A survey of integral α-helical membrane proteins

Journal of Structural and Functional Genomics

Volumn 10, Issue 4, 2009, Pages 269-280

  Kelly, Libusha ^a   Pieper, Ursula ^a   Eswar, Narayanan ^a   Hays, Franklin A ^a   Li, Min ^a   Roe Zurz, Zygy ^a   Kroetz, Deanna L ^a   Giacomini, Kathleen M ^a   Stroud, Robert M ^a   Sali, Andrej ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ABC transporters; Membrane proteins; Multidrug resistance; Superfamily analysis; Target selection

Indexed keywords

ABC TRANSPORTER; MEMBRANE PROTEIN; MULTIDRUG RESISTANCE PROTEIN;

ALPHA HELIX; ARTICLE; CLONE; FAMILY; GENOME; HUMAN; METHODOLOGY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; STRUCTURAL GENOMICS; YEAST;

ANIMALS; ATP-BINDING CASSETTE TRANSPORTERS; DRUG RESISTANCE, MULTIPLE; EVOLUTION, MOLECULAR; GENOME, HUMAN; GENOMICS; HUMANS; MEMBRANE PROTEINS; PROTEIN STRUCTURE, SECONDARY; RECEPTORS, G-PROTEIN-COUPLED;

EUKARYOTA; PROKARYOTA;

EID: 71049190929     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-009-9069-8     Document Type: Article

References (40)

