Publications | Structural Genomics Consortium

Apollo-NADP(+): a spectrally tunable family of genetically encoded sensors for NADP(.)

Cameron WD, Bui CV, Hutchinson A, Loppnau P, Gräslund S, Rocheleau JV

Nat. Methods. doi: 10.1038/nmeth.3764

Publication date: February 15, 2016

Citrullination-acetylation interplay guides E2F-1 activity during the inflammatory response.

Ghari F, Quirke AM, Munro S, Kawalkowska J, Picaud S, McGouran J, Subramanian V, Muth A, Williams R, Kessler B, Thompson PR, Fillipakopoulos P, Knapp S, Venables PJ, La Thangue NB

Sci Adv. 2(2):e1501257. doi: 10.1126/sciadv.1501257

Publication date: February 5, 2016

PMID: 26989780

Frapid: achieving full automation of FRAP for chemical probe validation.

Yapp C, Rogers C, Savitsky P, Philpott M, Müller S

Biomed Opt Express. 7(2):422-41. doi: 10.1364/BOE.7.000422

Publication date: February 1, 2016

PMID: 26977352

Lessons from ten years of crystallization experiments at the SGC.

Ng JT, Dekker C, Reardon P, von Delft F

Acta Crystallogr D Struct Biol. 72(Pt 2):224-235. doi: 10.1107/S2059798315024687

Publication date: February 1, 2016

PMID: 26894670

Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.

Ferreira de Freitas R, Eram MS, Szewczyk MM, Steuber H, Smil D, Wu H, Li F, Senisterra G, Dong A, Brown PJ, Hitchcock M, Moosmayer D, Stegmann CM, Egner U, Arrowsmith C, Barsyte-Lovejoy D, Vedadi M, Schapira M

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01772

Publication date: January 29, 2016

PMID: 26824386

Family-wide Structural Analysis of Human Numb-Associated Protein Kinases.

Sorrell FJ, Szklarz M, Abdul Azeez KR, Elkins JM, Knapp S

Structure. doi: 10.1016/j.str.2015.12.015

Publication date: January 29, 2016

PMID: 26853940

Identification of LACTB2, a metallo-β-lactamase protein, as a human mitochondrial endoribonuclease.

Levy S, Allerston CK, Liveanu V, Habib MR, Gileadi O, Schuster G

Nucleic Acids Res.. doi: 10.1093/nar/gkw050

Publication date: January 29, 2016

PMID: 26826708

A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1.

Stuckey JI, Dickson BM, Cheng N, Liu Y, Norris JL, Cholensky SH, Tempel W, Qin S, Huber KG, Sagum C, Black K, Li F, Huang XP, Roth BL, Baughman BM, Senisterra G, Pattenden SG, Vedadi M, Brown PJ, Bedford MT, Min J, Arrowsmith CH, James LI, Frye SV

Nat. Chem. Biol.. doi: 10.1038/nchembio.2007

Publication date: January 25, 2016

PMID: 26807715

EXD2 promotes homologous recombination by facilitating DNA end resection.

Broderick R, Nieminuszczy J, Baddock HT, Deshpande RA, Gileadi O, Paull TT, McHugh PJ, Niedzwiedz W

Nat. Cell Biol.. doi: 10.1038/ncb3303

Publication date: January 25, 2016

PMID: 26807646

Open Access Could Transform Drug Discovery: A Case Study of JQ1.

Arshad Z, Brindley D, Smith J, Roberts M, Lee WH, Davies B, Bure K, Hollander GA, Dopson S, Bountra C

Expert Opin Drug Discov. doi: 10.1517/17460441.2016.1144587

Publication date: January 21, 2016

PMID: 26791045

The Intersection of Structural and Chemical Biology - An Essential Synergy.

Zuercher WJ, Elkins JM, Knapp S

Cell Chem Biol. 23(1):173-82. doi: 10.1016/j.chembiol.2015.12.005

Publication date: January 21, 2016

PMID: 26933743

Accurate calculation of the absolute free energy of binding for drug molecules.

Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC

Chem Sci. 7(1):207-218. doi: 10.1039/c5sc02678d

Publication date: January 14, 2016

PMID: 26798447

8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.

Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall KJ, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England KS, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett JM, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown NA, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield CJ, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01635

Publication date: January 7, 2016

PMID: 26741168

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target.

