Publications | Structural Genomics Consortium

Structure of Cyclin G associated kinase (GAK) Trapped in different Conformations using Nanobodies.

Chaikuad A, Keates T, Vincke C, Kaufholz M, Zenn M, Zimmermann B, Gutiérrez C, Zhang RG, Hatzos-Skintges C, Joachimiak A, Muyldermans S, Herberg FW, Knapp S, Müller S

Biochem. J.. doi: 10.1042/BJ20131399

Publication date: January 17, 2014

PMID: 24438162

Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity.

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE

Mol. Cell. doi: 10.1016/j.molcel.2013.11.013

Publication date: December 24, 2013

PMID: 24374310

Stimulation of Hepatic Apolipoprotein A-I Production by Novel Thieno-Triazolodiazepines: Roles of the Classical Benzodiazepine Receptor, PAF Receptor, and Bromodomain Binding.

Kempen HJ, Bellus D, Fedorov O, Nicklisch S, Filippakopoulos P, Picaud S, Knapp S

Lipid Insights. 6:47-54. doi: 10.4137/Lpi.s13258

Publication date: December 22, 2013

PMID: 25278768

Diverse Levels of Sequence Selectivity and Catalytic Efficiency of Protein-Tyrosine Phosphatases.

Selner NG, Luechapanichkul R, Chen X, Neel BG, Zhang ZY, Knapp S, Bell CE, Pei D

Biochemistry. doi: 10.1021/bi401223r

Publication date: December 20, 2013

PMID: 24359314

Structure of the Catalytic Domain of EZH2 Reveals Conformational Plasticity in Cofactor and Substrate Binding Sites and Explains Oncogenic Mutations.

Wu H, Zeng H, Dong A, Li F, He H, Senisterra G, Seitova A, Duan S, Brown PJ, Vedadi M, Arrowsmith CH, Schapira M

PLoS ONE. 8(12):e83737. doi: 10.1371/journal.pone.0083737

Publication date: December 19, 2013

PMID: 24367611

[1,2,4]Triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains.

Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden B, Filippakopoulos P, Muller-Knapp S, Knapp S, Brennan PE

J. Med. Chem.. doi: 10.1021/jm401568s

Publication date: December 8, 2013

PMID: 24313754

ChromoHub V2: Cancer Genomics.

Shah MA, Denton EL, Liu L, Schapira M

Bioinformatics. doi: 10.1093/bioinformatics/btt710

Publication date: December 6, 2013

PMID: 24319001

Neculai D, Schwake M, Ravichandran M, Zunke F, Collins RF, Peters J, Neculai M, Plumb J, Loppnau P, Pizarro JC, Seitova A, Trimble WS, Saftig P, Grinstein S, Dhe-Paganon S.

Structure of LIMP-2 provides functional insights with implications for SR-BI and CD36.

Nature. 504(7478):172-176. doi: 10.1038/nature12684

Publication date: December 5, 2013

PMID: 24162852

Targeting low-druggability bromodomains: Fragment based screening and inhibitor design against the BAZ2B bromodomain.

Ferguson FM, Fedorov O, Chaikuad A, Philpott M, Muniz J, Felletar I, von Delft F, Heightman TD, Knapp S, Abell C, Ciulli A

J. Med. Chem.. doi: 10.1021/jm401582c

Publication date: December 4, 2013

PMID: 24304323

A versatile spectrophotometric protein tyrosine phosphatase assay based on 3-nitrophosphotyrosine containing substrates.

Ameijde JV, Overvoorde J, Knapp S, Hertog JD, Ruijtenbeek R, Liskamp RM

Anal. Biochem.. doi: 10.1016/j.ab.2013.11.023

Publication date: December 2, 2013

PMID: 24309020

Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2.

Wu H, Siarheyeva A, Zeng H, Lam R, Dong A, Wu XH, Li Y, Schapira M, Vedadi M, Min J

FEBS Lett.. 587(23):3859-68. doi: 10.1016/j.febslet.2013.10.020

Publication date: November 29, 2013

PMID: 24396869

Mutant prolactin receptor and familial hyperprolactinemia.

