Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics

Journal of Structural and Functional Genomics - Tập 8 - Trang 73-84 - 2007
George N. Phillips1, Brian G. Fox1, John L. Markley1, Brian F. Volkman2, Euiyoung Bae1, Eduard Bitto1, Craig A. Bingman1, Ronnie O. Frederick1, Jason G. McCoy1, Betsy L. Lytle3, Brad S. Pierce4, Jikui Song1, Simon N. Twigger5
1Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, USA
2Medical College of Wisconsin, Milwaukee, USA
3Medical College of Wisconsin, Milwaukee USA
4Department of Biochemistry, University of Wisconsin-Madison, Madison, USA
5Department of Physiology, Medical College of Wisconsin, Milwaukee, USA

Tóm tắt

The Center for Eukaryotic Structural Genomics (CESG) produces and solves the structures of proteins from eukaryotes. We have developed and operate a pipeline to both solve structures and to test new methodologies. Both NMR and X-ray crystallography methods are used for structure solution. CESG chooses targets based on sequence dissimilarity to known structures, medical relevance, and nominations from members of the scientific community. Many times proteins qualify in more than one of these categories. Here we review some of the structures that have connections to human health and disease.

Tài liệu tham khảo

Blommel PG, Martin PA, Wrobel RL, Steffen E, Fox BG (2006) Prot Exp Purif 47:562–570 Jeon WB, Aceti DJ, Bingman CA, Vojtik FC, Olson AC, Ellefson JM, McCombs JE, Sreenath HK, Blommel PG, Seder KD, Buchan BW, Burns BT, Geetha HV, Harms A, Sabat G, Sussman MR, Fox BG, Phillips GN Jr (2005) JSFG 6:143–147 Tyler RC, Aceti DJ, Bingman CB, Cornilescu CC, Fox BG, Frederick RO, Jeon WB, Lee MS, Newman CS, Peterson FC, Phillips GN Jr, Shahan MN, Singh S, Song J, Sreenath HK, Tyler EM, Ulrich EL, Vinarov DA, Vojtik FC, Volkman BF, Wrobel RL, Zhao Q, Markley JL (2005) Proteins 59:633–643 Zhao Q, Frederick RO, Seder KD, Thao S, Sreenath HK, Peterson FC, Volkman BF, Markley JL, Fox BG (2004) JSFG 5:87–93 Sreenath HK, Bingman CA, Buchan BW, Seder KD, Burns BT, Geetha HV, Jeon WB, Vojtik FC, Aceti DJ, Frederick RO, Phillips GN Jr, Fox BG (2005) Prot Expr Purif 40:256–267 Vinarov DA, Newman CL, Markley JL (2006) FEBS J 273:4160–4169 Zolnai Z, Lee PT, Li J, Chapman MR, Newman CS, Phillips GNJ, Rayment I, Ulrich EL, Volkman BF, Markley JL (2003) JSFG 4:11–23 Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL (2004) Nat Methods 1:149–153 Wang L, Eghbalnia HR, Markley JL (2006) J Biomol NMR 35:155–165 Jamrog DC, Zhang Y, Phillips GN Jr (2003) Acta Crystallogr D Biol Crystallogr 59:304–314 DiMaio F, Shavlik J, Phillips GN Jr (2006) Bioinformatics 22:e81–e89 Wrobel RL, Bingman CA, Jeon WB, Song J, Vinarov DA, Frederick RO, Aceti DJ, Sreenath HK, Zolnai Z, Vojtik FC, Bitto E, Fox BG, Phillips GN Jr, Markley JL (2006) In: Finnie C (ed) Plant proteomics. Blackwell Publishing, Oxford, pp 99–128 Birnbaum SM, Levintow