MW, Weise K, Ollesch J, Agrawal A, Stalz H, Stelzer W, Hulsbergen F, deGroot H, Gerwert K, Reed J, Langosch D ( 2004) De novo design of conformationally flexible transmembrane peptides driving membrane fusion. Proc Natl Acad Sci USA 101: 1477614781.
  • 218
    Hofmann MW, Poschner BC, Hauser S, Langosch D ( 2007) pH-activated fusogenic transmembrane LV-peptides. Biochemistry 46: 42044209.
  • 219
    Agrawal P, Kiihne S, Hollander J, Hulsbergen F, Hofmann M, Langosch D, de Groot H ( 2007) Solid state NMR investigation of the interaction between biomimetic lipid bilayers and de novo designed fusogenic peptides. ChemBiochem 8: 493496.