Newey PJ, Gorvin CM, Cleland SJ, Willberg CB, Bridge M, Azharuddin M, Drummond RS, van der Merwe PA, Klenerman P, Bountra C, Thakker RV

N. Engl. J. Med.. 369(21):2012-20. doi: 10.1056/NEJMoa1307557

Publication date: November 21, 2013

PMID: 24195502

Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate.

Harrington L, Cheley S, Alexander LT, Knapp S, Bayley H

Proc. Natl. Acad. Sci. U.S.A.. 110(47):E4417-26. doi: 10.1073/pnas.1312739110

Publication date: November 19, 2013

PMID: 24194548

RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain.

Picaud S, Wells C, Felletar I, Brotherton D, Martin S, Savitsky P, Diez-Dacal B, Philpott M, Bountra C, Lingard H, Fedorov O, Müller S, Brennan PE, Knapp S, Filippakopoulos P

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1310658110

Publication date: November 18, 2013

PMID: 24248379

Medium-throughput production of recombinant human proteins: ligation-independent cloning.

Strain-Damerell C, Mahajan P, Gileadi O, Burgess-Brown NA

Methods Mol. Biol.. 1091:55-72. doi: 10.1007/978-1-62703-691-7_4

Publication date: November 10, 2013

PMID: 24203324

Medium-Throughput Production of Recombinant Human Proteins: Protein Production in E. coli.

Burgess-Brown NA, Mahajan P, Strain-Damerell C, Gileadi O, Gräslund S

Methods Mol. Biol.. 1091:73-94. doi: 10.1007/978-1-62703-691-7_5

Publication date: November 10, 2013

PMID: 24203325

Medium-throughput production of recombinant human proteins: protein production in insect cells.

Mahajan P, Strain-Damerell C, Gileadi O, Burgess-Brown NA

Methods Mol. Biol.. 1091:95-121. doi: 10.1007/978-1-62703-691-7_6

Publication date: November 10, 2013

PMID: 24203326

Maintenance of muscle myosin levels in adult C. elegans requires both the double bromodomain protein BET-1 and sumoylation.

Fisher K, Gee F, Wang S, Xue F, Knapp S, Philpott M, Wells C, Rodriguez M, Snoek LB, Kammenga J, Poulin GB

Biol Open. doi: 10.1242/bio.20136007

Publication date: November 8, 2013

PMID: 24285704

Real-Time Monitoring of the Dephosphorylating Activity of Protein Tyrosine Phosphatases Using Microarrays with 3-Nitrophosphotyrosine Substrates.

van Ameijde J, Overvoorde J, Knapp S, den Hertog J, Ruijtenbeek R, Liskamp RMJ

Chempluschem. 78(11):1349-1357. doi: 10.1002/cplu.201300299

Publication date: November 1, 2013

PMID: 31986648

Structural determinants for ERK5 (MAPK7) and leucine rich repeat kinase 2 activities of benzo[e]pyrimido-[5,4-b]diazepine-6(11H)-ones.

Deng X, Elkins JM, Zhang J, Yang Q, Erazo T, Gomez N, Choi HG, Wang J, Dzamko N, Lee JD, Sim T, Kim N, Alessi DR, Lizcano JM, Knapp S, Gray NS

Eur J Med Chem. 70C:758-767. doi: 10.1016/j.ejmech.2013.10.052

Publication date: October 29, 2013

PMID: 24239623

Biochemical and Structural Studies of Conserved Maf Proteins Revealed Nucleotide Pyrophosphatases with a Preference for Modified Nucleotides.