1. A Andreeva D Howorth JM Chandonia SE Brenner TJ Hubbard C Chothia AG Murzin 2008 Data growth and its impact on the SCOP database: new developments Nucleic Acids Res 36 D419 D425 10.1093/nar/gkm993 1:CAS:528:DC%2BD1cXhtVSqt74%3D 18000004 (Pubitemid 351149760)
2. D Baker A Sali 2001 Protein structure prediction and structural genomics Science 294 93 96 10.1126/science.1065659 1:CAS:528:DC%2BD3MXnsFyisbY%3D 11588250 (Pubitemid 32952955)
3. JM Cuthbertson DA Doyle MS Sansom 2005 Transmembrane helix prediction: a comparative evaluation and analysis Protein Eng Des Sel 18 295 308 10.1093/protein/gzi032 1:CAS:528:DC%2BD2MXmt1ektbY%3D 15932905 (Pubitemid 40942576)
4. DO Daley M Rapp E Granseth K Melen D Drew G von Heijne 2005 Global topology analysis of the Escherichia coli inner membrane proteome Science 308 1321 1323 10.1126/science.1109730 1:CAS:528:DC%2BD2MXks1Ciurg%3D 15919996 (Pubitemid 40746130)
5. RJ Dawson KP Locher 2006 Structure of a bacterial multidrug ABC transporter Nature 443 180 185 10.1038/nature05155 1:CAS:528: DC%2BD28XpsVansLY%3D 16943773 (Pubitemid 44387602)
6. M Dean T Annilo 2005 Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates Annu Rev Genomics Hum Genet 6 123 142 10.1146/annurev.genom.6.080604.162122 1:CAS:528:DC%2BD2MXhtFWisrrI 16124856 (Pubitemid 41397078)
7. M Dean Y Hamon G Chimini 2001 The human ATP-binding cassette (ABC) transporter superfamily J Lipid Res 42 1007 1017 1:CAS:528:DC%2BD3MXlt1Kru7k%3D 11441126 (Pubitemid 32645780)
8. M Dean A Rzhetsky R Allikmets 2001 The human ATP-binding cassette (ABC) transporter superfamily Genome Res 11 1156 1166 10.1101/gr.GR-1649R 1:CAS:528:DC%2BD3MXltFaitL0%3D 11435397 (Pubitemid 32677289)
9. A Elofsson G von Heijne 2007 Membrane protein structure: prediction versus reality Annu Rev Biochem 76 125 140 10.1146/annurev.biochem.76.052705. 163539 1:CAS:528:DC%2BD2sXhtVehtb7I 17579561
10. O Emanuelsson S Brunak G von Heijne H Nielsen 2007 Locating proteins in the cell using TargetP, SignalP and related tools Nat Protoc 2 953 971 10.1038/nprot.2007.131 1:CAS:528:DC%2BD2sXhtFGnur%2FF 17446895 (Pubitemid 46745592)
11. RD Finn J Mistry B Schuster-Bockler S Griffiths-Jones V Hollich T Lassmann S Moxon M Marshall A Khanna R Durbin SR Eddy EL Sonnhammer A Bateman 2006 Pfam: clans, web tools and services Nucleic Acids Res 34 D247 D251 10.1093/nar/gkj149 1:CAS:528:DC%2BD28XisFylsA%3D%3D 16381856
12. SJ Fleishman N Ben-Tal 2006 Progress in structure prediction of alpha-helical membrane proteins Curr Opin Struct Biol 16 496 504 10.1016/j.sbi.2006.06.003 1:CAS:528:DC%2BD28XotFyltrY%3D 16822664 (Pubitemid 44149064)
13. JP Gillet T Efferth J Remacle 2007 Chemotherapy-induced resistance by ATP-binding cassette transporter genes Biochim Biophys Acta 1775 237 262 1:CAS:528:DC%2BD2sXmsFKmtLY%3D 17572300
14. BM Hasselbring JL Jordan RW Krause DC Krause 2006 Terminal organelle development in the cell wall-less bacterium Mycoplasma pneumoniae Proc Natl Acad Sci USA 103 16478 16483 10.1073/pnas.0608051103 1:CAS:528:DC%2BD28Xht1WmsLnO 17062751 (Pubitemid 44715221)
15. A Heger L Holm 2003 Exhaustive enumeration of protein domain families J Mol Biol 328 749 767 10.1016/S0022-2836(03)00269-9 1:CAS:528: DC%2BD3sXjtFeqsrk%3D 12706730 (Pubitemid 36438586)
16. JC Hermann R Marti-Arbona AA Fedorov E Fedorov SC Almo BK Shoichet FM Raushel 2007 Structure-based activity prediction for an enzyme of unknown function Nature 448 775 779 10.1038/nature05981 1:CAS:528:DC%2BD2sXptVGrs7w%3D 17603473 (Pubitemid 47266333)
17. F Horn E Bettler L Oliveira F Campagne FE Cohen G Vriend 2003 GPCRDB information system for G protein-coupled receptors Nucleic Acids Res 31 294 297 10.1093/nar/gkg103 1:CAS:528:DC%2BD3sXhvFSmsLs%3D 12520006 (Pubitemid 36150388)
18. TJ Hubbard BL Aken K Beal B Ballester M Caccamo Y Chen L Clarke G Coates F Cunningham T Cutts T Down SC Dyer S Fitzgerald J Fernandez-Banet S Graf S Haider M Hammond J Herrero R Holland K Howe K Howe N Johnson A Kahari D Keefe F Kokocinski E Kulesha D Lawson I Longden C Melsopp K Megy P Meidl B Ouverdin A Parker A Prlic S Rice D Rios M Schuster I Sealy J Severin G Slater D Smedley G Spudich S Trevanion A Vilella J Vogel S White M Wood T Cox V Curwen R Durbin XM Fernandez-Suarez P Flicek A Kasprzyk G Proctor S Searle J Smith A Ureta-Vidal E Birney 2007 Ensembl 2007 Nucleic Acids Res 35 D610 D617 10.1093/nar/gkl996 1:CAS:528:DC%2BD2sXivFKksw%3D%3D 17148474 (Pubitemid 46056279)
19. L Kall A Krogh EL Sonnhammer 2004 A combined transmembrane topology and signal peptide prediction method J Mol Biol 338 1027 1036 10.1016/j.jmb.2004.03. 016 1:CAS:528:DC%2BD2cXjtl2msLg%3D 15111065 (Pubitemid 38542831)
