Publications | Structural Genomics Consortium

Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis.

El-Hawari Y, Favia AD, Pilka ES, Kisiela M, Oppermann U, Martin HJ, Maser E

Chem. Biol. Interact.. 178(1-3):234-41. doi: 10.1016/j.cbi.2008.11.004

Publication date: March 16, 2009

PMID: 19061875

The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary.

Bray JE, Marsden BD, Oppermann U

Chem. Biol. Interact.. 178(1-3):99-109. doi: 10.1016/j.cbi.2008.10.058

Publication date: March 16, 2009

PMID: 19061874

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.

Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U

Chem. Biol. Interact.. 178(1-3):94-8. doi: 10.1016/j.cbi.2008.10.040

Publication date: March 16, 2009

PMID: 19027726

Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2.

Tong Y, Park I, Hong BS, Nedyalkova L, Tempel W, Park HW

Proteins. 75(4):1040-5. doi: 10.1002/prot.22378

Publication date: March 13, 2009

PMID: 19280598

Kinase domain insertions define distinct roles of CLK kinases in SR protein phosphorylation.

Bullock AN, Das S, Debreczeni JE, Rellos P, Fedorov O, Niesen FH, Guo K, Papagrigoriou E, Amos AL, Cho S, Turk BE, Ghosh G, Knapp S

Structure. 17(3):352-62. doi: 10.1016/j.str.2008.12.023

Publication date: March 11, 2009

PMID: 19278650

Discovery of indoline-based, natural-product-like compounds as probes of focal adhesion kinase signaling pathways.

Poondra RR, Kumar NN, Bijian K, Prakesch M, Campagna-Slater V, Reayi A, Reddy PT, Choudhry A, Barnes ML, Leek DM, Daroszewska M, Lougheed C, Xu B, Schapira M, Alaoui-Jamali MA, Arya P

J Comb Chem. 11(2):303-9. doi: 10.1021/cc8001525

Publication date: March 9, 2009

PMID: 19146410

Structural basis and specificity of human otubain 1-mediated deubiquitination.

Edelmann MJ, Iphöfer A, Akutsu M, Altun M, di Gleria K, Kramer HB, Fiebiger E, Dhe-Paganon S, Kessler BM

Biochem. J.. 418(2):379-90. doi: 10.1042/BJ20081318

Publication date: March 1, 2009

PMID: 18954305

Structure and function of histone methylation binding proteins.

Adams-Cioaba MA, Min J

Biochem. Cell Biol.. 87(1):93-105. doi: 10.1139/O08-129

Publication date: February 24, 2009

PMID: 19234526

The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.

Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A

PLoS Biol.. 7(2):e43. doi: 10.1371/journal.pbio.1000043

Publication date: February 24, 2009

PMID: 19243223

Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

Guo Y, Nady N, Qi C, Allali-Hassani A, Zhu H, Pan P, Adams-Cioaba MA, Amaya MF, Dong A, Vedadi M, Schapira M, Read RJ, Arrowsmith CH, Min J

Nucleic Acids Res.. 37(7):2204-10. doi: 10.1093/nar/gkp086

Publication date: February 20, 2009

PMID: 19233876

An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene.

Tempel W, Wu H, Dombrovsky L, Zeng H, Loppnau P, Zhu H, Plotnikov AN, Bochkarev A

Proteins. 74(3):789-93. doi: 10.1002/prot.22299

Publication date: February 15, 2009

PMID: 19089949

Distinguishing between calpain heterodimerization and homodimerization.

Ravulapalli R, Campbell RL, Gauthier SY, Dhe-Paganon S, Davies PL

FEBS J.. 276(4):973-82. doi: 10.1111/j.1742-4658.2008.06833.x

Publication date: February 14, 2009

PMID: 19215300

Structure of the human RECQ1 helicase reveals a putative strand-separation pin.

