The impact of extremophiles on structural genomics (and vice versa) (original) (raw)

References

• Abergel C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R, Maza C, Notredame C, Poirot O, Suhre K, Varagnol M, Claverie JM (2003) Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics 4:141–157
  Article PubMed CAS Google Scholar
• Acton TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GV, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Robotic cloning and protein production platform of the northeast structural genomics consortium. Methods Enzymol 394:210–243
  Article PubMed CAS Google Scholar
• Adams MW, Dailey HA, DeLucas LJ, Luo M, Prestegard JH, Rose JP, Wang BC (2003) The southeast collaboratory for structural genomics: a high-throughput gene to structure factory. Acc Chem Res 36:191–198
  Article PubMed CAS Google Scholar
• Almeida MS, Herrmann T, Peti W, Wilson IA, Wuthrich K (2005) NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins. Protein Sci 14:2880–2886
  Article PubMed CAS Google Scholar
• Alzari PM, Berglund H, Berrow NS, Blagova E, Busso D, Cambillau C, Campanacci V, Christodoulou E, Eiler S, Fogg MJ, Folkers G, Geerlof A, Hart D, Haouz A, Herman MD, Macieira S, Nordlund P, Perrakis A, Quevillon-Cheruel S, Tarandeau F, van Tilbeurgh H, Unger T, Luna-Vargas MP, Velarde M, Willmanns M, Owens RJ (2006) Implementation of semi-automated cloning and prokaryotic expression screening: the impact of SPINE. Acta Crystallogr D Biol Crystallogr 62:1103–1113
  Article PubMed CAS Google Scholar
• Arzt S, Beteva A, Cipriani F, Delageniere S, Felisaz F, Forstner G, Gordon E, Launer L, Lavault B, Leonard G, Mairs T, McCarthy A, McCarthy J, McSweeney S, Meyer J, Mitchell E, Monaco S, Nurizzo D, Ravelli R, Rey V, Shepard W, Spruce D, Svensson O, Theveneau P (2005) Automation of macromolecular crystallography beamlines. Prog Biophys Mol Biol 89:124–152
  Article PubMed CAS Google Scholar
• Atreya HS, Szyperski T (2005) Rapid NMR data collection. Methods Enzymol 394:78–108
  Article PubMed CAS Google Scholar
• Banci L, Bertini I, Cusack S, de Jong RN, Heinemann U, Jones EY, Kozielski F, Maskos K, Messerschmidt A, Owens R, Perrakis A, Poterszman A, Schneider G, Siebold C, Silman I, Sixma T, Stewart-Jones G, Sussman JL, Thierry JC, Moras D (2006) First steps towards effective methods in exploiting high-throughput technologies for the determination of human protein structures of high biomedical value. Acta Crystallogr D Biol Crystallogr 62:1208–1217
  Article PubMed CAS Google Scholar
• Berry IM, Dym O, Esnouf RM, Harlos K, Meged R, Perrakis A, Sussman JL, Walter TS, Wilson J, Messerschmidt A (2006) SPINE high-throughput crystallization, crystal imaging and recognition techniques: current state, performance analysis, new technologies and future aspects. Acta Crystallogr D Biol Crystallogr 62:1137–1149
  Article PubMed CAS Google Scholar
• Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D’Amico KL, Burley SK (2005) New York-structural genomix research consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics 6:225–232
  Article PubMed CAS Google Scholar
• Bravo J, Aloy P (2006) Target selection for complex structural genomics. Curr Opin Struct Biol 16:385–392
  Article PubMed CAS Google Scholar
• Brenner SE (2000) Target selection for structural genomics. Nat Struct Biol 7 Suppl:967–969
  Article PubMed CAS Google Scholar
• Brenner SE, Chothia C, Hubbard TJ (1997) Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 7:369–376
  Article PubMed CAS Google Scholar
• Brenner SE, Levitt M (2000) Expectations from structural genomics. Protein Sci 9:197–200
  Article PubMed CAS Google Scholar
• Burley SK (2000) An overview of structural genomics. Nat Struct Biol 7(Suppl):932–934
  Article PubMed CAS Google Scholar
• Canaves JM, Page R, Wilson IA, Stevens RC (2004) Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics. J Mol Biol 344:977–991
  Article PubMed CAS Google Scholar
• Chakravarty S, Varadarajan R (2002) Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41:8152–8161
