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  • 1
    Hediger MA, Romero MF, Peng JB, Rolfs A, Takanaga H, Bruford EA ( 2004) The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins—Introduction. Pflugers Arch 447: 465468.
  • 2
    Povey S, Lovering R, Bruford E, Wright M, Lush M, Wain H ( 2001) The HUGO Gene Nomenclature Committee (HGNC). Hum Genet 109: 678680.
  • 3
    Saier MH, Jr ( 2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 64: 354411.
  • 4
    Saier MH, Jr, Yen MR, Noto K, Tamang DG, Elkan C ( 2009) The Transporter Classification Database: recent advances. Nucl Acids Res 37: D274D278.
  • 5
    Fredriksson R, Nordstrom KJ, Stephansson O, Hagglund MG, Schioth HB ( 2008) The solute carrier (SLC) complement of the human genome: phylogenetic classification reveals four major families. FEBS Lett 582: 38113816.
  • 6
    Pebay-Peyroula E, Dahout-Gonzalez C, Kahn R, Trezeguet V, Lauquin GJ, Brandolin G ( 2003) Structure of mitochondrial ADP/ATP carrier in complex with carboxyatractyloside. Nature 426: 3944.
  • 7
    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.
  • 8
    Yamashita A, Singh SK, Kawate T, Jin Y, Gouaux E ( 2005) Crystal structure of a bacterial homologue of Na+/Cl—dependent neurotransmitter transporters. Nature 437: 215223.
  • 9
    Gether U, Andersen PH, Larsson OM, Schousboe A ( 2006) Neurotransmitter transporters: molecular function of important drug targets. Trends Pharmacol Sci 27: 375383.
  • 10
    Krishnamurthy H, Piscitelli CL, Gouaux E ( 2009) Unlocking the molecular secrets of sodium-coupled transporters. Nature 459: 347355.
  • 11
    Gao X, Lu F, Zhou L, Dang S, Sun L, Li X, Wang J, Shi Y ( 2009) Structure and mechanism of an amino acid antiporter. Science 324: 15651568.
  • 12
    Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, Miller C ( 2009) Structure of a prokaryotic virtual proton pump at 3.2 A resolution. Nature 460: 10401043.
  • 13
    Shaffer PL, Goehring A, Shankaranarayanan A, Gouaux E ( 2009) Structure and mechanism of a Na+-independent amino acid transporter. Science 325: 10101014.
  • 14
    Ressl S, Terwisscha van Scheltinga AC, Vonrhein C, Ott V, Ziegler C ( 2009) Molecular basis of transport and regulation in the Na(+)/betaine symporter BetP. Nature 458: 4752.
  • 15
    Yernool D, Boudker O, Jin Y, Gouaux E ( 2004) Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature 431: 811818.
  • 16
    Huang Y, Lemieux MJ, Song J, Auer M, Wang DN ( 2003) Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301: 616620.
  • 17
    Mirza O, Guan L, Verner G, Iwata S, Kaback HR ( 2006) Structural evidence for induced fit and a mechanism for sugar/H+ symport in LacY. EMBO J 25: 11771183.
  • 18
    Yin Y, He X, Szewczyk P, Nguyen T, Chang G ( 2006) Structure of the multidrug transporter EmrD from Escherichia coli. Science 312: 741744.
  • 19
    Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, Iwata S ( 2003) Structure and mechanism of the lactose permease of Escherichia coli. Science 301: 610615.
  • 20
    Abramson J, Iwata S, Kaback HR ( 2004) Lactose permease as a paradigm for membrane transport proteins (Review). Mol Membr Biol 21: 227236.
  • 21
    Guan L, Kaback HR ( 2006) Lessons from lactose permease. Annu Rev Biophys Biomol Struct 35: 6791.
  • 22
    Karpowich NK, Wang DN ( 2008) Structural biology: symmetric transporters for asymmetric transport. Science 321: 781782.
  • 23
    Forrest LR, Zhang YW, Jacobs MT, Gesmonde J, Xie L, Honig BH, Rudnick G ( 2008) Mechanism for alternating access in neurotransmitter transporters. Proc Natl Acad Sci USA 105: 1033810343.
  • 24
    Weyand S, Shimamura T, Yajima S, Suzuki S, Mirza O, Krusong K, Carpenter EP, Rutherford NG, Hadden JM, O'Reilly J, Ma P, Saidijam M, Patching SG, Hope RJ, Norbertczak HT, Roach PC, Iwata S, Henderson PJ, Cameron AD ( 2008) Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter. Science 322: 709713.
  • 25
    Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI ( 2006) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623625.
  • 26
    Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A ( 2009) Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel 22: 569574.