Pike AC, Shrestha B, Popuri V, Burgess-Brown N, Muzzolini L, Costantini S, Vindigni A, Gileadi O

Proc. Natl. Acad. Sci. U.S.A.. 106(4):1039-44. doi: 10.1073/pnas.0806908106

Publication date: January 27, 2009

PMID: 19151156

Large-scale structural analysis of the classical human protein tyrosine phosphatome.

Barr AJ, Ugochukwu E, Lee WH, King ON, Filippakopoulos P, Alfano I, Savitsky P, Burgess-Brown NA, Müller S, Knapp S

Cell. 136(2):352-63. doi: 10.1016/j.cell.2008.11.038

Publication date: January 23, 2009

PMID: 19167335

Targeting group II PAKs in cancer and metastasis.

Eswaran J, Soundararajan M, Knapp S

Cancer Metastasis Rev.. 28(1-2):209-17. doi: 10.1007/s10555-008-9181-4

Publication date: January 23, 2009

PMID: 19160016

Discovery of a potent and selective inhibitor for human carbonyl reductase 1 from propionate scanning applied to the macrolide zearalenone.

Zimmermann TJ, Niesen FH, Pilka ES, Knapp S, Oppermann U, Maier ME

Bioorg. Med. Chem.. 17(2):530-6. doi: 10.1016/j.bmc.2008.11.076

Publication date: January 15, 2009

PMID: 19097799

Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site.

Scheeff ED, Eswaran J, Bunkoczi G, Knapp S, Manning G

Structure. 17(1):128-38. doi: 10.1016/j.str.2008.10.018

Publication date: January 14, 2009

PMID: 19141289

Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis.

Artz JD, Dunford JE, Arrowood MJ, Dong A, Chruszcz M, Kavanagh KL, Minor W, Russell RG, Ebetino FH, Oppermann U, Hui R

Chem. Biol.. 15(12):1296-306. doi: 10.1016/j.chembiol.2008.10.017

Publication date: December 22, 2008

PMID: 19101474

Extremely tight binding of a ruthenium complex to glycogen synthase kinase 3.

Atilla-Gokcumen GE, Pagano N, Streu C, Maksimoska J, Filippakopoulos P, Knapp S, Meggers E

Chembiochem. 9(18):2933-6. doi: 10.1002/cbic.200800489

Publication date: December 15, 2008

PMID: 19035373

Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases.

Rose NR, Ng SS, Mecinović J, Liénard BM, Bello SH, Sun Z, McDonough MA, Oppermann U, Schofield CJ

J. Med. Chem.. 51(22):7053-6. doi: 10.1021/jm800936s

Publication date: November 27, 2008

PMID: 18942826

Structural basis for parasite-specific functions of the divergent profilin of Plasmodium falciparum.

Kursula I, Kursula P, Ganter M, Panjikar S, Matuschewski K, Schüler H

Structure. 16(11):1638-48. doi: 10.1016/j.str.2008.09.008

Publication date: November 12, 2008

PMID: 19000816

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

Huang X, Finerty P, Walker JR, Butler-Cole C, Vedadi M, Schapira M, Parker SA, Turk BE, Thompson DA, Dhe-Paganon S

J. Struct. Biol.. 165(2):88-96. doi: 10.1016/j.jsb.2008.10.003

Publication date: November 5, 2008

PMID: 19028587

Building skeletally diverse architectures on the Indoline Scaffold: the discovery of a chemical probe of focal adhesion kinase signaling networks.

Prakesch M, Bijian K, Campagna-Slater V, Quevillon S, Joseph R, Wei CQ, Sesmilo E, Reayi A, Poondra RR, Barnes ML, Leek DM, Xu B, Lougheed C, Schapira M, Alaoui-Jamali M, Arya P

Bioorg. Med. Chem.. 16(21):9596-602. doi: 10.1016/j.bmc.2008.09.025

Publication date: November 1, 2008

PMID: 18835181

Structural and kinetic differences between human and Aspergillus fumigatus D-glucosamine-6-phosphate N-acetyltransferase.