  Article PubMed CAS Google Scholar
• Chandonia JM, Brenner SE (2006) The impact of structural genomics: expectations and outcomes. Science 311:347–351
  Article PubMed CAS Google Scholar
• Chandonia JM, Kim SH, Brenner SE (2006) Target selection and deselection at the Berkeley structural genomics center. Proteins 62:356–370
  Article PubMed CAS Google Scholar
• Chen S, Yakunin AF, Kuznetsova E, Busso D, Pufan R, Proudfoot M, Kim R, Kim SH (2004) Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii. J Biol Chem 279:31854–31862
  Article PubMed CAS Google Scholar
• Christendat D, Yee A, Dharamsi A, Kluger Y, Savchenko A, Cort JR, Booth V, Mackereth CD, Saridakis V, Ekiel I, Kozlov G, Maxwell KL, Wu N, McIntosh LP, Gehring K, Kennedy MA, Davidson AR, Pai EF, Gerstein M, Edwards AM, Arrowsmith CH (2000) Structural proteomics of an archaeon. Nat Struct Biol 7:903–909
  Article PubMed CAS Google Scholar
• Cianci M, Antonyuk S, Bliss N, Bailey MW, Buffey SG, Cheung KC, Clarke JA, Derbyshire GE, Ellis MJ, Enderby MJ, Grant AF, Holbourn MP, Laundy D, Nave C, Ryder R, Stephenson P, Helliwell JR, Hasnain SS (2005) A high-throughput structural biology/proteomics beamline at the SRS on a new multipole wiggler. J Synchrotron Radiat 12:455–466
  Article PubMed CAS Google Scholar
• Cohen GN, Barbe V, Flament D, Galperin M, Heilig R, Lecompte O, Poch O, Prieur D, Querellou J, Ripp R, Thierry JC, Van der Oost J, Weissenbach J, Zivanovic Y, Forterre P (2003) An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 47:1495–1512
  Article PubMed CAS Google Scholar
• Collins B, Stevens RC, Page R (2005) Crystallization optimum solubility screening: using crystallization results to identify the optimal buffer for protein crystal formation. Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1035–1038
  Article PubMed CAS Google Scholar
• Cornvik T, Dahlroth SL, Magnusdottir A, Flodin S, Engvall B, Lieu V, Ekberg M, Nordlund P (2006) An efficient and generic strategy for producing soluble human proteins and domains in E. coli by screening construct libraries. Proteins 65:266–273
  Article PubMed CAS Google Scholar
• Cyranoski D (2006) ‘Big science’ protein project under fire. Nature 443:382
  Article PubMed CAS Google Scholar
• DiDonato M, Deacon AM, Klock HE, McMullan D, Lesley SA (2004) A scaleable and integrated crystallization pipeline applied to mining the Thermotoga maritima proteome. J Struct Funct Genomics 5:133–146
  Article PubMed CAS Google Scholar
• Dieckman LJ, Hanly WC, Collart ER (2006) Strategies for high-throughput gene cloning and expression. Genet Eng (N Y) 27:179–190
  Article CAS Google Scholar
• Douris V, Swevers L, Labropoulou V, Andronopoulou E, Georgoussi Z, Iatrou K (2006) Stably transformed insect cell lines: tools for expression of secreted and membrane-anchored proteins and high-throughput screening platforms for drug and insecticide discovery. Adv Virus Res 68:113–156
  Article PubMed CAS Google Scholar
• Endo Y, Sawasaki T (2006) Cell-free expression systems for eukaryotic protein production. Curr Opin Biotechnol 17:373–380
  Article PubMed CAS Google Scholar
• Esposito D, Chatterjee DK (2006) Enhancement of soluble protein expression through the use of fusion tags. Curr Opin Biotechnol 17:353–358
  Article PubMed CAS Google Scholar
• Fiala G, Stetter KO (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch Microbio 145:56–60
  Article CAS Google Scholar
• Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512
  Article PubMed CAS Google Scholar
• Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15:352–363
  Article PubMed CAS Google Scholar
• Gaasterland T (1998) Structural genomics: bioinformatics in the driver’s seat. Nat Biotechnol 16:625–627
  Article PubMed CAS Google Scholar
• Ginalski K, Grishin NV, Godzik A, Rychlewski L (2005) Practical lessons from protein structure prediction. Nucleic Acids Res 33:1874–1891
  Article PubMed CAS Google Scholar