20. L Kelly R Karchin A Sali 2007 Protein interactions and disease phenotypes in the ABC transporter superfamily Pac Symp Biocomput 5 1 63
21. A Krogh B Larsson G von Heijne EL Sonnhammer 2001 Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J Mol Biol 305 567 580 10.1006/jmbi.2000.4315 1:CAS:528:DC%2BD3MXisFCguw%3D%3D 11152613 (Pubitemid 33032862)
22. MK Leabman CC Huang J DeYoung EJ Carlson TR Taylor M de la Cruz SJ Johns D Stryke M Kawamoto TJ Urban DL Kroetz TE Ferrin AG Clark N Risch I Herskowitz KM Giacomini 2003 Natural variation in human membrane transporter genes reveals evolutionary and functional constraints Proc Natl Acad Sci USA 100 5896 5901 10.1073/pnas.0730857100 1:CAS:528:DC%2BD3sXjvFOlsbY%3D 12719533 (Pubitemid 36576904)
23. M Li FA Hays Z Roe-Zurz L Vuong L Kelly C-M Ho R Robbins U Pieper J Oconnell L Miercke 2008 Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening J Mol Biol 385 820 830 10.1016/j.jmb.2008.11.021 19061901
24. KS Makarova EV Koonin 2005 Evolutionary and functional genomics of the Archaea Curr Opin Microbiol 8 586 594 10.1016/j.mib.2005.08.003 1:CAS:528:DC%2BD2MXhtVehs7jI 16111915 (Pubitemid 41355040)
25. AJ Martin-Galiano D Frishman 2006 Defining the fold space of membrane proteins: the CAMPS database Proteins 64 906 922 10.1002/prot.21081 1:CAS:528:DC%2BD28XovVOjs78%3D 16802318 (Pubitemid 44420932)
26. McKusick-Nathans Institute of Genetic Medicine, (J. H. U. B., MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD) (2008)
27. JP Miller RS Lo A Ben-Hur C Desmarais I Stagljar WS Noble S Fields 2005 Large-scale identification of yeast integral membrane protein interactions Proc Natl Acad Sci USA 102 12123 12128 10.1073/pnas.0505482102 1:CAS:528: DC%2BD2MXps1yqsrs%3D 16093310 (Pubitemid 41291139)
28. A Oberai Y Ihm S Kim JU Bowie 2006 A limited universe of membrane protein families and folds Protein Sci 15 1723 1734 10.1110/ps.062109706 1:CAS:528:DC%2BD28XmvVajsLs%3D 16815920
29. U Pieper N Eswar FP Davis H Braberg MS Madhusudhan A Rossi M Marti-Renom R Karchin BM Webb D Eramian MY Shen L Kelly F Melo A Sali 2006 MODBASE: a database of annotated comparative protein structure models and associated resources Nucleic Acids Res 34 D291 D295 10.1093/nar/gkj059 1:CAS:528: DC%2BD28XisFOksQ%3D%3D 16381869
30. U Pieper N Eswar BM Webb D Eramian L Kelly DT Barkan H Carter P Mankoo R Karchin MA Marti-Renom FP Davis A Sali 2009 MODBASE, a database of annotated comparative protein structure models and associated resources Nucleic Acids Res 37 D347 D354 10.1093/nar/gkn791 1:CAS:528:DC%2BD1cXhsFejtLfE 18948282
31. HW Pinkett AT Lee P Lum KP Locher DC Rees 2007 An inward-facing conformation of a putative metal-chelate-type ABC transporter Science 315 373 377 10.1126/science.1133488 1:CAS:528:DC%2BD2sXmt1KgsA%3D%3D 17158291 (Pubitemid 46175517)
32. Q Ren K Chen IT Paulsen 2007 TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels Nucleic Acids Res 35 D274 D279 10.1093/nar/gkl925 1:CAS:528: DC%2BD2sXivFKhtQ%3D%3D 17135193 (Pubitemid 46056214)
33. MH Saier Jr CV Tran RD Barabote 2006 TCDB: the transporter classification database for membrane transport protein analyses and information Nucleic Acids Res 34 D181 D186 10.1093/nar/gkj001 1:CAS:528:DC%2BD28XisFOitw%3D%3D 16381841
34. A Sali 1998 100,000 protein structures for the biologist Nat Struct Biol 5 1029 1032 10.1038/4136 1:CAS:528:DyaK1cXnvFOlurY%3D 9846869 (Pubitemid 28546262)
35. F Servant C Bru S Carrere E Courcelle J Gouzy D Peyruc D Kahn 2002 ProDom: automated clustering of homologous domains Brief Bioinform 3 246 251 10.1093/bib/3.3.246 1:CAS:528:DC%2BD38XnsFOhtbk%3D 12230033
36. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker 2003 Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res 13 2498 2504 10.1101/gr.1239303 1:CAS:528:DC%2BD3sXovFWrtr4%3D 14597658 (Pubitemid 37428274)
37. R Development Core Team (2008) R: a language and environment for statistical computing
38. UniProt Consortium 2007 The Universal Protein Resource (UniProt) Nucleic Acids Res 35 D193 D197 10.1093/nar/gkl929 (Pubitemid 46056197)
39. MF Vickers SY Yao SA Baldwin JD Young CE Cass 2000 Nucleoside transporter proteins of Saccharomyces cerevisiae. Demonstration of a transporter (FUI1) with high uridine selectivity in plasma membranes and a transporter (FUN26) with broad nucleoside selectivity in intracellular membranes J Biol Chem 275 25931 25938 10.1074/jbc.M000239200 1:CAS:528:DC%2BD3cXmt1Olu7g%3D 10827169 (Pubitemid 30676631)
40. White S (2007) http://blanco.biomol.uci.edu/Membrane-Proteins-xtal.html