Hurtado-Guerrero R, Raimi OG, Min J, Zeng H, Vallius L, Shepherd S, Ibrahim AF, Wu H, Plotnikov AN, van Aalten DM

Biochem. J.. 415(2):217-23. doi: 10.1042/BJ20081000

Publication date: October 15, 2008

PMID: 18601654

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S

Nature. 455(7214):822-5. doi: 10.1038/nature07273

Publication date: October 9, 2008

PMID: 18772889

A pilot project to generate affinity reagents to human proteins.

Uhlen M, Gräslund S, Sundström M

Nat. Methods. 5(10):854-5. doi: 10.1038/nmeth1008-854

Publication date: October 1, 2008

PMID: 18825127

Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

Eydoux C, Spinelli S, Davis TL, Walker JR, Seitova A, Dhe-Paganon S, De Caro A, Cambillau C, Carrière F

Biochemistry. 47(36):9553-64. doi: 10.1021/bi8005576

Publication date: September 9, 2008

PMID: 18702514

Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation.

Filippakopoulos P, Kofler M, Hantschel O, Gish GD, Grebien F, Salah E, Neudecker P, Kay LE, Turk BE, Superti-Furga G, Pawson T, Knapp S

Cell. 134(5):793-803. doi: 10.1016/j.cell.2008.07.047

Publication date: September 5, 2008

PMID: 18775312

Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10.

Wu X, Oppermann M, Berndt KD, Bergman T, Jörnvall H, Knapp S, Oppermann U

Biochem. Biophys. Res. Commun.. 373(4):482-7. doi: 10.1016/j.bbrc.2008.06.030

Publication date: September 5, 2008

PMID: 18571501

Linear motif atlas for phosphorylation-dependent signaling.

Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R

Sci Signal. 1(35):ra2. doi: 10.1126/scisignal.1159433

Publication date: September 4, 2008

PMID: 18765831

The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site.

Trésaugues L, Stenmark P, Schüler H, Flodin S, Welin M, Nyman T, Hammarström M, Moche M, Gräslund S, Nordlund P

Proteins. 73(4):1047-52. doi: 10.1002/prot.22198

Publication date: September 4, 2008

PMID: 18767156

Structural and functional characterization of human Iba proteins.

Schulze JO, Quedenau C, Roske Y, Adam T, Schüler H, Behlke J, Turnbull AP, Sievert V, Scheich C, Mueller U, Heinemann U, Büssow K

FEBS J.. 275(18):4627-40. doi: 10.1111/j.1742-4658.2008.06605.x

Publication date: September 1, 2008

PMID: 18699778

FKBP family proteins: immunophilins with versatile biological functions.

Kang CB, Hong Y, Dhe-Paganon S, Yoon HS

Neurosignals. 16(4):318-25. doi: 10.1159/000123041

Publication date: July 18, 2008

PMID: 18635947

UnPAKing the class differences among p21-activated kinases.

Eswaran J, Soundararajan M, Kumar R, Knapp S

Trends Biochem. Sci.. 33(8):394-403. doi: 10.1016/j.tibs.2008.06.002

Publication date: July 17, 2008

PMID: 18639460

The structure of the PP2A regulatory subunit B56 gamma: the remaining piece of the PP2A jigsaw puzzle.

Magnusdottir A, Stenmark P, Flodin S, Nyman T, Kotenyova T, Gräslund S, Ogg D, Nordlund P

Proteins. 74(1):212-21. doi: 10.1002/prot.22150

Publication date: July 12, 2008

PMID: 18618707

The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.

Baumli S, Lolli G, Lowe ED, Troiani S, Rusconi L, Bullock AN, Debreczeni JE, Knapp S, Johnson LN

EMBO J.. 27(13):1907-18. doi: 10.1038/emboj.2008.121

Publication date: July 9, 2008

PMID: 18566585

Actin/myosin-based gliding motility in apicomplexan parasites.

Matuschewski K, Schüler H

Subcell. Biochem.. 47:110-20.

Publication date: July 1, 2008

PMID: 18512346

Structural analysis of CYP2R1 in complex with vitamin D3.

