Publications | Structural Genomics Consortium

Linking of 2-oxoglutarate and substrate binding sites enables potent and highly selective inhibition of JmjC histone demethylases.

Woon EC, Tumber A, Kawamura A, Hillringhaus L, Ge W, Rose NR, Ma JH, Chan MC, Walport LJ, Che KH, Ng SS, Marsden BD, Oppermann U, McDonough MA, Schofield CJ

Angew. Chem. Int. Ed. Engl.. 51(7):1631-4. doi: 10.1002/anie.201107833

Publication date: February 13, 2012

PMID: 22241642

Structural and functional insights into the DNA replication factor Cdc45 reveal an evolutionary relationship to the DHH family of phosphoesterases.

Krastanova I, Sannino V, Amenitsch H, Gileadi O, Pisani FM, Onesti S

J. Biol. Chem.. 287(6):4121-8. doi: 10.1074/jbc.M111.285395

Publication date: February 3, 2012

PMID: 22147708

Structural insights into the allosteric effects of 4EBP1 on the eukaryotic translation initiation factor eIF4E.

Siddiqui N, Tempel W, Nedyalkova L, Volpon L, Wernimont AK, Osborne MJ, Park HW, Borden KL

J. Mol. Biol.. 415(5):781-92. doi: 10.1016/j.jmb.2011.12.002

Publication date: February 3, 2012

PMID: 22178476

Crystallization and preliminary X-ray diffraction analysis of human dipeptidyl peptidase 10 (DPPY), a component of voltage-gated potassium channels.

Bezerra GA, Dobrovetsky E, Seitova A, Dhe-Paganon S, Gruber K

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.. 68(Pt 2):214-7. doi: 10.1107/S1744309111055230

Publication date: February 1, 2012

PMID: 22298003

Biochemical discrimination between selenium and sulfur 1: a single residue provides selenium specificity to human selenocysteine lyase.

Collins R, Johansson AL, Karlberg T, Markova N, van den Berg S, Olesen K, Hammarström M, Flores A, Schüler H, Schiavone LH, Brzezinski P, Arnér ES, Högbom M

PLoS ONE. 7(1):e30581. doi: 10.1371/journal.pone.0030581

Publication date: January 25, 2012

PMID: 22295093

Protein aggregates are recruited to aggresome by histone deacetylase 6 via unanchored ubiquitin C termini.

Ouyang H, Ali YO, Ravichandran M, Dong A, Qiu W, MacKenzie F, Dhe-Paganon S, Arrowsmith CH, Zhai RG

J. Biol. Chem.. 287(4):2317-27. doi: 10.1074/jbc.M111.273730

Publication date: January 20, 2012

PMID: 22069321

Structural and kinetic evidence that catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates.

Egger S, Chaikuad A, Klimacek M, Kavanagh KL, Oppermann U, Nidetzky B

J. Biol. Chem.. 287(3):2119-29. doi: 10.1074/jbc.M111.313015

Publication date: January 13, 2012

PMID: 22123821

7,8-dichloro-1-oxo-β-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes.

Huber K, Brault L, Fedorov O, Gasser C, Filippakopoulos P, Bullock AN, Fabbro D, Trappe J, Schwaller J, Knapp S, Bracher F

J. Med. Chem.. 55(1):403-13. doi: 10.1021/jm201286z

Publication date: January 12, 2012

PMID: 22136433

Conformational plasticity of glycogenin and its maltosaccharide substrate during glycogen biogenesis.

Chaikuad A, Froese DS, Berridge G, von Delft F, Oppermann U, Yue WW

Proc. Natl. Acad. Sci. U.S.A.. 108(52):21028-33. doi: 10.1073/pnas.1113921108

Publication date: December 27, 2011

PMID: 22160680

Druggability of methyl-lysine binding sites.

Santiago C, Nguyen K, Schapira M

J. Comput. Aided Mol. Des.. 25(12):1171-8. doi: 10.1007/s10822-011-9505-2

Publication date: December 7, 2011

PMID: 22146969

Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family.