  • 27
    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ ( 1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 33893402.
  • 28
    Abramson J, Wright EM ( 2009) Structure and function of Na(+)-symporters with inverted repeats. Curr Opin Struct Biol 19: 425432.
  • 29
    Murzin AG, Brenner SE, Hubbard T, Chothia C ( 1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536540.
  • 30
    Blakely RD, DeFelice LJ ( 2007) All aglow about presynaptic receptor regulation of neurotransmitter transporters. Mol Pharmacol 71: 12061208.
  • 31
    Chen NH, Reith ME, Quick MW ( 2004) Synaptic uptake and beyond: the sodium- and chloride-dependent neurotransmitter transporter family SLC6. Pflugers Arch 447: 519531.
  • 32
    Manji HK, Drevets WC, Charney DS ( 2001) The cellular neurobiology of depression. Nat Med 7: 541547.
  • 33
    Nestler EJ, Barrot M, DiLeone RJ, Eisch AJ, Gold SJ, Monteggia LM ( 2002) Neurobiology of depression. Neuron 34: 1325.
  • 34
    Leabman MK, Huang CC, DeYoung J, Carlson EJ, Taylor TR, de la Cruz M, Johns SJ, Stryke D, Kawamoto M, Urban TJ, Kroetz DL, Ferrin TE, Clark AG, Risch N, Herskowitz I, Giacomini KM; Pharmacogenetics of Membrane Transporters Investigators ( 2003) Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc Natl Acad Sci USA 100: 58965901.
  • 35
    Koepsell H, Schmitt BM, Gorboulev V ( 2003) Organic cation transporters. Rev Physiol Biochem Pharmacol 150: 3690.
  • 36
    Shu Y, Brown C, Castro RA, Shi RJ, Lin ET, Owen RP, Sheardown SA, Yue L, Burchard EG, Brett CM, Giacomini KM ( 2008) Effect of genetic variation in the organic cation transporter 1, OCT1, on metformin pharmacokinetics. Clin Pharmacol Ther 83: 273280.
  • 37
    Shu Y, Sheardown SA, Brown C, Owen RP, Zhang S, Castro RA, Ianculescu AG, Yue L, Lo JC, Burchard EG, Brett CM, Giacomini KM ( 2007) Effect of genetic variation in the organic cation transporter 1 (OCT1) on metformin action. J Clin Invest 117: 14221431.
  • 38
    Shu Y, Leabman MK, Feng B, Mangravite LM, Huang CC, Stryke D, Kawamoto M, Johns SJ, DeYoung J, Carlson E, Ferrin TE, Herskowitz I, Giacomini KM; Pharmacogenetics of Membrane Transporters Investigators ( 2003) Evolutionary conservation predicts function of variants of the human organic cation transporter, OCT1. Proc Natl Acad Sci USA 100: 59025907.
  • 39
    Dresser MJ, Gray AT, Giacomini KM ( 2000) Kinetic and selectivity differences between rodent, rabbit, and human organic cation transporters (OCT1). J Pharmacol Exp Ther 292: 11461152.
  • 40
    Hilgemann DW, Lu CC ( 1999) GAT1 (GABA:Na+:Cl) cotransport function. Database reconstruction with an alternating access model. J Gen Physiol 114: 459475.
  • 41
    Jardetzky O ( 1966) Simple allosteric model for membrane pumps. Nature 211: 969970.
  • 42
    Singh SK, Piscitelli CL, Yamashita A, Gouaux E ( 2008) A competitive inhibitor traps LeuT in an open-to-out conformation. Science 322: 16551661.
  • 43
    Andersen J, Kristensen AS, Bang-Andersen B, Stromgaard K ( 2009) Recent advances in the understanding of the interaction of antidepressant drugs with serotonin and norepinephrine transporters. Chem Commun (Camb) 25: 36773692.
  • 44
    Singh SK, Yamashita A, Gouaux E ( 2007) Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature 448: 952956.
  • 45
    Zhou Z, Zhen J, Karpowich NK, Goetz RM, Law CJ, Reith ME, Wang DN ( 2007) LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake. Science 317: 13901393.
  • 46
    Shi L, Quick M, Zhao Y, Weinstein H, Javitch JA ( 2008) The mechanism of a neurotransmitter:sodium symporter—inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell 30: 667677.
  • 47
    Quick M, Winther AM, Shi L, Nissen P, Weinstein H, Javitch JA ( 2009) Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci USA 106: 55635568.
  • 48
    Chothia C, Lesk AM ( 1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823826.
  • 49
    Sander C, Schneider R ( 1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 5668.