Strushkevich N, Usanov SA, Plotnikov AN, Jones G, Park HW

J. Mol. Biol.. 380(1):95-106. doi: 10.1016/j.jmb.2008.03.065

Publication date: June 27, 2008

PMID: 18511070

Autoregulation by the juxtamembrane region of the human ephrin receptor tyrosine kinase A3 (EphA3).

Davis TL, Walker JR, Loppnau P, Butler-Cole C, Allali-Hassani A, Dhe-Paganon S

Structure. 16(6):873-84. doi: 10.1016/j.str.2008.03.008

Publication date: June 13, 2008

PMID: 18547520

High throughput crystallography at SGC Toronto: an overview.

Bochkarev A, Tempel W

Methods Mol. Biol.. 426:515-21. doi: 10.1007/978-1-60327-058-8_34

Publication date: June 11, 2008

PMID: 18542887

High throughput production of recombinant human proteins for crystallography.

Gileadi O, Burgess-Brown NA, Colebrook SM, Berridge G, Savitsky P, Smee CE, Loppnau P, Johansson C, Salah E, Pantic NH

Methods Mol. Biol.. 426:221-46. doi: 10.1007/978-1-60327-058-8_14

Publication date: June 11, 2008

PMID: 18542867

Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.

Wu H, Min J, Zeng H, McCloskey DE, Ikeguchi Y, Loppnau P, Michael AJ, Pegg AE, Plotnikov AN

J. Biol. Chem.. 283(23):16135-46. doi: 10.1074/jbc.M710323200

Publication date: June 6, 2008

PMID: 18367445

A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research.

Nady N, Min J, Kareta MS, Chédin F, Arrowsmith CH

Trends Biochem. Sci.. 33(7):305-13. doi: 10.1016/j.tibs.2008.04.014

Publication date: June 4, 2008

PMID: 18538573

Structural and biophysical characterization of human myo-inositol oxygenase.

Thorsell AG, Persson C, Voevodskaya N, Busam RD, Hammarström M, Gräslund S, Gräslund A, Hallberg BM

J. Biol. Chem.. 283(22):15209-16. doi: 10.1074/jbc.M800348200

Publication date: May 30, 2008

PMID: 18364358

Zinc binding catalytic domain of human tankyrase 1.

Lehtiö L, Collins R, van den Berg S, Johansson A, Dahlgren LG, Hammarström M, Helleday T, Holmberg-Schiavone L, Karlberg T, Weigelt J

J. Mol. Biol.. 379(1):136-45. doi: 10.1016/j.jmb.2008.03.058

Publication date: May 23, 2008

PMID: 18436240

The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1).

Davis TL, Walker JR, Ouyang H, MacKenzie F, Butler-Cole C, Newman EM, Eisenmesser EZ, Dhe-Paganon S

FEBS J.. 275(9):2283-95. doi: 10.1111/j.1742-4658.2008.06381.x

Publication date: May 1, 2008

PMID: 18397323

Application of high-throughput isothermal denaturation to assess protein stability and screen for ligands.

Senisterra GA, Soo Hong B, Park HW, Vedadi M

J Biomol Screen. 13(5):337-42. doi: 10.1177/1087057108317825

Publication date: April 30, 2008

PMID: 18448703

Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity.

Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R, Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH

J. Biol. Chem.. 283(17):11355-63. doi: 10.1074/jbc.M707362200

Publication date: April 25, 2008

PMID: 18285338

Similar biological activities of two isostructural ruthenium and osmium complexes.

Maksimoska J, Williams DS, Atilla-Gokcumen GE, Smalley KS, Carroll PJ, Webster RD, Filippakopoulos P, Knapp S, Herlyn M, Meggers E

Chemistry. 14(16):4816-22. doi: 10.1002/chem.200800294

Publication date: April 22, 2008

PMID: 18425743

Crystal structure of the methyltransferase domain of human TARBP1.

Wu H, Min J, Zeng H, Plotnikov AN

Proteins. 72(1):519-25. doi: 10.1002/prot.22065

Publication date: April 17, 2008

PMID: 18412263