Hillringhaus L, Yue WW, Rose NR, Ng SS, Gileadi C, Loenarz C, Bello SH, Bray JE, Schofield CJ, Oppermann U

J. Biol. Chem.. 286(48):41616-25. doi: 10.1074/jbc.M111.283689

Publication date: December 2, 2011

PMID: 21914792

Cofactor mobility determines reaction outcome in the IMPDH and GMPR (β-α)8 barrel enzymes.

Patton GC, Stenmark P, Gollapalli DR, Sevastik R, Kursula P, Flodin S, Schuler H, Swales CT, Eklund H, Himo F, Nordlund P, Hedstrom L

Nat. Chem. Biol.. 7(12):950-8. doi: 10.1038/nchembio.693

Publication date: December 1, 2011

PMID: 22037469

Recombinant protein quality evaluation: proposal for a minimal information standard.

Buckle AM, Bate MA, Androulakis S, Cinquanta M, Basquin J, Bonneau F, Chatterjee DK, Cittaro D, Gräslund S, Gruszka A, Page R, Suppmann S, Wheeler JX, Agostini D, Taussig M, Taylor CF, Bottomley SP, Villaverde A, de Marco A

Stand Genomic Sci. 5(2):195-7. doi: 10.4056/sigs.1834511

Publication date: November 30, 2011

PMID: 22180821

Thermal denaturation assays in chemical biology.

Senisterra G, Chau I, Vedadi M

Assay Drug Dev Technol. 10(2):128-36. doi: 10.1089/adt.2011.0390

Publication date: November 8, 2011

PMID: 22066913

Actin regulation in the malaria parasite.

Sattler JM, Ganter M, Hliscs M, Matuschewski K, Schüler H

Eur. J. Cell Biol.. 90(11):966-71. doi: 10.1016/j.ejcb.2010.11.011

Publication date: November 1, 2011

PMID: 21256619

Critical role for a stage-specific actin in male exflagellation of the malaria parasite.

Deligianni E, Morgan RN, Bertuccini L, Kooij TW, Laforge A, Nahar C, Poulakakis N, Schüler H, Louis C, Matuschewski K, Siden-Kiamos I

Cell. Microbiol.. 13(11):1714-30. doi: 10.1111/j.1462-5822.2011.01652.x

Publication date: November 1, 2011

PMID: 21790945

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.

Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T

Proteins. 79 Suppl 10:6-20. doi: 10.1002/prot.23196

Publication date: October 21, 2011

PMID: 22020785

3,5-dimethylisoxazoles act as acetyl-lysine-mimetic bromodomain ligands.

Hewings DS, Wang M, Philpott M, Fedorov O, Uttarkar S, Filippakopoulos P, Picaud S, Vuppusetty C, Marsden B, Knapp S, Conway SJ, Heightman TD

J. Med. Chem.. 54(19):6761-70. doi: 10.1021/jm200640v

Publication date: October 13, 2011

PMID: 21851057

Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9.

Li J, Li Z, Ruan J, Xu C, Tong Y, Pan PW, Tempel W, Crombet L, Min J, Zang J

PLoS ONE. 6(10):e25104. doi: 10.1371/journal.pone.0025104

Publication date: October 12, 2011

PMID: 22022377

Fluorescence-based methods for screening writers and readers of histone methyl marks.

Allali-Hassani A, Wasney GA, Siarheyeva A, Hajian T, Arrowsmith CH, Vedadi M

J Biomol Screen. 17(1):71-84. doi: 10.1177/1087057111422256

Publication date: October 4, 2011

PMID: 21972038

A centrifugation-free high-throughput protein purification system using in-line microfluidization.

Alenkin D, Yermekbayeva L, Mujib S, Vesterberg A, Newman E, Yamazaki K, Cossar D, Dhe-Paganon S

Protein Expr. Purif.. 79(2):204-9. doi: 10.1016/j.pep.2011.05.006

Publication date: October 1, 2011

PMID: 21605681

Analysis of conditions affecting auto-phosphorylation of human kinases during expression in bacteria.