  • 50
    Brenner SE, Chothia C, Hubbard TJ ( 1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 95: 60736078.
  • 51
    Rost B ( 1999) Twilight zone of protein sequence alignments. Protein Eng 12: 8594.
  • 52
    Atkinson HJ, Morris JH, Ferrin TE, Babbitt PC ( 2009) Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. PLoS ONE 4: e4345.
  • 53
    The UniProt Consortium ( 2008) The universal protein resource (UniProt). Nucl Acids Res 36: D190D195.
  • 54
    Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW ( 2010) GenBank. Nucl Acids Res D4651.
  • 55
    Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T ( 2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 24982504.
  • 56
    Palacin M, Kanai Y ( 2004) The ancillary proteins of HATs: SLC3 family of amino acid transporters. Pflugers Arch 447: 490494.
  • 57
    Manolescu AR, Augustin R, Moley K, Cheeseman C ( 2007) A highly conserved hydrophobic motif in the exofacial vestibule of fructose transporting SLC2A proteins acts as a critical determinant of their substrate selectivity. Mol Membr Biol 24: 455463.
  • 58
    Vitart V, Rudan I, Hayward C, Gray NK, Floyd J, Palmer CN, Knott SA, Kolcic I, Polasek O, Graessler J, et al. ( 2008) SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout. Nat Genet 40: 437442.
  • 59
    Caulfield MJ, Munroe PB, O'Neill D, Witkowska K, Charchar FJ, Doblado M, Evans S, Eyheramendy S, Onipinla A, Howard P, Shaw-Hawkins S, Dobson RJ, Wallace C, Newhouse SJ, Brown M, Connell JM, Dominiczak A, Farrall M, Lathrop GM, Samani NJ, Kumari M, Marmot M, Brunner E, Chambers J, Elliott P, Kooner J, Laan M, Org E, Veldre G, Viigimaa M, Cappuccio FP, Ji C, Iacone R, Strazzullo P, Moley KH, Cheeseman C ( 2008) SLC2A9 is a high-capacity urate transporter in humans. PLoS Med 5: e197.
  • 60
    Uldry M, Thorens B ( 2004) The SLC2 family of facilitated hexose and polyol transporters. Pflugers Arch 447: 480489.
  • 61
    Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, Ophir R, Bar-Even A, Horn-Saban S, Safran M, Domany E, Lancet D, Shmueli O ( 2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650659.
  • 62
    Theissen G ( 2002) Secret life of genes. Nature 415: 741.
  • 63
    Jeffery CJ ( 2003) Moonlighting proteins: old proteins learning new tricks. Trends Genet 19: 415417.
  • 64
    Hegyi H, Gerstein M ( 2001) Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. Genome Res 11: 16321640.
  • 65
    Ofran Y, Punta M, Schneider R, Rost B ( 2005) Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discov Today 10: 14751482.
  • 66
    Rost B ( 2002) Enzyme function less conserved than anticipated. J Mol Biol 318: 595608.
  • 67
    Hubbard TJ, Aken BL, Ayling S, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Clarke L, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Holland R, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Rios D, Schuster M, Slater G, Smedley D, Spooner W, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wilder S, Zadissa A, Birney E, Cunningham F, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Kasprzyk A, Proctor G, Smith J, Searle S, Flicek P ( 2009) Ensembl 2009. Nucl Acids Res 37: D690D697.
  • 68
    Krogh A ( 2008) What are artificial neural networks? Nat Biotechnol 26: 195197.
  • 69
    Jacobsson JA, Haitina T, Lindblom J, Fredriksson R ( 2007) Identification of six putative human transporters with structural similarity to the drug transporter SLC22 family. Genomics 90: 595609.
  • 70
    Bailey TL, Williams N, Misleh C, Li WW ( 2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucl Acids Res 34: W369W373.
  • 71
    Bashton M, Chothia C ( 2007) The generation of new protein functions by the combination of domains. Structure 15: 8599.
  • 72
    Kasho VN, Smirnova IN, Kaback HR ( 2006) Sequence alignment and homology threading reveals prokaryotic and eukaryotic proteins similar to lactose permease. J Mol Biol 358: 10601070.
  • 73
    Vadyvaloo V, Smirnova IN, Kasho VN, Kaback HR ( 2006) Conservation of residues involved in sugar/H(+) symport by the sucrose permease of Escherichia coli relative to lactose permease. J Mol Biol 358: 10511059.
  • 74
    Sorgen PL, Hu Y, Guan L, Kaback HR, Girvin ME ( 2002) An approach to membrane protein structure without crystals. Proc Natl Acad Sci USA 99: 1403714040.
  • 75
    Eisen JA ( 1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163167.
  • 76
    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.