• Gonzalez JM, Masuchi Y, Robb FT, Ammerman JW, Maeder DL, Yanagibayashi M, Tamaoka J, Kato C (1998) Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles 2:123–130
  Article PubMed CAS Google Scholar
• Hart DJ, Tarendeau F (2006) Combinatorial library approaches for improving soluble protein expression in Escherichia coli. Acta Crystallogr D Biol Crystallogr 62:19–26
  Article PubMed CAS Google Scholar
• Hashimoto Y, Yano T, Kuramitsu S, Kagamiyama H (2001) Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett 506:231–234
  Article PubMed CAS Google Scholar
• Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, Merkl R, Gottschalk G, Fritz HJ (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22:547–553
  Article PubMed CAS Google Scholar
• Holden JF, Poole FL, Tollaksen SL, Giometti CS, Lim H, Yates JR, Adams MWW (2001) Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs. Comp Funct Genomics 2:275–288
  Article CAS PubMed Google Scholar
• Holm L, Sander C (1994) Searching protein structure databases has come of age. Proteins 19:165–173
  Article PubMed CAS Google Scholar
• Holm L, Sander C (1997) New structure—novel fold?. Structure 5:165–171
  Article PubMed CAS Google Scholar
• Hondoh T, Kato A, Yokoyama S, Kuroda Y (2006) Computer-aided NMR assay for detecting natively folded structural domains. Protein Sci 15:871–883
  Article PubMed CAS Google Scholar
• Huber R, Langworthy TA, Konig H, Thomm M, Woese CR, Sleytr UB, Stetter KO (1986) Thermotoga-maritima sp-nov represents a new genus of unique extremely thermophilic eubacteria growing up to 90-degrees-C. Arch Microbiol 144:324–333
  Article CAS Google Scholar
• Ito K, Arai R, Fusatomi E, Kamo-Uchikubo T, Kawaguchi SI, Akasaka R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S (2006) Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 angstrom resolution: a CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD. Protein Sci 15:1187–1192
  Article PubMed CAS Google Scholar
• Jenney FE, Brereton PS, Izumi M, Poole FL, Shah C, Sugar FJ, Lee HS, Adams MWW (2005) High-throughput production of Pyrococcus furiosus proteins: considerations for metalloproteins. J Synchrotron Radiat 12:8–12
  Article PubMed CAS Google Scholar
• Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A (2002) The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol 9:27–31
  Article PubMed CAS Google Scholar
• Koyama Y, Hoshino T, Tomizuka N, Furukawa K (1986) Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166:338–340
  PubMed CAS Google Scholar
• Lecompte O, Ripp R, Puzos-Barbe V, Duprat S, Heilig R, Dietrich J, Thierry JC, Poch O (2001) Genome evolution at the genus level: comparison of three complete genomes of hyperthermophilic archaea. Genome Res 11:981–993
  Article PubMed CAS Google Scholar
• Lee CH, Jung JW, Yee A, Arrowsmith CH, Lee W (2004) Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum. Protein Sci 13:1148–1154
  Article PubMed CAS Google Scholar
• Lesley SA, Kuhn P, Godzik A, Deacon AM, Mathews I, Kreusch A, Spraggon G, Klock HE, McMullan D, Shin T, Vincent J, Robb A, Brinen LS, Miller MD, McPhillips TM, Miller MA, Scheibe D, Canaves JM, Guda C, Jaroszewski L, Selby TL, Elsliger MA, Wooley J, Taylor SS, Hodgson KO, Wilson IA, Schultz PG, Stevens RC (2002) Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc Natl Acad Sci USA 99:11664–11669
  Article PubMed CAS Google Scholar
• Liu JY, Huang CD, Shin DH, Yokota H, Jancarik J, Kim JS, Adams PD, Kim R, Kim SH (2005) Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization. J Mol Biol 350:987–996
  Article PubMed CAS Google Scholar
• Liu X, Fan K, Wang W (2004) The number of protein folds and their distribution over families in nature. Proteins 54:491–499
  Article PubMed CAS Google Scholar
• Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D (2000) Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. Proc Natl Acad Sci USA 97:2450–2455
  Article PubMed CAS Google Scholar
• Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA (2006) Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. Nucleic Acids Res 34:1066–1080
