Publications | Structural Genomics Consortium

A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases.

Fedorov O, Marsden B, Pogacic V, Rellos P, Müller S, Bullock AN, Schwaller J, Sundström M, Knapp S

Proc. Natl. Acad. Sci. U.S.A.. 104(51):20523-8. doi: 10.1073/pnas.0708800104

Publication date: December 18, 2007

PMID: 18077363

Evaluation of micro-parallel liquid chromatography as a method for HTS-coupled actives verification.

Simeonov A, Yasgar A, Klumpp C, Zheng W, Shafqat N, Oppermann U, Austin CP, Inglese J

Assay Drug Dev Technol. 5(6):815-24. doi: 10.1089/adt.2007.097

Publication date: December 15, 2007

PMID: 18078381

Bisphosphonates: an update on mechanisms of action and how these relate to clinical efficacy.

Russell RG, Xia Z, Dunford JE, Oppermann U, Kwaasi A, Hulley PA, Kavanagh KL, Triffitt JT, Lundy MW, Phipps RJ, Barnett BL, Coxon FP, Rogers MJ, Watts NB, Ebetino FH

Ann. N. Y. Acad. Sci.. 1117:209-57. doi: 10.1196/annals.1402.089

Publication date: December 7, 2007

PMID: 18056045

The use of systematic N- and C-terminal deletions to promote production and structural studies of recombinant proteins.

Gräslund S, Sagemark J, Berglund H, Dahlgren LG, Flores A, Hammarström M, Johansson I, Kotenyova T, Nilsson M, Nordlund P, Weigelt J

Protein Expr. Purif.. 58(2):210-21. doi: 10.1016/j.pep.2007.11.008

Publication date: November 22, 2007

PMID: 18171622

Mechanism and substrate recognition of human holo ACP synthase.

Bunkoczi G, Pasta S, Joshi A, Wu X, Kavanagh KL, Smith S, Oppermann U

Chem. Biol.. 14(11):1243-53. doi: 10.1016/j.chembiol.2007.10.013

Publication date: November 21, 2007

PMID: 18022563

L3MBTL1 recognition of mono- and dimethylated histones.

Min J, Allali-Hassani A, Nady N, Qi C, Ouyang H, Liu Y, MacKenzie F, Vedadi M, Arrowsmith CH

Nat. Struct. Mol. Biol.. 14(12):1229-30. doi: 10.1038/nsmb1340

Publication date: November 18, 2007

PMID: 18026117

Structure of the SOCS4-ElonginB/C complex reveals a distinct SOCS box interface and the molecular basis for SOCS-dependent EGFR degradation.

Bullock AN, Rodriguez MC, Debreczeni JE, Songyang Z, Knapp S

Structure. 15(11):1493-504. doi: 10.1016/j.str.2007.09.016

Publication date: November 14, 2007

PMID: 17997974

In situ proteolysis for protein crystallization and structure determination.

Dong A, Xu X, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Evdokimova E, Filippova E, Gu J, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Kim Y, Korniyenko Y, Minor W, Que Q, Savchenko A, Skarina T, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H

Nat. Methods. 4(12):1019-21. doi: 10.1038/nmeth1118

Publication date: November 4, 2007

PMID: 17982461

Structure determination of the motor domain of yeast kinesin kar3 by x-ray crystallography.

Park HW

Methods Mol. Biol.. 392:199-211. doi: 10.1007/978-1-59745-490-2_14

Publication date: October 24, 2007

PMID: 17951720

Structural and functional characterization of the human protein kinase ASK1.

Bunkoczi G, Salah E, Filippakopoulos P, Fedorov O, Müller S, Sobott F, Parker SA, Zhang H, Min W, Turk BE, Knapp S

Structure. 15(10):1215-26. doi: 10.1016/j.str.2007.08.011

Publication date: October 17, 2007

PMID: 17937911

Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.

Dufe VT, Qiu W, Müller IB, Hui R, Walter RD, Al-Karadaghi S

J. Mol. Biol.. 373(1):167-77. doi: 10.1016/j.jmb.2007.07.053

Publication date: October 12, 2007

PMID: 17822713

Structural basis of substrate-binding specificity of human arylamine N-acetyltransferases.