L, Kingsley RB, Greenstein JP (1952) J Biol Chem 194:455–470 Matalon R (1997) Genet Test 1:21–25 Matalon R, Michals-Matalon K (1999) Neurochem Res 24:507–513 Tsai G, Coyle JT (1995) Prog Neurobiol 46:531–540 Moffett JR, Ross B, Arun P, Madhavarao CN, Namboodiri AM (2007) Prog Neurobiol 81:89–131 Gujar SK, Maheshwari S, Bjorkman-Burtscher I, Sundgren PC (2005) J Neuroophthalmol 25:217–226 Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr (2007) Proc Natl Acad Sci USA 104:456–461 Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWeese-Scott C, Geer LY, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Marchler GH, Mullokandov M, Shoemaker BA, Simonyan V, Song JS, Thiessen PA, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2005) Nucleic Acids Res 33:D192-D196 Bitto E, Wesenberg GE, Phillips GN Jr, Mccoy JG, Bingman CA (2006b) Protein data bank (http://www.rcsb.org/pdb/home) PDB ID: 2I3C, DOI: 10.2210/pdb2i3c/pdb LeCoq J, An HJ, Lebrilla C, Viola RE (2006) Biochemistry 45:5878–5884 Stipanuk MH (2004) Annu Rev Nutr 24:539–77 Ewetz L, Sorbo B (1966) Biochemica Et Biophysical Acta 128:296–305 Sorbo B, Ewetz L (1965) Biochem Biophys Res Comm 18:359–363 Lombardini JB, Singer TP, Boyer PD (1969) J Biol Chem 244:1172–1175 Simmons CR, Hirschberger LL, Machi MS, Stipanuk MH (2006) Prot Expr Purif 47:74–81 Kwon YH, Stipanuk MH (2001) Am J Physiol Endocrinol Metab 280:E804–E815 Cooper AJ (1983) Annu Rev Biochem 52:187–222 Bagley PJ, Hirschberger LL, Stipanuk MH (1995) Anal Biochem 227:40–48 Gordon C, Emery P, Bradley H, Waring H (1992) Lancett 229:25–26 Heafield MT, Fearn S, Steventon GB, Waring RH, Williams AC, Sturman SG (1990) Neurosci Lett 110:216–220 Wesenberg, GE, Phillips, GN Jr, Mccoy JG, Bitto E, Bingman CA, Allard STM (2005c) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2ATF, DOI: 10.2210/pdb2atf/pdb Simmons CR, Liu Q, Huang Q, Hao Q, Begley TP, Karplus PA, Stipanuk MH (2005) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2B5H, DOI: 10.2210/pdb2b5h/pdb Ye S, Wu X, Wei L, Tang D, Sun P, Rao Z (2006) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2IC1, DOI: 10.2210/pdb2ic1/pdb McCoy JG, Bailey LJ, Bitto E, Bingman CA, Aceti DJ, Fox BG, Phillips GN Jr (2006a) Proc Natl Acad Sci USA 103:3084–3089 Simmons CR, Liu Q, Huang Q, Hao Q, Begley TP, Karplus P, Stipanuk MH (2006b) J Biol Chem 281:1872333 Ye S, Wu X, Wei L, Tang D, Sun P, Bartlam M, Rao Z (2007) J Biol Chem 282:3391–3402 Straganz GD, Nidetzky B (2006) ChemBioChem 37:1536–1548 Whittaker JW (2003) Chem Rev 103:2347–2363 Whittaker MM, Whittaker JW (1990) J Biol Chem 265:9610–9613 Ito N, Phillips SEV, Stevens C, Ogel ZB, McPherson MJ, Keen JN, Yadav KDS, Knowles PF (1991) Nature 350:87–90 Costas M, Mehn MP, Jensen MP, Que LJ (2004) Chem Rev 104:939–986 Solomon EI, Decker A, Lehnert N (2003) Proc Natl Acad Sci USA 100:3589–3594 Solomon EI, Brunold TCI, Davis MI, Kemsley JN, Lee S-K, Lehnert