Publications | Structural Genomics Consortium

Pyruvate kinase M2 activators promote tetramer formation and suppress tumorigenesis.

Anastasiou D, Yu Y, Israelsen WJ, Jiang JK, Boxer MB, Hong BS, Tempel W, Dimov S, Shen M, Jha A, Yang H, Mattaini KR, Metallo CM, Fiske BP, Courtney KD, Malstrom S, Khan TM, Kung C, Skoumbourdis AP, Veith H, Southall N, Walsh MJ, Brimacombe KR, Leister W, Lunt SY, Johnson ZR, Yen KE, Kunii K, Davidson SM, Christofk HR, Austin CP, Inglese J, Harris MH, Asara JM, Stephanopoulos G, Salituro FG, Jin S, Dang L, Auld DS, Park HW, Cantley LC, Thomas CJ, Vander Heiden MG

Nat. Chem. Biol.. 8(10):839-47. doi: 10.1038/nchembio.1060

Publication date: August 26, 2012

PMID: 22922757

Fragment screening of cyclin G-associated kinase by weak affinity chromatography.

Meiby E, Knapp S, Elkins JM, Ohlson S

Anal Bioanal Chem. 404(8):2417-25. doi: 10.1007/s00216-012-6335-6

Publication date: August 24, 2012

PMID: 22918538

Small-molecule inhibition of BRDT for male contraception.

Matzuk MM, McKeown MR, Filippakopoulos P, Li Q, Ma L, Agno JE, Lemieux ME, Picaud S, Yu RN, Qi J, Knapp S, Bradner JE

Cell. 150(4):673-84. doi: 10.1016/j.cell.2012.06.045

Publication date: August 17, 2012

PMID: 22901802

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.

Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H, Eberhard D, Hutchinson S, Jones E, Katso R, Leveridge M, Mander PK, Mosley J, Ramirez-Molina C, Rowland P, Schofield CJ, Sheppard RJ, Smith JE, Swales C, Tanner R, Thomas P, Tumber A, Drewes G, Oppermann U, Patel DJ, Lee K, Wilson DM

Nature. 488(7411):404-8. doi: 10.1038/nature11262

Publication date: August 16, 2012

PMID: 22842901

ChromoHub: a data hub for navigators of chromatin-mediated signalling.

Liu L, Zhen XT, Denton E, Marsden BD, Schapira M

Bioinformatics. 28(16):2205-6. doi: 10.1093/bioinformatics/bts340

Publication date: August 15, 2012

PMID: 22718786

The bromodomain interaction module.

Filippakopoulos P, Knapp S

FEBS Lett.. 586(17):2692-704. doi: 10.1016/j.febslet.2012.04.045

Publication date: August 14, 2012

PMID: 22710155

An allosteric inhibitor of protein arginine methyltransferase 3.

Siarheyeva A, Senisterra G, Allali-Hassani A, Dong A, Dobrovetsky E, Wasney GA, Chau I, Marcellus R, Hajian T, Liu F, Korboukh I, Smil D, Bolshan Y, Min J, Wu H, Zeng H, Loppnau P, Poda G, Griffin C, Aman A, Brown PJ, Jin J, Al-Awar R, Arrowsmith CH, Schapira M, Vedadi M

Structure. 20(8):1425-35. doi: 10.1016/j.str.2012.06.001

Publication date: August 8, 2012

PMID: 22795084

Characterization of the human SNM1A and SNM1B/Apollo DNA repair exonucleases.

Sengerová B, Allerston CK, Abu M, Lee SY, Hartley J, Kiakos K, Schofield CJ, Hartley JA, Gileadi O, McHugh PJ

J. Biol. Chem.. 287(31):26254-67. doi: 10.1074/jbc.M112.367243

Publication date: July 27, 2012

PMID: 22692201

Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases.

Rose NR, Woon EC, Tumber A, Walport LJ, Chowdhury R, Li XS, King ON, Lejeune C, Ng SS, Krojer T, Chan MC, Rydzik AM, Hopkinson RJ, Che KH, Daniel M, Strain-Damerell C, Gileadi C, Kochan G, Leung IK, Dunford J, Yeoh KK, Ratcliffe PJ, Burgess-Brown N, von Delft F, Muller S, Marsden B, Brennan PE, McDonough MA, Oppermann U, Klose RJ, Schofield CJ, Kawamura A

J. Med. Chem.. 55(14):6639-43. doi: 10.1021/jm300677j

Publication date: July 26, 2012

PMID: 22724510

Development and application of a fluoride-detection-based fluorescence assay for γ-butyrobetaine hydroxylase.