Shrestha A, Hamilton G, O'Neill E, Knapp S, Elkins JM

Protein Expr. Purif.. 81(1):136-43. doi: 10.1016/j.pep.2011.09.012

Publication date: October 1, 2011

PMID: 21985771

Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery.

Philpott M, Yang J, Tumber T, Fedorov O, Uttarkar S, Filippakopoulos P, Picaud S, Keates T, Felletar I, Ciulli A, Knapp S, Heightman TD

Mol Biosyst. 7(10):2899-908. doi: 10.1039/c1mb05099k

Publication date: October 1, 2011

PMID: 21804994

Kinase inhibitor selectivity profiling using differential scanning fluorimetry.

Fedorov O, Niesen FH, Knapp S

Methods Mol. Biol.. 795:109-18. doi: 10.1007/978-1-61779-337-0_7

Publication date: October 1, 2011

PMID: 21960218

The Cryptosporidium parvum kinome.

Artz JD, Wernimont AK, Allali-Hassani A, Zhao Y, Amani M, Lin YH, Senisterra G, Wasney GA, Fedorov O, King O, Roos A, Lunin VV, Qiu W, Finerty P, Hutchinson A, Chau I, von Delft F, MacKenzie F, Lew J, Kozieradzki I, Vedadi M, Schapira M, Zhang C, Shokat K, Heightman T, Hui R

BMC Genomics. 12:478. doi: 10.1186/1471-2164-12-478

Publication date: September 30, 2011

PMID: 21962082

Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A.

Lemak A, Yee A, Bezsonova I, Dhe-Paganon S, Arrowsmith CH

J. Biomol. NMR. 51(1-2):185-90. doi: 10.1007/s10858-011-9552-y

Publication date: September 27, 2011

PMID: 21947926

Oligomeric structure of the MALT1 tandem Ig-like domains.

Qiu L, Dhe-Paganon S

PLoS ONE. 6(9):e23220. doi: 10.1371/journal.pone.0023220

Publication date: September 23, 2011

PMID: 21966355

Bromodomains as therapeutic targets.

Muller S, Filippakopoulos P, Knapp S

Expert Rev Mol Med. 13:e29. doi: 10.1017/S1462399411001992

Publication date: September 22, 2011

PMID: 21933453

Crystal structure of the Cys2His2-type zinc finger domain of human DPF2.

Zhang W, Xu C, Bian C, Tempel W, Crombet L, MacKenzie F, Min J, Liu Z, Qi C

Biochem. Biophys. Res. Commun.. 413(1):58-61. doi: 10.1016/j.bbrc.2011.08.043

Publication date: September 16, 2011

PMID: 21888896

Optimization of cellular activity of G9a inhibitors 7-aminoalkoxy-quinazolines.

Liu F, Barsyte-Lovejoy D, Allali-Hassani A, He Y, Herold JM, Chen X, Yates CM, Frye SV, Brown PJ, Huang J, Vedadi M, Arrowsmith CH, Jin J

J. Med. Chem.. 54(17):6139-50. doi: 10.1021/jm200903z

Publication date: September 8, 2011

PMID: 21780790

Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair.

Wang AT, Sengerová B, Cattell E, Inagawa T, Hartley JM, Kiakos K, Burgess-Brown NA, Swift LP, Enzlin JH, Schofield CJ, Gileadi O, Hartley JA, McHugh PJ

Genes Dev.. 25(17):1859-70. doi: 10.1101/gad.15699211

Publication date: September 1, 2011

PMID: 21896658

Structural biology of human metal-dependent histone deacetylases.

Schapira M

Handb Exp Pharmacol. 206:225-40. doi: 10.1007/978-3-642-21631-2_10

Publication date: September 1, 2011

PMID: 21879452

Normalizing molecular docking rankings using virtually generated decoys.