N, Neese F, Skulan AJ, Yang Y-S, Zhou J (2000) Chem Rev 100:235–349 Koehntop KD, Emerson JP, Que LJ (2005) J Biol Inorg Chem 10:97–93 Tiranti V, D’Adamo P, Briem E, Ferrari G, Mineri R, Lamantea E, Mandel H, Balestri P, Garcia-Silva MT, Vollmer B, Rinaldo P, Hahn SH, Leonard J, Rahman S, Dionisi-Vici C, Garavaglia B, Gasparini P, Zeviani M (2004) Am J Hum Genet 74:239–252 Burlina A, Zacchello F, Dionisi-Vici C, Bertini E, Sabetta G, Bennet MJ, Hale DE, Schmidt-Sommerfeld E, Rinaldo P (1991) Lancet 338:1522–1523 Burlina AB, Dionisi-Vici C, Bennett MJ, Gibson KM, Servidei S, Bertini E, Hale DE, Schmidt-Sommerfeld E, Sabetta G, Zacchello F et al (1994) J Pediatr 124:79–86 McCoy JG, Wesenberg GE, Phillips GN Jr, Bitto E, Bingman CA (2006c) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2GCU, DOI: 10.2210/pdb2gcu/pdb McCoy JG, Bingman CA, Bitto E, Holdorf MM, Makaroff CA, Phillips GN Jr (2006b) Acta Crystallogr D Biol Crystallogr D62:964–970 Tiranti V, Briem E, Lamantea E, Mineri R, Papaleo E, Degioia L, Forlani F, Rinaldo P, Dickson P, Abu-Libdeh B, Cindro-Heberle L, Owaidha M, Jack RM, Christensen E, Burlina A, Zeviani M (2005) J Med Genet 43:340–346 Kobe B, Deisenhofer J (1996) J Mol Biol 264:1028–1043 Darzynkiewicz Z, Carter SP, Mikulski SM, Ardelt WJ, Shogen K (1988) Cell Tissue Kinet 21:169–182 Haigis MC, Kurten EL, Abel RL, Raines RT (2002) J Biol Chem 277:11576–11581 Erickson HA, Jund MD, Pennell CA (2006) Protein Eng Des Sel 19:37–45 Dickson KA, Dahlberg CL, Raines RT (2003) Arch Biochem Biophys 415:172-177 Lee JE, Raines RT (2003) Biochemistry 42:11443-11450 Campbell EM, Hope TJ (2005) Gene Ther 12:1353–1359 Milisav I (1998) Cell Motil Cytoskeleton 39:261–272 Bae E, Wesenberg GE, Phillips GN Jr, Bitto E, Bingman, CA (2006a) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2I5S, DOI: 10.2210/pdb2i5s/pdb Bae E, Wesenberg GE, Phillips GN, Jr, Bitto E, Bingman, CA (2006b) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2GMK, DOI: 10.2210/pdb2gmk/pdb Wesenberg GE, Phillips GN JrMcCoy JG, Bitto E, Bingman CA, Allard STM (2005b) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2AMY, DOI: 10.2210/pdb2amy/pdb Matthijs G, Schollen E, Pardon E, Veiga-Da-Cunha M, Jaeken J, Cassiman JJ, Van Schaftingen E (1997) Nat Genet 16:88–92 Tayebi N, Andrews DQ, Park JK, Orvisky E, McReynolds J, Sidransky E, Krasnewich DM (2002) Am J Med Genet 108:241–246 Jaeken J, Stibler H, Hagberg B (1991) Acta Paediatr Scand Suppl 375:1–71 Lehle L, Strahl S, Tanner W (2006) Angew Chem Int Ed Engl 45:6802–6818 Pirard M, Achouri Y, Collet JF, Schollen E, Matthijs G, Van Schaftingen E (1999) Biochem J 339 (Pt 1):201–207 Kjaergaard S, Skovby F, Schwartz M (1999) Eur J Hum Genet 7:884–888 Matthijs G, Schollen E, Van Schaftingen E, Cassiman JJ, Jaeken J (1998) Am J Hum Genet 62:542–550 Matthijs G, Schollen E, Heykants L, Grunewald S (1999) Mol Genet Metab 68:220–226 Silvaggi NR, Zhang