Rydzik AM, Leung IK, Kochan GT, Thalhammer A, Oppermann U, Claridge TD, Schofield CJ

Chembiochem. 13(11):1559-63. doi: 10.1002/cbic.201200256

Publication date: July 23, 2012

PMID: 22730246

Crystal structure of human ADP-ribose transferase ARTD15/PARP16 reveals a novel putative regulatory domain.

Karlberg T, Thorsell AG, Kallas Å, Schüler H

J. Biol. Chem.. 287(29):24077-81. doi: 10.1074/jbc.M112.379289

Publication date: July 13, 2012

PMID: 22661712

Phosphoglucomutase is absent in Trypanosoma brucei and redundantly substituted by phosphomannomutase and phospho-N-acetylglucosamine mutase.

Bandini G, Mariño K, Güther ML, Wernimont AK, Kuettel S, Qiu W, Afzal S, Kelner A, Hui R, Ferguson MA

Mol. Microbiol.. 85(3):513-34. doi: 10.1111/j.1365-2958.2012.08124.x

Publication date: July 12, 2012

PMID: 22676716

Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.

Campbell SJ, Edwards RA, Leung CC, Neculai D, Hodge CD, Dhe-Paganon S, Glover JN

J. Biol. Chem.. 287(28):23900-10. doi: 10.1074/jbc.M112.359653

Publication date: July 6, 2012

PMID: 22589545

WITHDRAWN: Epigallocatechin-3-gallate up-regulates tumor suppressor gene expression via a reactive oxygen species-dependent down-regulation of UHRF1.

Achour M, Mousli M, Alhosin M, Ibrahim A, Peluso J, Muller CD, Schini-Kerth VB, Hamiche A, Dhe-Paganon S

Biochem. Biophys. Res. Commun.. doi: 10.1016/j.bbrc.2012.06.130

Publication date: July 4, 2012

PMID: 22771810

IQGAP proteins reveal an atypical phosphoinositide (aPI) binding domain with a pseudo C2 domain fold.

Dixon MJ, Gray A, Schenning M, Agacan M, Tempel W, Tong Y, Nedyalkova L, Park HW, Leslie NR, van Aalten DM, Downes CP, Batty IH

J. Biol. Chem.. 287(27):22483-96. doi: 10.1074/jbc.M112.352773

Publication date: June 29, 2012

PMID: 22493426

Structure of MMACHC reveals an arginine-rich pocket and a domain-swapped dimer for its B12 processing function.

Froese DS, Krojer T, Wu X, Shrestha R, Kiyani W, von Delft F, Gravel RA, Oppermann U, Yue WW

Biochemistry. 51(25):5083-90. doi: 10.1021/bi300150y

Publication date: June 26, 2012

PMID: 22642810

Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family.

Chaikuad A, Pilka ES, De Riso A, von Delft F, Kavanagh KL, Vénien-Bryan C, Oppermann U, Yue WW

BMC Struct. Biol.. 12:14. doi: 10.1186/1472-6807-12-14

Publication date: June 21, 2012

PMID: 22720794

Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation.

Keates T, Cooper CD, Savitsky P, Allerston CK, Phillips C, Hammarström M, Daga N, Berridge G, Mahajan P, Burgess-Brown NA, Müller S, Gräslund S, Gileadi O

N Biotechnol. 29(5):515-25. doi: 10.1016/j.nbt.2011.10.007

Publication date: June 15, 2012

PMID: 22027370

The corky root rot pathogen Pyrenochaeta lycopersici secretes a proteinaceous inducer of cell death affecting host plants differentially.

Clergeot PH, Schuler H, Mørtz E, Brus M, Vintila S, Ekengren S

Phytopathology.

Publication date: June 6, 2012

PMID: 22671025

Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1.

Wu H, Moshkina N, Min J, Zeng H, Joshua J, Zhou MM, Plotnikov AN

Proc. Natl. Acad. Sci. U.S.A.. 109(23):8925-30. doi: 10.1073/pnas.1114117109

Publication date: June 5, 2012

PMID: 22615379

3-methylcrotonyl-CoA carboxylase deficiency: clinical, biochemical, enzymatic and molecular studies in 88 individuals.

Grünert SC, Stucki M, Morscher RJ, Suormala T, Bürer C, Burda P, Christensen E, Ficicioglu C, Herwig J, Kölker S, Möslinger D, Pasquini E, Santer R, Schwab KO, Wilcken B, Fowler B, Yue WW, Baumgartner MR

Orphanet J Rare Dis. 7:31. doi: 10.1186/1750-1172-7-31

Publication date: May 29, 2012

PMID: 22642865

Sequence-specific recognition of a PxLPxI/L motif by an ankyrin repeat tumbler lock.