Agarwal P, Alzrigat M, Párraga AA, Enroth S, Singh U, Ungerstedt J, Österborg A, Brown PJ, Ma A, Jin J, Nilsson K, Öberg F, Kalushkova A, Jernberg-Wiklund H

Oncotarget. doi: 10.18632/oncotarget.6843

Publication date: January 7, 2016

PMID: 26755663

Exploring Selective Inhibition of the First Bromodomain of the Human Bromodomain and Extra-terminal Domain (BET) Proteins.

Raux B, Voitovich Y, Derviaux C, Lugari A, Rebuffet E, Milhas S, Priet S, Roux T, Trinquet E, Guillemot JC, Knapp S, Brunel JM, Fedorov AY, Collette Y, Roche P, Betzi S, Combes S, Morelli X

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01708

Publication date: January 6, 2016

PMID: 26735842

Structure-based identification of inhibitory fragments targeting the p300/CBP-associated factor bromodomain.

Chaikuad A, Lang S, Brennan PE, Temperini C, Fedorov O, Hollander J, Nachane R, Abell C, Müller S, Siegal G, Knapp S

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01719

Publication date: January 5, 2016

PMID: 26731131

Use of Methylmalonyl-CoA epimerase in Enhancing Crotonase Stereoselectivity.

Hamed RB, Gomez-Castellanos JR, Froese DS, Krysztofinska E, Yue WW, Schofield CJ

Chembiochem. doi: 10.1002/cbic.201500644

Publication date: December 30, 2015

PMID: 26716911

Recent Progress in Histone Demethylase Inhibitors.

McAllister TE, England KS, Hopkinson RJ, Brennan PE, Kawamura A, Schofield CJ

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01758

Publication date: December 28, 2015

PMID: 26710088

Profiling of Small Molecules by Chemical Proteomics.

Huber KV, Superti-Furga G

Methods Mol. Biol.. 1394:211-8. doi: 10.1007/978-1-4939-3341-9_15

Publication date: December 25, 2015

PMID: 26700051

A Radioactivity-Based Assay for Screening Human m6A-RNA Methyltransferase, METTL3-METTL14 Complex, and Demethylase ALKBH5.

Li F, Kennedy S, Hajian T, Gibson E, Seitova A, Xu C, Arrowsmith CH, Vedadi M

J Biomol Screen. doi: 10.1177/1087057115623264

Publication date: December 23, 2015

PMID: 26701100

Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors.

Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG

J. Med. Chem.. doi: 10.1021/acs.jmedchem.5b01527

Publication date: December 23, 2015

PMID: 26699912

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination.

Yanling Zhao D, Gish G, Braunschweig U, Li Y, Ni Z, Schmitges FW, Zhong G, Liu K, Li W, Moffat J, Vedadi M, Min J, Pawson TJ, Blencowe BJ, Greenblatt JF

Nature. doi: 10.1038/nature16469

Publication date: December 23, 2015

PMID: 26700805

Role of reverse phenotyping in interpretation of next generation sequencing data and a review of INPP5E related disorders.

de Goede C, Yue WW, Yan G, Ariyaratnam S, Chandler KE, Downes L, Khan N, Mohan M, Lowe M, Banka S

Eur. J. Paediatr. Neurol.. doi: 10.1016/j.ejpn.2015.11.012

Publication date: December 18, 2015

PMID: 26748598

Human ISPD Is a Cytidyltransferase Required for Dystroglycan O-Mannosylation.

Riemersma M, Froese DS, van Tol W, Engelke UF, Kopec J, van Scherpenzeel M, Ashikov A, Krojer T, von Delft F, Tessari M, Buczkowska A, Swiezewska E, Jae LT, Brummelkamp TR, Manya H, Endo T, van Bokhoven H, Yue WW, Lefeber DJ

Chem. Biol.. 22(12):1643-52. doi: 10.1016/j.chembiol.2015.10.014

Publication date: December 17, 2015

PMID: 26687144

Structure of the Helicase Domain of DNA Polymerase Theta Reveals a Possible Role in the Microhomology-Mediated End-Joining Pathway.

Newman JA, Cooper CD, Aitkenhead H, Gileadi O

Structure. 23(12):2319-30. doi: 10.1016/j.str.2015.10.014

Publication date: December 1, 2015

PMID: 26636256

Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding.

Dixon-Clarke SE, Elkins JM, Cheng SW, Morin GB, Bullock AN

Sci Rep. 5:17122. doi: 10.1038/srep17122

Publication date: November 26, 2015

PMID: 26597175

Evidence That Compound I Is the Active Species in Both the Hydroxylase and Lyase Steps by Which P450scc Converts Cholesterol to Pregnenolone: EPR/ENDOR/Cryoreduction/Annealing Studies.