  Article PubMed CAS Google Scholar
• Marsischky G, LaBaer J (2004) Many paths to many clones: a comparative look at high-throughput cloning methods. Genome Res 14:2020–2028
  Article PubMed CAS Google Scholar
• Martinez-Cruz LA, Dreyer MK, Boisvert DC, Yokota H, Martinez-Chantar ML, Kim R, Kim SH (2002) Crystal structure of MJ1247 protein from M. jannaschii at 2.0 A resolution infers a molecular function of 3-hexulose-6-phosphate isomerase. Structure (Camb) 10:195–204
  Article CAS Google Scholar
• Mayer KL, Qu Y, Bansal S, LeBlond PD, Jenney FE, Brereton PS, Adams MWW, Xu Y, Prestegard JH (2006) Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction. Proteins Struct Funct Bioinform 65:480–489
  Article CAS Google Scholar
• McPherson A (2004) Protein crystallization in the structural genomics era. J Struct Funct Genomics 5:3–12
  Article PubMed CAS Google Scholar
• Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323–329
  Article PubMed CAS Google Scholar
• Orengo CA, Todd AE, Thornton JM (1999) From protein structure to function. Curr Opin Struct Biol 9:374–382
  Article PubMed CAS Google Scholar
• Oshima T, Imahori K (1971) Isolation of an extreme thermophile and thermostability of its transfer ribonucleic-acid and ribosomes. J Gen Appl Microbiol 17:513–517
  Google Scholar
• Peti W, Etezady-Esfarjani T, Herrmann T, Klock HE, Lesley SA, Wuthrich K (2004) NMR for structural proteomics of Thermotoga maritima: screening and structure determination. J Struct Funct Genomics 5:205–215
  Article PubMed CAS Google Scholar
• Poole FL 2nd, Gerwe BA, Hopkins RC, Schut GJ, Weinberg MV, Jenney FE Jr, Adams MW (2005) Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes. J Bacteriol 187:7325–7332
  Article PubMed CAS Google Scholar
• Protein Structure Initiative P (2005) http://www.nigms.nih.gov/psi/, vol 2005. NIGMS/NIH Protein Structure Initiative
• Pusey ML, Liu ZJ, Tempel W, Praissman J, Lin D, Wang BC, Gavira JA, Ng JD (2005) Life in the fast lane for protein crystallization and X-ray crystallography. Prog Biophys Mol Biol 88:359–386
  Article PubMed CAS Google Scholar
• Rees DC (2001) Crystallographic analyses of hyperthermophilic proteins. Methods Enzymol 334:423–437
  PubMed CAS Google Scholar
• Robb FT, Maeder DL, Brown JR, DiRuggiero J, Stump MD, Yeh RK, Weiss RB, Dunn DM (2001) Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Methods Enzymol 330:134–157
  Article PubMed CAS Google Scholar
• Robinson-Rechavi M, Alibes A, Godzik A (2006) Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima. J Mol Biol 356:547–557
  Article PubMed CAS Google Scholar
• Robinson-Rechavi M, Godzik A (2005) Structural genomics of Thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure (Camb) 13:857–860
  Article CAS Google Scholar
• Sadeghi M, Naderi-Manesh H, Zarrabi M, Ranjbar B (2006) Effective factors in thermostability of thermophilic proteins. Biophys Chem 119:256–270
  Article PubMed CAS Google Scholar
• Sanishvili R, Yakunin AF, Laskowski RA, Skarina T, Evdokimova E, Doherty-Kirby A, Lajoie GA, Thornton JM, Arrowsmith CH, Savchenko A, Joachimiak A, Edwards AM (2003) Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem 278:26039–26045
  Article PubMed CAS Google Scholar
• Saridakis V, Christendat D, Kimber MS, Dharamsi A, Edwards AM, Pai EF (2001) Insights into ligand binding and catalysis of a central step in NAD+ synthesis: structures of Methanobacterium thermoautotrophicum NMN adenylyltransferase complexes. J Biol Chem 276:7225–7232
  Article PubMed CAS Google Scholar
• Savchenko A, Yee A, Khachatryan A, Skarina T, Evdokimova E, Pavlova M, Semesi A, Northey J, Beasley S, Lan N, Das R, Gerstein M, Arrowmith CH, Edwards AM (2003) Strategies for structural proteomics of prokaryotes: quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches. Proteins 50:392–399
  Article PubMed CAS Google Scholar
• Service R (2005) Structural biology. Structural genomics, round 2. Science 307:1554–1558
  Article PubMed CAS Google Scholar
• Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN et al (1997) Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol 179:7135–7155
  PubMed CAS Google Scholar
• Sugar FJ, Jenney FE Jr, Poole FL 2nd, Brereton PS, Izumi M, Shah C, Adams MW (2005) Comparison of small- and large-scale expression of selected Pyrococcus furiosus genes as an aid to high-throughput protein production. J Struct Funct Genomics 6:149–158
  Article PubMed CAS Google Scholar
• Szilagyi A, Zavodszky P (2000) Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Structure 8:493–504
  Article PubMed CAS Google Scholar
• Tempel W, Liu ZJ, Schubot FD, Shah A, Weinberg MV, Jenney FE Jr, Arendall WB 3rd, Adams MW, Richardson JS, Richardson DC, Rose JP, Wang BC (2004) Structural genomics of Pyrococcus furiosus: X-ray crystallography reveals 3D domain swapping in rubrerythrin. Proteins 57:878–882
  Article PubMed CAS Google Scholar
• Todd AE, Marsden RL, Thornton JM, Orengo CA (2005) Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 348:1235–1260
  Article PubMed CAS Google Scholar
• Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH (2004) Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target. J Struct Funct Genomics 5:241–254
  Article PubMed CAS Google Scholar
• Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al (2001) The sequence of the human genome. Science 291:1304–1351
  Article PubMed CAS Google Scholar
• Vincentelli R, Canaan S, Offant J, Cambillau C, Bignon C (2005) Automated expression and solubility screening of His-tagged proteins in 96-well format. Anal Biochem 346:77–84
  Article PubMed CAS Google Scholar
• Wang BC, Adams MW, Dailey H, DeLucas L, Luo M, Rose J, Bunzel R, Dailey T, Habel J, Horanyi P, Jenney FE Jr, Kataeva I, Lee HS, Li S, Li T, Lin D, Liu ZJ, Luan CH, Mayer M, Nagy L, Newton MG, Ng J, Poole FL 2nd, Shah A, Shah C, Sugar FJ, Xu H (2005) Protein production and crystallization at SECSG—an overview. J Struct Funct Genomics 6:233–243
  Article PubMed CAS Google Scholar
• Wolfson HJ, Shatsky M, Schneidman-Duhovny D, Dror O, Shulman-Peleg A, Ma BY, Nussinov R (2005) From structure to function: methods and applications. Curr Protein Pept Sci 6:171–183
  Article PubMed CAS Google Scholar
• Yakunin AF, Yee AA, Savchenko A, Edwards AM, Arrowsmith CH (2004) Structural proteomics: a tool for genome annotation. Curr Opin Chem Biol 8:42–48
  Article PubMed CAS Google Scholar
• Yang Z, Savchenko A, Yakunin A, Zhang R, Edwards A, Arrowsmith C, Tong L (2003) Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643. J Biol Chem 278:8804–8808
  Article PubMed CAS Google Scholar
• Yokoyama S (2003) Protein expression systems for structural genomics and proteomics. Curr Opin Chem Biol 7:39–43
  Article PubMed CAS Google Scholar
• Yokoyama S (2005) [Large-scale structural proteomics project at RIKEN: present and future]. Tanpakushitsu Kakusan Koso 50:836–845
  PubMed CAS Google Scholar
• Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S (2000) Structural genomics projects in Japan. Nat Struct Biol 7(Suppl):943–945
  Article PubMed CAS Google Scholar
• Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH (1998) Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics. Proc Natl Acad Sci USA 95:15189–193
  Article PubMed CAS Google Scholar
• Zeikus JG, Wolfe RS (1972) Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J Bacteriol 109:707–715
  PubMed CAS Google Scholar
• Zhang R, Skarina T, Evdokimova E, Edwards A, Savchenko A, Laskowski R, Cuff ME, Joachimiak A (2006) Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer. Acta Crystallogr Sect F Struct Biol Cryst Commun 62:335–339
  Article PubMed CAS Google Scholar
• Zhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, Arrowsmith CH, Clarke S, Edwards A, Joachimiak A, Savchenko A (2001) Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure (Camb) 9:1095–1106
  Article CAS Google Scholar
• Zhou CZ, Chen YX (2004) Developments in structural genomics: protein purification and function interpretation. Curr Genomics 5:37–48
  Article CAS Google Scholar

Download references