Xu C, Jin J, Bian C, Lam R, Tian R, Weist R, You L, Nie J, Bochkarev A, Tempel W, Tan CS, Wasney GA, Vedadi M, Gish GD, Arrowsmith CH, Pawson T, Yang XJ, Min J

Sci Signal. 5(226):ra39. doi: 10.1126/scisignal.2002979

Publication date: May 29, 2012

PMID: 22649097

Pan-pathway based interaction profiling of FDA-approved nucleoside and nucleobase analogs with enzymes of the human nucleotide metabolism.

Egeblad L, Welin M, Flodin S, Gräslund S, Wang L, Balzarini J, Eriksson S, Nordlund P

PLoS ONE. 7(5):e37724. doi: 10.1371/journal.pone.0037724

Publication date: May 25, 2012

PMID: 22662200

Rapid determination of multiple linear kinase substrate motifs by mass spectrometry.

Kettenbach AN, Wang T, Faherty BK, Madden DR, Knapp S, Bailey-Kellogg C, Gerber SA

Chem. Biol.. 19(5):608-18. doi: 10.1016/j.chembiol.2012.04.011

Publication date: May 25, 2012

PMID: 22633412

The Role of Protein Structural Analysis in the Next Generation Sequencing Era.

Yue WW, Froese DS, Brennan PE

Top Curr Chem. doi: 10.1007/128_2012_326

Publication date: May 20, 2012

PMID: 22610134

The structure of the full-length tetrameric PKA regulatory RIIβ complex reveals the mechanism of allosteric PKA activation.

Elkins JM, Knapp S

Sci Signal. 5(224):pe21. doi: 10.1126/scisignal.2003053

Publication date: May 17, 2012

PMID: 22589386

Structural basis for the allosteric inhibitory mechanism of human kidney-type glutaminase (KGA) and its regulation by Raf-Mek-Erk signaling in cancer cell metabolism.

Thangavelu K, Pan CQ, Karlberg T, Balaji G, Uttamchandani M, Suresh V, Schüler H, Low BC, Sivaraman J

Proc. Natl. Acad. Sci. U.S.A.. 109(20):7705-10. doi: 10.1073/pnas.1116573109

Publication date: May 15, 2012

PMID: 22538822

Fold of the conserved DTC domain in Deltex proteins.

Obiero J, Walker JR, Dhe-Paganon S

Proteins. 80(5):1495-9. doi: 10.1002/prot.24054

Publication date: May 1, 2012

PMID: 22411408

Novel insights into the regulation of malarial calcium-dependent protein kinase 1.

Ahmed A, Gaadhe K, Sharma GP, Kumar N, Neculai M, Hui R, Mohanty D, Sharma P

FASEB J.. 26(8):3212-21. doi: 10.1096/fj.12-203877

Publication date: April 25, 2012

PMID: 22539638

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.

Bezerra GA, Dobrovetsky E, Viertlmayr R, Dong A, Binter A, Abramic M, Macheroux P, Dhe-Paganon S, Gruber K

Proc. Natl. Acad. Sci. U.S.A.. 109(17):6525-30. doi: 10.1073/pnas.1118005109

Publication date: April 24, 2012

PMID: 22493238

Small-molecule inhibitors of the c-Fes protein-tyrosine kinase.

Hellwig S, Miduturu CV, Kanda S, Zhang J, Filippakopoulos P, Salah E, Deng X, Choi HG, Zhou W, Hur W, Knapp S, Gray NS, Smithgall TE

Chem. Biol.. 19(4):529-40. doi: 10.1016/j.chembiol.2012.01.020

Publication date: April 20, 2012

PMID: 22520759

Epigenetic protein families: a new frontier for drug discovery.

Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M

Nat Rev Drug Discov. 11(5):384-400. doi: 10.1038/nrd3674

Publication date: April 13, 2012

PMID: 22498752

Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.

Ruan J, Ouyang H, Amaya MF, Ravichandran M, Loppnau P, Min J, Zang J

PLoS ONE. 7(4):e35376. doi: 10.1371/journal.pone.0035376

Publication date: April 13, 2012

PMID: 22514736

A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.

Sheng Y, Hong JH, Doherty R, Srikumar T, Shloush J, Avvakumov GV, Walker JR, Xue S, Neculai D, Wan JW, Kim SK, Arrowsmith CH, Raught B, Dhe-Paganon S

Mol. Cell Proteomics. 11(8):329-41. doi: 10.1074/mcp.O111.013706

Publication date: April 10, 2012

PMID: 22496338

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