Davydov R, Strushkevich N, Smil D, Yantsevich A, Gilep A, Usanov S, Hoffman BM

Biochemistry. doi: 10.1021/acs.biochem.5b00903

Publication date: November 25, 2015

PMID: 26603348

MLL5 Orchestrates a Cancer Self-Renewal State by Repressing the Histone Variant H3.3 and Globally Reorganizing Chromatin.

Gallo M, Coutinho FJ, Vanner RJ, Gayden T, Mack SC, Murison A, Remke M, Li R, Takayama N, Desai K, Lee L, Lan X, Park NI, Barsyte-Lovejoy D, Smil D, Sturm D, Kushida MM, Head R, Cusimano MD, Bernstein M, Clarke ID, Dick JE, Pfister SM, Rich JN, Arrowsmith CH, Taylor MD, Jabado N, Bazett-Jones DP, Lupien M, Dirks PB

Cancer Cell. doi: 10.1016/j.ccell.2015.10.005

Publication date: November 25, 2015

PMID: 26626085

A Potent, Selective and Cell-active Inhibitor of Human Type I Protein Arginine Methyltransferases.

Eram MS, Shen Y, Szewczyk M, Wu H, Senisterra G, Li F, Butler KV, Kaniskan HÜ, Speed BA, Dela Seña C, Dong A, Zeng H, Schapira M, Brown PJ, Arrowsmith CH, Barsyte-Lovejoy D, Liu J, Vedadi M, Jin J

ACS Chem. Biol.. doi: 10.1021/acschembio.5b00839

Publication date: November 24, 2015

PMID: 26598975

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins.

Kamps JJ, Huang J, Poater J, Xu C, Pieters BJ, Dong A, Min J, Sherman W, Beuming T, Matthias Bickelhaupt F, Li H, Mecinović J

Nat Commun. 6:8911. doi: 10.1038/ncomms9911

Publication date: November 19, 2015

PMID: 26578293

The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities.

Allerston CK, Lee SY, Newman JA, Schofield CJ, McHugh PJ, Gileadi O

Nucleic Acids Res.. doi: 10.1093/nar/gkv1256

Publication date: November 17, 2015

PMID: 26582912

Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance.

Fedorov O, Castex J, Tallant C, Owen DR, Martin S, Aldeghi M, Monteiro O, Filippakopoulos P, Picaud S, Trzupek JD, Gerstenberger BS, Bountra C, Willmann D, Wells C, Philpott M, Rogers C, Biggin PC, Brennan PE, Bunnage ME, Schüle R, Günther T, Knapp S, Müller S

Sci Adv. 1(10):e1500723. doi: 10.1126/sciadv.1500723

Publication date: November 13, 2015

PMID: 26702435

Structural Chemistry of Human RNA Methyltransferases.

Schapira M

ACS Chem. Biol.. doi: 10.1021/acschembio.5b00781

Publication date: November 13, 2015

PMID: 26566070

Emerging Target Families: Intractable Targets.

Knapp S

Handb Exp Pharmacol. doi: 10.1007/164_2015_28

Publication date: November 10, 2015

PMID: 26552403

Generation of a selective small molecule inhibitor of the CBP/p300 bromodomain for leukemia therapy.

Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, Olzscha H, Monteiro O, Martin S, Philpott M, Tumber A, Filippakopoulos P, Yapp C, Wells C, Hing Che K, Bannister A, Robson S, Kumar U, Parr N, Lee K, Lugo D, Jeffrey P, Taylor S, Vecellio ML, Bountra C, Brennan P, O'Mahony A, Velichko S, Muller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S

Cancer Res.. doi: 10.1158/0008-5472.CAN-15-0236

Publication date: November 9, 2015

PMID: 26552700

Design of a fluorescent ligand targeting the S-adenosylmethionine binding site of the histone methyltransferase MLL1.

Luan Y, Blazer LL, Hu H, Hajian T, Zhang J, Wu H, Houliston S, Arrowsmith CH, Vedadi M, Zheng YG

Org. Biomol. Chem.. doi: 10.1039/c5ob01794g

Publication date: November 6, 2015

PMID: 26541578

Structural basis for substrate recognition by the human N-terminal methyltransferase 1.

Dong C, Mao Y, Tempel W, Qin S, Li L, Loppnau P, Huang R, Min J

Genes Dev.. doi: 10.1101/gad.270611.115

Publication date: November 5, 2015

PMID: 26543161

Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP.