  • 77
    Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, III, Miercke LJ, Giacomini KM, Sali A, Stroud RM ( 2009) Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 385: 820830.
  • 78
    Punta M, Forrest LR, Bigelow H, Kernytsky A, Liu J, Rost B ( 2007) Membrane protein prediction methods. Methods 41: 460474.
  • 79
    Kelly L, Karchin R, Sali A ( 2007) Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput 5163.
  • 80
    Feng B, Dresser MJ, Shu Y, Johns SJ, Giacomini KM ( 2001) Arginine 454 and lysine 370 are essential for the anion specificity of the organic anion transporter, rOAT3. Biochemistry 40: 55115520.
  • 81
    Zhang S, Lovejoy KS, Shima JE, Lagpacan LL, Shu Y, Lapuk A, Chen Y, Komori T, Gray JW, Chen X, Lippard SJ, Giacomini KM ( 2006) Organic cation transporters are determinants of oxaliplatin cytotoxicity. Cancer Res 66: 88478857.
  • 82
    Ahlin G, Karlsson J, Pedersen JM, Gustavsson L, Larsson R, Matsson P, Norinder U, Bergstrom CA, Artursson P ( 2008) Structural requirements for drug inhibition of the liver specific human organic cation transport protein 1. J Med Chem 51: 59325942.
  • 83
    Blundell TL, Sibanda BL, Montalvao RW, Brewerton S, Chelliah V, Worth CL, Harmer NJ, Davies O, Burke D ( 2006) Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Philos Trans R Soc Lond B Biol Sci 361: 413423.
  • 84
    Shoichet BK ( 2004) Virtual screening of chemical libraries. Nature 432: 862865.
  • 85
    Kitchen DB, Decornez H, Furr JR, Bajorath J ( 2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3: 935949.
  • 86
    Sanchez R, Sali A ( 1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 95: 1359713602.
  • 87
    Koehl P, Levitt M ( 1999) A brighter future for protein structure prediction. Nat Struct Biol 6: 108111.
  • 88
    Baker D, Sali A ( 2001) Protein structure prediction and structural genomics. Science 294: 9396.
  • 89
    Landau M, Herz K, Padan E, Ben-Tal N ( 2007) Model structure of the Na+/H+ exchanger 1 (NHE1): functional and clinical implications. J Biol Chem 282: 3785437863.
  • 90
    Forrest LR, Tavoulari S, Zhang YW, Rudnick G, Honig B ( 2007) Identification of a chloride ion binding site in Na+/Cl dependent transporters. Proc Natl Acad Sci USA 104: 1276112766.
  • 91
    Celik L, Sinning S, Severinsen K, Hansen CG, Moller MS, Bols M, Wiborg O, Schiott B ( 2008) Binding of serotonin to the human serotonin transporter. Molecular modeling and experimental validation. J Am Chem Soc 130: 38533865.
  • 92
    Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, Gether U, Loland CJ ( 2008) The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci 11: 780789.
  • 93
    Beuming T, Shi L, Javitch JA, Weinstein H ( 2006) A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Mol Pharmacol 70: 16301642.
  • 94
    Macarron R ( 2006) Critical review of the role of HTS in drug discovery. Drug Discov Today 11: 277279.
  • 95
    Enright AJ, van Dongen S, Ouzounis CA ( 2002) An efficient algorithm for large-scale detection of protein families. Nucl Acids Res 30: 15751584.
  • 96
    Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA ( 2001) Database resources of the National Center for Biotechnology Information. Nucl Acids Res 29: 1116.
  • 97
    Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB ( 2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA 101: 60626067.
  • 98
    Sonnhammer EL, von Heijne G, Krogh A ( 1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6: 175182.
  • 99
    Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A ( 2009) A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics 10: 269280.
  • 100
    Sali A, Blundell TL ( 1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779815.
  • 101
    Pearson WR ( 1998) Empirical statistical estimates for sequence similarity searches. J Mol Biol 276: 7184.
  • 102
    Edgar RC ( 2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32: 17921797.
  • 103
    Retief JD ( 2000) Phylogenetic analysis using PHYLIP. Methods Mol Biol 132: 243258.
  • 104
    Clamp M, Cuff J, Searle SM, Barton GJ ( 2004) The Jalview Java alignment editor. Bioinformatics 20: 426427.
  • 105
    Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A ( 2003) Tools for comparative protein structure modeling and analysis. Nucleic Acids Res 31: 33753380.
  • 106
    Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A ( 2009) MODBASE, a database of annotated comparative protein structure models and associated resources. Nucl Acids Res 37: D347D354.
  • 107
    Shen MY, Sali A ( 2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15: 25072524.