C, Lu Z, Dai J, Dunaway-Mariano D, Allen KN (2006) J Biol Chem 281:14918–14926 Kedzierski L, Malby RL, Smith BJ, Perugini MA, Hodder AN, Ilg T, Colman PM, Handman E (2006) J Mol Biol 363:215–227 Amici A, Emanuelli M, Magni G, Raffaelli N, Ruggieri S (1997) FEBS Lett 419:263–267 Valentine WN, Fink K, Paglia DE, Harris SR, Adams WS (1974) J Clin Invest 54:866–879 Valentine WN, Paglia DE, Fink K, Madokoro G (1976) J Clin Invest 58:926–932 Rees DC, Duley JA, Marinaki AM (2003) Br J Haematol 120:375–383 Zanella A, Bianchi P, Fermo E, Valentini G (2006) Br J Haematol 133:113–123 Hokari S, Miyazaki T, Hasegawa M, Komoda T (1998) Biol Chem 379:329–333 Swanson MS, Markin RS, Stohs SJ, Angle CR (1984) Blood 63:665–670 Wesenberg GE, Phillips GN Jr, Han BW, Bitto E, Bingman CA, Bae E (2005a) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2BDU, DOI: 10.2210/pdb2bdu/pdb Bitto E, Bingman CA, Wesenberg GE, McCoy JG, Phillips GN Jr (2006a) J Biol Chem 281:20521–20529 Collet JF, Stroobant V, Pirard M, Delpierre G, Van Schaftingen E (1998) J Biol Chem 273:14107–14112 Kim HY, Heo YS, Kim JH, Park MH, Moon J, Kim E, Kwon D, Yoon J, Shin D, Jeong EJ, Park SY, Lee TG, Jeon YH, Ro S, Cho JM, Hwang KY (2002) J Biol Chem 277:46651–46658 Chiarelli LR, Bianchi P, Fermo E, Galizzi A, Iadarola P, Mattevi A, Zanella A, Valentini G (2005) Blood 105:3340–3345 Paglia DE, Valentine WN (1975) J Biol Chem 250:7973–7979 Ledoux L (1955a) Nature 176:36–37 Ledoux L (1955b) Nature 175:258–259 Leland PA, Schultz LW, Kim BM, Raines RT (1998) Proc Natl Acad Sci USA 95:10407–10412 Rutkoski TJ, Kurten EL, Mitchell JC, Raines RT (2005) J Mol Biol 354:41–54 Di Donato A, Cafaro V, D’Alessio G (1994) J Biol Chem 269:17394–17396 Leich F, Koditz J, Ulbrich-Hofman R, Arnold U (2006) J Mol Biol 358:1305–1313 Jinno H, Ueda M, Ozawa S, Ikeda T, Enomoto K, Psarras K, Kitajima M, Yamada H, Seno M (1996) Life Sci 58:1901–1908 Jinno H, Ueda M, Ozawa S, Ikeda T, Kitajima M, Maeda T, Seno M (2002) Anticancer Res 22:4141–4145 Psarras K, Ueda M, Yamamura T, Ozawa S, Kitajima M, Aiso S, Komatsu S, Seno M (1998) Protein Eng 11:1285–1292 Futami J, Seno M, Ueda M, Tada H, Yamada H (1999) Protein Eng 12:1013–1019 Hayashida T, Ueda M, Aiura K, Tada H, Onizuka M, Seno M, Yamada H, Kitajima M (2005) Protein Eng Des Sel 18:321–327 Tada H, Onizuka M, Muraki K, Masuzawa W, Futami J, Kosaka M, Seno M, Yamada H (2004) FEBS Lett 568:39–43 Piccoli R, Di Gaetano S, De Lorenzo C, Grauso M, Monaco C, Spalletti-Cernia D, Laccetti P, Cinatl J, Matousek J, D’Alessio G (1999) Proc Natl Acad Sci USA 96:7768–7773 Leland PA, Staniszewski KE, Kim BM, Raines RT (2001) J Biol Chem 276:43095–43102 McCoy JG, Wesenberg GE, Phillips GN Jr, Bitto E, Bingman CA, Allard STM (2005) Protein Data Bank (http://www.rcsb.org/pdb/home) PDBID: 1Z7X, DOI: 10.2210/pdb1z7x/pdb Johnson RJ, McCoy JG, Bingman CA, Phillips GN Jr, Raines RT (2007) J Mol Biol 