Tchigvintsev A, Tchigvintsev D, Flick R, Popovic A, Dong A, Xu X, Brown G, Lu W, Wu H, Cui H, Dombrowski L, Joo JC, Beloglazova N, Min J, Savchenko A, Caudy AA, Rabinowitz JD, Murzin AG, Yakunin AF

Chem. Biol.. doi: 10.1016/j.chembiol.2013.09.011

Publication date: October 22, 2013

PMID: 24210219

Exploring the Trypanosoma brucei Hsp83 Potential as a Target for Structure Guided Drug Design.

Pizarro JC, Hills T, Senisterra G, Wernimont AK, Mackenzie C, Norcross NR, Ferguson MA, Wyatt PG, Gilbert IH, Hui R

PLoS Negl Trop Dis. 7(10):e2492. doi: 10.1371/journal.pntd.0002492

Publication date: October 17, 2013

PMID: 24147171

Small-Molecule Modulators for Epigenetics Targets.

Knapp S, Weinmann H

ChemMedChem. doi: 10.1002/cmdc.201300344

Publication date: October 14, 2013

PMID: 24127276

Identification of Novel Functionally Selective Kappa Opioid Receptor Scaffolds.

White KL, Scopton AP, Rives ML, Bikbulatov RV, Polepally PR, Brown PJ, Kenakin T, Javitch JA, Zjawiony JK, Roth BL

Mol. Pharmacol.. doi: 10.1124/mol.113.089649

Publication date: October 10, 2013

PMID: 24113749

Discovery of an in vivo Chemical Probe of the Lysine Methyltransferases G9a and GLP.

Liu F, Barsyte-Lovejoy D, Li F, Xiong Y, Korboukh VK, Huang X, Allali-Hassani A, Janzen WP, Roth BL, Frye SV, Arrowsmith CH, Brown PJ, Vedadi M, Jin J

J. Med. Chem.. doi: 10.1021/jm401480r

Publication date: October 8, 2013

PMID: 24102134

Structural insights into functional overlapping and differentiation among myosin V motors.

Nascimento AF, Trindade DM, Tonoli CC, de Giuseppe PO, Assis LH, Honorato RV, de Oliveira PS, Mahajan P, Burgess-Brown NA, von Delft F, Larson RE, Murakami MT

J. Biol. Chem.. doi: 10.1074/jbc.M113.507202

Publication date: October 4, 2013

PMID: 24097982

Discovery of Novel Small-Molecule Inhibitors of BRD4 Using Structure-Based Virtual Screening.

Vidler LR, Filippakopoulos P, Fedorov O, Picaud S, Martin S, Tomsett M, Woodward H, Brown N, Knapp S, Hoelder S

J. Med. Chem.. doi: 10.1021/jm4011302

Publication date: October 3, 2013

PMID: 24090311

Molecular Basis for the Regulation of the H3K4 Methyltransferase Activity of PRDM9.

Wu H, Mathioudakis N, Diagouraga B, Dong A, Dombrovski L, Baudat F, Cusack S, de Massy B, Kadlec J

Cell Rep. doi: 10.1016/j.celrep.2013.08.035

Publication date: October 2, 2013

PMID: 24095733

Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation.

Islam K, Chen Y, Wu H, Bothwell IR, Blum GJ, Zeng H, Dong A, Zheng W, Min J, Deng H, Luo M

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1216365110

Publication date: September 30, 2013

PMID: 24082136

Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases.

Canning P, Cooper CD, Krojer T, Murray JW, Pike AC, Chaikuad A, Keates T, Thangaratnarajah C, Hojzan V, Ayinampudi V, Marsden BD, Gileadi O, Knapp S, von Delft F, Bullock AN

J. Biol. Chem.. 288(39):28304.

Publication date: September 27, 2013

PMID: 24078033

Highly Functionalized Terpyridines as Competitive Inhibitors of AKAP-PKA Interactions.

Schäfer G, Milić J, Eldahshan A, Götz F, Zühlke K, Schillinger C, Kreuchwig A, Elkins JM, Abdul Azeez KR, Oder A, Moutty MC, Masada N, Beerbaum M, Schlegel B, Niquet S, Schmieder P, Krause G, von Kries JP, Cooper DM, Knapp S, Rademann J, Rosenthal W, Klussmann E

Angew. Chem. Int. Ed. Engl.. doi: 10.1002/anie.201304686

Publication date: September 23, 2013

PMID: 24115519

Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1.