Liu Y, Lau J, Li W, Tempel W, Li L, Dong A, Narula A, Qin S, Min J

Biochem. J.. doi: 10.1042/BJ20150830

Publication date: November 2, 2015

PMID: 26527736

Inflammation activation and resolution in human tendon disease.

Dakin SG, Martinez FO, Yapp C, Wells G, Oppermann U, Dean BJ, Smith RD, Wheway K, Watkins B, Roche L, Carr AJ

Sci Transl Med. 7(311):311ra173. doi: 10.1126/scitranslmed.aac4269

Publication date: October 28, 2015

PMID: 26511510

Comprehensive characterization of the Published Kinase Inhibitor Set.

Elkins JM, Fedele V, Szklarz M, Abdul Azeez KR, Salah E, Mikolajczyk J, Romanov S, Sepetov N, Huang XP, Roth BL, Al Haj Zen A, Fourches D, Muratov E, Tropsha A, Morris J, Teicher BA, Kunkel M, Polley E, Lackey KE, Atkinson FL, Overington JP, Bamborough P, Müller S, Price DJ, Willson TM, Drewry DH, Knapp S, Zuercher WJ

Nat. Biotechnol.. doi: 10.1038/nbt.3374

Publication date: October 26, 2015

PMID: 26501955

New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins.

Zhang Q, Fan L, Hou F, Dong A, Wang YX, Tong Y

Sci Rep. 5:15660. doi: 10.1038/srep15660

Publication date: October 23, 2015

PMID: 26489670

The ins and outs of selective kinase inhibitor development.

Müller S, Chaikuad A, Gray NS, Knapp S

Nat. Chem. Biol.. 11(11):818-21. doi: 10.1038/nchembio.1938

Publication date: October 20, 2015

PMID: 26485069

Structural basis of metallo-β-lactamase inhibition by captopril stereoisomers.

Brem J, van Berkel SS, Zollman D, Lee SY, Gileadi O, McHugh PJ, Walsh TR, McDonough MA, Schofield CJ

Antimicrob. Agents Chemother.. doi: 10.1128/AAC.01335-15

Publication date: October 19, 2015

PMID: 26482303

Structural insights into the MMACHC-MMADHC protein complex involved in vitamin B12 trafficking.

Froese DS, Kopec J, Fitzpatrick F, Schuller M, McCorvie TJ, Chalk R, Plessl T, Fettelschoss V, Fowler B, Baumgartner MR, Yue WW

J. Biol. Chem.. doi: 10.1074/jbc.M115.683268

Publication date: October 19, 2015

PMID: 26483544

STRUCTURAL BIOLOGY. Chromatin complex, crystal clear.

Schapira M

Science. 350(6258):278-9. doi: 10.1126/science.aad5203

Publication date: October 16, 2015

PMID: 26472895

WDR5 supports an N-Myc transcriptional complex that drives a pro-tumorigenic gene expression signature in neuroblastoma.

Sun Y, Bell JL, Carter DR, Gherardi S, Poulos RC, Milazzo G, Wong JW, Al-Awar R, Tee AE, Liu PY, Liu B, Atmadibrata B, Wong M, Trahair T, Zhao Q, Shohet JM, Haupt Y, Schulte JH, Brown PJ, Arrowsmith CH, Vedadi M, MacKenzie KL, Huttelmaier S, Perini G, Marshall GM, Braithwaite A, Liu T

Cancer Res.. doi: 10.1158/0008-5472.CAN-15-0423

Publication date: October 15, 2015

PMID: 26471359

Targeting RIPK1,2,3 to combat inflammation.

Bullock AN, Degterev A

Oncotarget. doi: 10.18632/oncotarget.6106

Publication date: October 13, 2015

PMID: 26472031

Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells.

Morozumi Y, Boussouar F, Tan M, Chaikuad A, Jamshidikia M, Colak G, He H, Nie L, Petosa C, de Dieuleveult M, Curtet S, Vitte AL, Rabatel C, Debernardi A, Cosset FL, Verhoeyen E, Emadali A, Schweifer N, Gianni D, Gut M, Guardiola P, Rousseaux S, Gérard M, Knapp S, Zhao Y, Khochbin S

J Mol Cell Biol. doi: 10.1093/jmcb/mjv060

Publication date: October 12, 2015

PMID: 26459632

Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step.

Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK

Int J Mol Sci. 16(10):23587-603. doi: 10.3390/ijms161023587

Publication date: October 6, 2015

PMID: 26437402

Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins.

Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S

PLoS ONE. 10(10):e0139695. doi: 10.1371/journal.pone.0139695

Publication date: October 5, 2015

PMID: 26437229