Wallach I, Jaitly N, Nguyen K, Schapira M, Lilien R

J Chem Inf Model. 51(8):1817-30. doi: 10.1021/ci200175h

Publication date: August 22, 2011

PMID: 21699246

Structural Chemistry of Human SET Domain Protein Methyltransferases.

Schapira M

Curr Chem Genomics. 5(Suppl 1):85-94. doi: 10.2174/1875397301005010085

Publication date: August 22, 2011

PMID: 21966348

Crystal structures explain functional differences in the two actin depolymerization factors of the malaria parasite.

Singh BK, Sattler JM, Chatterjee M, Huttu J, Schüler H, Kursula I

J. Biol. Chem.. 286(32):28256-64. doi: 10.1074/jbc.M111.211730

Publication date: August 12, 2011

PMID: 21832095

Characterization of 14-3-3 proteins from Cryptosporidium parvum.

Brokx SJ, Wernimont AK, Dong A, Wasney GA, Lin YH, Lew J, Vedadi M, Lee WH, Hui R

PLoS ONE. 6(8):e14827. doi: 10.1371/journal.pone.0014827

Publication date: August 11, 2011

PMID: 21853016

High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors.

Miduturu CV, Deng X, Kwiatkowski N, Yang W, Brault L, Filippakopoulos P, Chung E, Yang Q, Schwaller J, Knapp S, King RW, Lee JD, Herrgard S, Zarrinkar P, Gray NS

Chem. Biol.. 18(7):868-79. doi: 10.1016/j.chembiol.2011.05.010

Publication date: July 29, 2011

PMID: 21802008

Structural basis of Rnd1 binding to plexin Rho GTPase binding domains (RBDs).

Wang H, Hota PK, Tong Y, Li B, Shen L, Nedyalkova L, Borthakur S, Kim S, Tempel W, Buck M, Park HW

J. Biol. Chem.. 286(29):26093-106. doi: 10.1074/jbc.M110.197053

Publication date: July 22, 2011

PMID: 21610070

Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation.

Bian C, Xu C, Ruan J, Lee KK, Burke TL, Tempel W, Barsyte D, Li J, Wu M, Zhou BO, Fleharty BE, Paulson A, Allali-Hassani A, Zhou JQ, Mer G, Grant PA, Workman JL, Zang J, Min J

EMBO J.. 30(14):2829-42. doi: 10.1038/emboj.2011.193

Publication date: July 20, 2011

PMID: 21685874

A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.

Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J

Nat. Chem. Biol.. 7(8):566-74. doi: 10.1038/nchembio.599

Publication date: July 10, 2011

PMID: 21743462

Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility.

Evans DM, Spencer CC, Pointon JJ, Su Z, Harvey D, Kochan G, Oppermann U, Opperman U, Dilthey A, Pirinen M, Stone MA, Appleton L, Moutsianas L, Moutsianis L, Leslie S, Wordsworth T, Kenna TJ, Karaderi T, Thomas GP, Ward MM, Weisman MH, Farrar C, Bradbury LA, Danoy P, Inman RD, Maksymowych W, Gladman D, Rahman P, Morgan A, Marzo-Ortega H, Bowness P, Gaffney K, Gaston JS, Smith M, Bruges-Armas J, Couto AR, Sorrentino R, Paladini F, Ferreira MA, Xu H, Liu Y, Jiang L, Lopez-Larrea C, Díaz-Peña R, López-Vázquez A, Zayats T, Band G, Bellenguez C, Blackburn H, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Corvin A, Craddock N, Deloukas P, Dronov S, Duncanson A, Edkins S, Freeman C, Gillman M, Gray E, Gwilliam R, Hammond N, Hunt SE, Jankowski J, Jayakumar A, Langford C, Liddle J, Markus HS, Mathew CG, McCann OT, McCarthy MI, Palmer CN, Peltonen L, Plomin R, Potter SC, Rautanen A, Ravindrarajah R, Ricketts M, Samani N, Sawcer SJ, Strange A, Trembath RC, Viswanathan AC, Waller M, Weston P, Whittaker P, Widaa S, Wood NW, McVean G, Reveille JD, Wordsworth BP, Brown MA, Donnelly P

Nat. Genet.. 43(8):761-7. doi: 10.1038/ng.873

Publication date: July 10, 2011

PMID: 21743469

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.

Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S

J. Biol. Chem.. 286(27):24300-11. doi: 10.1074/jbc.M111.234104

Publication date: July 8, 2011

PMID: 21489993

Structure and mechanism of human UDP-glucose 6-dehydrogenase.

Egger S, Chaikuad A, Kavanagh KL, Oppermann U, Nidetzky B

J. Biol. Chem.. 286(27):23877-87. doi: 10.1074/jbc.M111.234682

Publication date: July 8, 2011

PMID: 21502315

PRC2 complexes with JARID2, MTF2, and esPRC2p48 in ES cells to modulate ES cell pluripotency and somatic cell reprogramming.

Zhang Z, Jones A, Sun CW, Li C, Chang CW, Joo HY, Dai Q, Mysliwiec MR, Wu LC, Guo Y, Yang W, Liu K, Pawlik KM, Erdjument-Bromage H, Tempst P, Lee Y, Min J, Townes TM, Wang H

Stem Cells. 29(2):229-40. doi: 10.1002/stem.578

Publication date: July 7, 2011

PMID: 21732481

Composition, recruitment and regulation of the PRC2 complex.

Nayak V, Xu C, Min J

Nucleus. 2(4):277-82. doi: 10.4161/nucl.2.4.16266

Publication date: July 1, 2011

PMID: 21941108

Comparative structural analysis of lipid binding START domains.

Thorsell AG, Lee WH, Persson C, Siponen MI, Nilsson M, Busam RD, Kotenyova T, Schüler H, Lehtiö L

PLoS ONE. 6(6):e19521. doi: 10.1371/journal.pone.0019521

Publication date: June 30, 2011

PMID: 21738568

An allosteric inhibitor of the human Cdc34 ubiquitin-conjugating enzyme.

Ceccarelli DF, Tang X, Pelletier B, Orlicky S, Xie W, Plantevin V, Neculai D, Chou YC, Ogunjimi A, Al-Hakim A, Varelas X, Koszela J, Wasney GA, Vedadi M, Dhe-Paganon S, Cox S, Xu S, Lopez-Girona A, Mercurio F, Wrana J, Durocher D, Meloche S, Webb DR, Tyers M, Sicheri F

Cell. 145(7):1075-87. doi: 10.1016/j.cell.2011.05.039

Publication date: June 24, 2011

PMID: 21683433

Leucettines, a class of potent inhibitors of cdc2-like kinases and dual specificity, tyrosine phosphorylation regulated kinases derived from the marine sponge leucettamine B: modulation of alternative pre-RNA splicing.

Debdab M, Carreaux F, Renault S, Soundararajan M, Fedorov O, Filippakopoulos P, Lozach O, Babault L, Tahtouh T, Baratte B, Ogawa Y, Hagiwara M, Eisenreich A, Rauch U, Knapp S, Meijer L, Bazureau JP

J. Med. Chem.. 54(12):4172-86. doi: 10.1021/jm200274d

Publication date: June 23, 2011

PMID: 21615147

A selective inhibitor and probe of the cellular functions of Jumonji C domain-containing histone demethylases.

Luo X, Liu Y, Kubicek S, Myllyharju J, Tumber A, Ng S, Che KH, Podoll J, Heightman TD, Oppermann U, Schreiber SL, Wang X

J. Am. Chem. Soc.. 133(24):9451-6. doi: 10.1021/ja201597b

Publication date: June 22, 2011

PMID: 21585201

Leveraging crowdsourcing to facilitate the discovery of new medicines.

Norman TC, Bountra C, Edwards AM, Yamamoto KR, Friend SH

Sci Transl Med. 3(88):88mr1. doi: 10.1126/scitranslmed.3002678

Publication date: June 22, 2011

PMID: 21697527