368:434–449 Kobe B, Deisenhofer J (1997) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 1DFJ, DOI: 10.2210/pdb1dfj/pdb Gartner W, Lang W, Leutmetzer F, Domanovits H, Waldhausl W, Wagner L (2001) Cereb Cortex 11:1161–1169 Nicolls MR, D’Antonio JM, Hutton JC, Gill RG, Czwornog JL, Duncan MW (2003) J Proteome Res 2:199–205 Adolf K, Wagner L, Bergh A, Stattin P, Ottosen P, Borre M, Birkenkamp-Demtroder K, Orntoft TF, Torring N (2007) Prostate 67:472–484 Birkenkamp-Demtroder K, Wagner L, Brandt Sorensen F, Bording Astrup L, Gartner W, Scherubl H, Heine B, Christiansen P, Orntoft TF (2005) Neuroendocrinology 82:121–138 Rogstam A, Linse S, Lindqvist A, James P, Wagner L, Berggard T (2007) Biochem J 401:353–363 Wesenberg GE, Phillips GN Jr, Han BW, Bitto E, Bingman CA, Bae E (2005d) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2BE4, DOI: 10.2210/pdb2be4/pdb Bowman AB, Patel-King RS, Benashski SE, McCaffery JM, Goldstein LS, King SM (1999) J Cell Biol 146:165–180 Jiang J, Yu L, Huang X, Chen X, Li D, Zhang Y, Tang L, Zhao S (2001) Gene Ther 281:103–113 DiBella LM, Sakato M, Patel-King RS, Pazour GJ, King SM (2004) Mol Biol Cell 15:4633–4646 Susalka SJ, Nikulina K, Salata MW, Vaughan PS, King SM, Vaughan KT, Pfister KK (2002) J Biol Chem 277:32939–32946 Tang Q, Staub CM, Gao G, Jin Q, Wang Z, Ding W, Aurigemma RE, Mulder KM (2002) Mol Biol Cell 13:4484–4496 Song J, Tyler RC, Lee MS, Tyler EM, Markley JL (2005) J Mol Biol 354:1043–1051 Terunuma A, Shiba K, Noda T (1997) Nucleic Acids Res 25:1984–1990 Phillips K, Luisi B (2000) J Mol Biol 302:1023–1039 Lytle BL, Peterson FC, Volkman BF (2005) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 1ZR9, DOI: 10.2210/pdb1zr9/pdb Omichinski JG, Clore GM, Robien M, Sakaguchi K, Appella E, Gronenborn AM (1992) Biochemistry 31:3907–3917 Omichinski JG, Clore GM, Appella E, Sakaguchi K, Gronenborn AM (1990) Biochemistry 29:9324–9334 Moller HM, Martinez-Yamout MA, Dyson HJ, Wright PE (2005) J Mol Biol 351:718–730 de la Cruz NB, Peterson FC, Lytle BL, Volkman BF (2007) Protein Sci (in press) Volkman BF, de la Cruz NB, Lytle BL, Peterson FC (2006) Protein Data Bank (http://www.rcsb.org/pdb/home) PDB ID: 2GOW, DOI: 10.2210/pdb2gow/pdb Downes BP, Saracco SA, Lee SS, Crowell DN, Vierstra RD (2006) J Biol Chem 281:27145–27157 Chadwick BP, Kidd T, Sgouros J, Ish-Horowicz D, Frischauf AM (1999) Gene Ther 233:189–195 Beyer K, Nickel R, Freidhoff L, Bjorksten B, Huang SK, Barnes KC, MacDonald S, Forster J, Zepp F, Wahn V (2000) J Invest Dermatol 115:906–908 Bu LM, Bradley M, Soderhall C, Wahlgren CF, Kockum I, Nordenskjold M (2006) Allergy 61:617–621 Knoblauch H, Muller-Myhsok B, Busjahn A, Ben Avi L, Bahring S, Baron H, Heath SC, Uhlmann R, Faulhaber HD, Shpitzen S, Aydin A, Reshef A, Rosenthal M, Eliav O, Muhl A, Lowe A, Schurr D, Harats D, Jeschke E, Friedlander Y, Schuster H, Luft FC, Leitersdorf E (2000) Am J Hum Genet 66:157–166