De Nicola GF, Martin ED, Chaikuad A, Bassi R, Clark J, Martino L, Verma S, Sicard P, Tata R, Atkinson RA, Knapp S, Conte MR, Marber MS

Nat. Struct. Mol. Biol.. 20(10):1182-1190. doi: 10.1038/nsmb.2668

Publication date: September 15, 2013

PMID: 24037507

Suppressor of Cytokine Signaling (SOCS) 5 Utilises Distinct Domains for Regulation of JAK1 and Interaction with the Adaptor Protein Shc-1.

Linossi EM, Chandrashekaran IR, Kolesnik TB, Murphy JM, Webb AI, Willson TA, Kedzierski L, Bullock AN, Babon JJ, Norton RS, Nicola NA, Nicholson SE

PLoS ONE. 8(8):e70536. doi: 10.1371/journal.pone.0070536

Publication date: August 21, 2013

PMID: 23990909

Synthesis and SAR studies of 5-(pyridin-4-yl)-1,3,4-thiadiazol-2-amine derivatives as potent inhibitors of Bloom helicase.

Rosenthal AS, Dexheimer TS, Gileadi O, Nguyen GH, Chu WK, Hickson ID, Jadhav A, Simeonov A, Maloney DJ

Bioorg. Med. Chem. Lett.. doi: 10.1016/j.bmcl.2013.08.025

Publication date: August 13, 2013

PMID: 24012121

Testis specific gene expression drives disease progression and Rituximab resistance in lymphoma.

Knapp S

EMBO Mol Med. 5(8):1149-50. doi: 10.1002/emmm.201303018

Publication date: August 7, 2013

PMID: 23918227

5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.

Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JB, King ON, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer T, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller-Knapp S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A

Chem Sci. 4(8):3110-3117. doi: 10.1039/C3SC51122G

Publication date: August 1, 2013

PMID: 26682036

Discovery of a Potent and Selective DDR1 Receptor Tyrosine Kinase Inhibitor.

Kim HG, Tan L, Weisberg EL, Liu F, Canning P, Choi HG, Ezell SA, Wu H, Zhao Z, Wang J, Mandinova A, Griffin JD, Bullock AN, Liu Q, Lee SW, Gray NS

ACS Chem. Biol.. doi: 10.1021/cb400430t

Publication date: July 30, 2013

PMID: 23899692

Topical anti-angiogenic SRPK1 inhibitors reduce choroidal neovascularization in rodent models of exudative-AMD.

Gammons MV, Federov O, Ivison D, Du C, Clark TL, Hopkins C, Hagiwara M, Dick AD, Cox RJ, Harper SJ, Hancox JC, Knapp S, Bates DO

Invest. Ophthalmol. Vis. Sci.. doi: 10.1167/iovs.13-12422

Publication date: July 25, 2013

PMID: 23887803

Control of the Hippo Pathway by Set7-Dependent Methylation of Yap.

Oudhoff MJ, Freeman SA, Couzens AL, Antignano F, Kuznetsova E, Min PH, Northrop JP, Lehnertz B, Barsyte-Lovejoy D, Vedadi M, Arrowsmith CH, Nishina H, Gold MR, Rossi FM, Gingras AC, Zaph C

Dev. Cell. doi: 10.1016/j.devcel.2013.05.025

Publication date: July 9, 2013

PMID: 23850191

Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP2) from Haloferax volcanii.

Liao S, Zhang W, Fan K, Ye K, Zhang X, Zhang J, Xu C, Tu X

Sci Rep. 3:2136. doi: 10.1038/srep02136

Publication date: July 5, 2013

PMID: 23823798

Substrate Specificity and Oligomerization of Human GMP Synthetase.

