Publications | Structural Genomics Consortium

Histone recognition and large-scale structural analysis of the human bromodomain family.

Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Müller S, Pawson T, Gingras AC, Arrowsmith CH, Knapp S

Cell. 149(1):214-31. doi: 10.1016/j.cell.2012.02.013

Publication date: March 30, 2012

PMID: 22464331

Crystal structures of the tetratricopeptide repeat domains of kinesin light chains: insight into cargo recognition mechanisms.

Zhu H, Lee HY, Tong Y, Hong BS, Kim KP, Shen Y, Lim KJ, Mackenzie F, Tempel W, Park HW

PLoS ONE. 7(3):e33943. doi: 10.1371/journal.pone.0033943

Publication date: March 28, 2012

PMID: 22470497

Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins.

Adams-Cioaba MA, Li Z, Tempel W, Guo Y, Bian C, Li Y, Lam R, Min J

FEBS Lett.. 586(6):859-65. doi: 10.1016/j.febslet.2012.02.012

Publication date: March 23, 2012

PMID: 22449972

Crystal structures from the Plasmodium peroxiredoxins: new insights into oligomerization and product binding.

Qiu W, Dong A, Pizarro JC, Botchkarsev A, Min J, Wernimont AK, Hills T, Hui R, Artz JD

BMC Struct. Biol.. 12:2. doi: 10.1186/1472-6807-12-2

Publication date: March 19, 2012

PMID: 22429898

Crystal structure of the secretory isozyme of mammalian carbonic anhydrases CA VI: implications for biological assembly and inhibitor development.

Pilka ES, Kochan G, Oppermann U, Yue WW

Biochem. Biophys. Res. Commun.. 419(3):485-9. doi: 10.1016/j.bbrc.2012.02.038

Publication date: March 16, 2012

PMID: 22366092

Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family.

Filippakopoulos P, Picaud S, Fedorov O, Keller M, Wrobel M, Morgenstern O, Bracher F, Knapp S

Bioorg. Med. Chem.. 20(6):1878-86. doi: 10.1016/j.bmc.2011.10.080

Publication date: March 15, 2012

PMID: 22137933

Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima.

Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SW, Wilson IA

Proteins. 80(6):1545-59. doi: 10.1002/prot.24041

Publication date: March 13, 2012

PMID: 22411095

Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.

No JH, de Macedo Dossin F, Zhang Y, Liu YL, Zhu W, Feng X, Yoo JA, Lee E, Wang K, Hui R, Freitas-Junior LH, Oldfield E

Proc. Natl. Acad. Sci. U.S.A.. 109(11):4058-63. doi: 10.1073/pnas.1118215109

Publication date: March 13, 2012

PMID: 22392982

The p53 cofactor Strap exhibits an unexpected TPR motif and oligonucleotide-binding (OB)-fold structure.

Adams CJ, Pike AC, Maniam S, Sharpe TD, Coutts AS, Knapp S, La Thangue NB, Bullock AN

Proc. Natl. Acad. Sci. U.S.A.. 109(10):3778-83. doi: 10.1073/pnas.1113731109

Publication date: March 6, 2012

PMID: 22362889

Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors.

Wahlberg E, Karlberg T, Kouznetsova E, Markova N, Macchiarulo A, Thorsell AG, Pol E, Frostell Å, Ekblad T, Öncü D, Kull B, Robertson GM, Pellicciari R, Schüler H, Weigelt J

Nat. Biotechnol.. 30(3):283-8. doi: 10.1038/nbt.2121

Publication date: March 1, 2012

PMID: 22343925

On the need for an international effort to capture, share and use crystallization screening data.

Newman J, Bolton EE, Müller-Dieckmann J, Fazio VJ, Gallagher DT, Lovell D, Luft JR, Peat TS, Ratcliffe D, Sayle RA, Snell EH, Taylor K, Vallotton P, Velanker S, von Delft F

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.. 68(Pt 3):253-8. doi: 10.1107/S1744309112002618

Publication date: March 1, 2012

PMID: 22442216

Structural stability of human protein tyrosine phosphatase ρ catalytic domain: effect of point mutations.

Pasquo A, Consalvi V, Knapp S, Alfano I, Ardini M, Stefanini S, Chiaraluce R

PLoS ONE. 7(2):e32555. doi: 10.1371/journal.pone.0032555

Publication date: February 28, 2012

PMID: 22389709

Crystal structure of inactive form of Rab3B.

Zhang W, Shen Y, Jiao R, Liu Y, Deng L, Qi C

Biochem. Biophys. Res. Commun.. 418(4):841-4. doi: 10.1016/j.bbrc.2012.01.124

Publication date: February 24, 2012

PMID: 22321395

Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30.

Liu K, Guo Y, Liu H, Bian C, Lam R, Liu Y, Mackenzie F, Rojas LA, Reinberg D, Bedford MT, Xu RM, Min J

PLoS ONE. 7(2):e30375. doi: 10.1371/journal.pone.0030375

Publication date: February 17, 2012

PMID: 22363433

Crystal structures of the coil 2B fragment and the globular tail domain of human lamin B1.

Ruan J, Xu C, Bian C, Lam R, Wang JP, Kania J, Min J, Zang J

FEBS Lett.. 586(4):314-8. doi: 10.1016/j.febslet.2012.01.007

Publication date: February 17, 2012

PMID: 22265972

Two ZnF-UBP domains in isopeptidase T (USP5).

Avvakumov GV, Walker JR, Xue S, Allali-Hassani A, Asinas A, Nair UB, Fang X, Zuo X, Wang YX, Wilkinson KD, Dhe-Paganon S

Biochemistry. 51(6):1188-98. doi: 10.1021/bi200854q

Publication date: February 14, 2012

PMID: 22283393

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