Publications | Structural Genomics Consortium

Large-scale structural biology of the human proteome.

Edwards A

Annu. Rev. Biochem.. 78:541-68. doi: 10.1146/annurev.biochem.78.070907.103305

Publication date: June 6, 2009

PMID: 19489729

Forward genetics in Toxoplasma gondii reveals a family of rhoptry kinases that mediates pathogenesis.

Sibley LD, Qiu W, Fentress S, Taylor SJ, Khan A, Hui R

Eukaryotic Cell. 8(8):1085-93. doi: 10.1128/EC.00107-09

Publication date: May 22, 2009

PMID: 19465561

Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.

Kochan G, Pilka ES, von Delft F, Oppermann U, Yue WW

J. Mol. Biol.. 388(5):997-1008. doi: 10.1016/j.jmb.2009.03.064

Publication date: May 22, 2009

PMID: 19345228

Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands.

Crowther GJ, Napuli AJ, Thomas AP, Chung DJ, Kovzun KV, Leibly DJ, Castaneda LJ, Bhandari J, Damman CJ, Hui R, Hol WG, Buckner FS, Verlinde CL, Zhang Z, Fan E, van Voorhis WC

J Biomol Screen. 14(6):700-7. doi: 10.1177/1087057109335749

Publication date: May 21, 2009

PMID: 19470714

Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.

Lehtiö L, Jemth AS, Collins R, Loseva O, Johansson A, Markova N, Hammarström M, Flores A, Holmberg-Schiavone L, Weigelt J, Helleday T, Schüler H, Karlberg T

J. Med. Chem.. 52(9):3108-11. doi: 10.1021/jm900052j

Publication date: May 14, 2009

PMID: 19354255

Girls homozygous for an IL-2-inducible T cell kinase mutation that leads to protein deficiency develop fatal EBV-associated lymphoproliferation.

Huck K, Feyen O, Niehues T, Rüschendorf F, Hübner N, Laws HJ, Telieps T, Knapp S, Wacker HH, Meindl A, Jumaa H, Borkhardt A

J. Clin. Invest.. 119(5):1350-8. doi: 10.1172/JCI37901

Publication date: May 9, 2009

PMID: 19425169

The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch.

Collins R, Karlberg T, Lehtiö L, Schütz P, van den Berg S, Dahlgren LG, Hammarström M, Weigelt J, Schüler H

J. Biol. Chem.. 284(16):10296-300. doi: 10.1074/jbc.C900018200

Publication date: April 17, 2009

PMID: 19244245

Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.

Min T, Vedadi M, Watson DC, Wasney GA, Munger C, Cygler M, Matte A, Young NM

Biochemistry. 48(14):3057-67. doi: 10.1021/bi802195d

Publication date: April 14, 2009

PMID: 19236052

Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii.

Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, Fentress S, Hui R, Sibley LD

EMBO J.. 28(7):969-79. doi: 10.1038/emboj.2009.24

Publication date: April 8, 2009

PMID: 19197235

In situ proteolysis to generate crystals for structure determination: an update.

Wernimont A, Edwards A

PLoS ONE. 4(4):e5094. doi: 10.1371/journal.pone.0005094

Publication date: April 7, 2009

PMID: 19352432

HD-PTP is a catalytically inactive tyrosine phosphatase due to a conserved divergence in its phosphatase domain.

Gingras MC, Zhang YL, Kharitidi D, Barr AJ, Knapp S, Tremblay ML, Pause A

PLoS ONE. 4(4):e5105. doi: 10.1371/journal.pone.0005105

Publication date: April 2, 2009

PMID: 19340315

Novel mutations in ACVR1 result in atypical features in two fibrodysplasia ossificans progressiva patients.

Petrie KA, Lee WH, Bullock AN, Pointon JJ, Smith R, Russell RG, Brown MA, Wordsworth BP, Triffitt JT

PLoS ONE. 4(3):e5005. doi: 10.1371/journal.pone.0005005

Publication date: March 30, 2009

PMID: 19330033

Short-term glucocorticoid treatment increases insulin secretion in islets derived from lean mice through multiple pathways and mechanisms.

Hult M, Ortsäter H, Schuster G, Graedler F, Beckers J, Adamski J, Ploner A, Jörnvall H, Bergsten P, Oppermann U

Mol. Cell. Endocrinol.. 301(1-2):109-16. doi: 10.1016/j.mce.2008.09.038

Publication date: March 25, 2009

PMID: 18984029

Structure of dystrophia myotonica protein kinase.

Elkins JM, Amos A, Niesen FH, Pike AC, Fedorov O, Knapp S

Protein Sci.. 18(4):782-91. doi: 10.1002/pro.82

Publication date: March 25, 2009

PMID: 19309729

Structure-activity relationships of human AKR-type oxidoreductases involved in bile acid synthesis: AKR1D1 and AKR1C4.

Lee WH, Lukacik P, Guo K, Ugochukwu E, Kavanagh KL, Marsden B, Oppermann U

Mol. Cell. Endocrinol.. 301(1-2):199-204. doi: 10.1016/j.mce.2008.09.042

Publication date: March 25, 2009

PMID: 19013211

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