Welin M, Lehtiö L, Johansson A, Flodin S, Nyman T, Trésaugues L, Hammarström M, Gräslund S, Nordlund P

J. Mol. Biol.. doi: 10.1016/j.jmb.2013.06.032

Publication date: June 28, 2013

PMID: 23816837

Molecular architecture of the ankyrin SOCS box family of Cul5-dependent E3 ubiquitin ligases.

Muniz JR, Guo K, Kershaw NJ, Ayinampudi V, von Delft F, Babon JJ, Bullock AN

J. Mol. Biol.. doi: 10.1016/j.jmb.2013.06.015

Publication date: June 24, 2013

PMID: 23806657

Crystal Structures of Malonyl-Coenzyme A Decarboxylase Provide Insights into Its Catalytic Mechanism and Disease-Causing Mutations.

Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L

Structure. doi: 10.1016/j.str.2013.05.001

Publication date: June 18, 2013

PMID: 23791943

Squeezing the most from every crystal: the fine details of data collection.

Krojer T, Pike AC, von Delft F

Acta Crystallogr. D Biol. Crystallogr.. 69(Pt 7):1303-13. doi: 10.1107/S0907444913013280

Publication date: June 18, 2013

PMID: 23793157

Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states.

Shintre CA, Pike AC, Li Q, Kim JI, Barr AJ, Goubin S, Shrestha L, Yang J, Berridge G, Ross J, Stansfeld PJ, Sansom MS, Edwards AM, Bountra C, Marsden BD, von Delft F, Bullock AN, Gileadi O, Burgess-Brown NA, Carpenter EP

Proc. Natl. Acad. Sci. U.S.A.. 110(24):9710-5. doi: 10.1073/pnas.1217042110

Publication date: June 11, 2013

PMID: 23716676

Effect of single amino Acid substitution observed in cancer on pim-1 kinase thermodynamic stability and structure.

Lori C, Lantella A, Pasquo A, Alexander LT, Knapp S, Chiaraluce R, Consalvi V

PLoS ONE. 8(6):e64824. doi: 10.1371/journal.pone.0064824

Publication date: June 5, 2013

PMID: 23755147

Structures of Down Syndrome Kinases, DYRKs, Reveal Mechanisms of Kinase Activation and Substrate Recognition.

Soundararajan M, Roos AK, Savitsky P, Filippakopoulos P, Kettenbach AN, Olsen JV, Gerber SA, Eswaran J, Knapp S, Elkins JM

Structure. 21(6):986-96. doi: 10.1016/j.str.2013.03.012

Publication date: June 4, 2013

PMID: 23665168

PFI-1, a Highly Selective Protein Interaction Inhibitor, Targeting BET Bromodomains.

Picaud S, Da Costa D, Thanasopoulou A, Filippakopoulos P, Fish PV, Philpott M, Fedorov O, Brennan P, Bunnage ME, Owen DR, Bradner JE, Taniere P, O'Sullivan B, Müller S, Schwaller J, Stankovic T, Knapp S

Cancer Res.. 73(11):3336-3346. doi: 10.1158/0008-5472.CAN-12-3292

Publication date: June 1, 2013

PMID: 23576556

Quantitative Analysis of Histone Demethylase Probes Using Fluorescence Polarization.

Xu W, Podoll JD, Dong X, Tumber A, Oppermann UC, Wang X

J. Med. Chem.. doi: 10.1021/jm3018628

Publication date: May 30, 2013

PMID: 23725560

Homozygous mutations in a predicted endonuclease cause Congenital Dyserythropoietic Anemia Type I.

Babbs C, Roberts NA, Sanchez-Pulido L, McGowan SJ, Ahmed MR, Brown JM, Sabry MA, Bentley DR, McVean GA, Donnelly P, Gileadi O, Ponting CP, Higgs DR, Buckle VJ

Haematologica. doi: 10.3324/haematol.2013.089490

Publication date: May 28, 2013

PMID: 23716552