Wu H, Dombrovsky L, Tempel W, Martin F, Loppnau P, Goodfellow GH, Grant DM, Plotnikov AN

J. Biol. Chem.. 282(41):30189-97. doi: 10.1074/jbc.M704138200

Publication date: October 12, 2007

PMID: 17656365

The scientific impact of the Structural Genomics Consortium: a protein family and ligand-centered approach to medically-relevant human proteins.

Gileadi O, Knapp S, Lee WH, Marsden BD, Müller S, Niesen FH, Kavanagh KL, Ball LJ, von Delft F, Doyle DA, Oppermann UC, Sundström M

J. Struct. Funct. Genomics. 8(2-3):107-19. doi: 10.1007/s10969-007-9027-2

Publication date: October 12, 2007

PMID: 17932789

Nicotinamide riboside kinase structures reveal new pathways to NAD+.

Tempel W, Rabeh WM, Bogan KL, Belenky P, Wojcik M, Seidle HF, Nedyalkova L, Yang T, Sauve AA, Park HW, Brenner C

PLoS Biol.. 5(10):e263. doi: 10.1371/journal.pbio.0050263

Publication date: October 2, 2007

PMID: 17914902

Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder.

Hong BS, Senisterra G, Rabeh WM, Vedadi M, Leonardi R, Zhang YM, Rock CO, Jackowski S, Park HW

J. Biol. Chem.. 282(38):27984-93. doi: 10.1074/jbc.M701915200

Publication date: September 21, 2007

PMID: 17631502

The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability.

Niesen FH, Berglund H, Vedadi M

Nat Protoc. 2(9):2212-21. doi: 10.1038/nprot.2007.321

Publication date: September 15, 2007

PMID: 17853878

Structure and mechanism of spermidine synthases.

Wu H, Min J, Ikeguchi Y, Zeng H, Dong A, Loppnau P, Pegg AE, Plotnikov AN

Biochemistry. 46(28):8331-9. doi: 10.1021/bi602498k

Publication date: July 17, 2007

PMID: 17585781

Structural analysis identifies imidazo[1,2-b]pyridazines as PIM kinase inhibitors with in vitro antileukemic activity.

Pogacic V, Bullock AN, Fedorov O, Filippakopoulos P, Gasser C, Biondi A, Meyer-Monard S, Knapp S, Schwaller J

Cancer Res.. 67(14):6916-24. doi: 10.1158/0008-5472.CAN-07-0320

Publication date: July 15, 2007

PMID: 17638903

Activation segment exchange: a common mechanism of kinase autophosphorylation?

Oliver AW, Knapp S, Pearl LH

Trends Biochem. Sci.. 32(8):351-6. doi: 10.1016/j.tibs.2007.06.004

Publication date: July 12, 2007

PMID: 17627826

Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.

Ng SS, Kavanagh KL, McDonough MA, Butler D, Pilka ES, Lienard BM, Bray JE, Savitsky P, Gileadi O, von Delft F, Rose NR, Offer J, Scheinost JC, Borowski T, Sundstrom M, Schofield CJ, Oppermann U

Nature. 448(7149):87-91. doi: 10.1038/nature05971

Publication date: July 5, 2007

PMID: 17589501

Crystal structure of a binary complex between human GCN5 histone acetyltransferase domain and acetyl coenzyme A.

Schuetz A, Bernstein G, Dong A, Antoshenko T, Wu H, Loppnau P, Bochkarev A, Plotnikov AN

Proteins. 68(1):403-7. doi: 10.1002/prot.21407

Publication date: July 1, 2007

PMID: 17410582

Crystallization and preliminary X-ray analysis of phage Mu activator protein C in a complex with promoter DNA.

Shanmuganatham KK, Ravichandran M, Howe MM, Park HW

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.. 63(Pt 7):620-3. doi: 10.1107/S1744309107025286

Publication date: July 1, 2007

PMID: 17620727

Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.

Walldén K, Stenmark P, Nyman T, Flodin S, Gräslund S, Loppnau P, Bianchi V, Nordlund P

J. Biol. Chem.. 282(24):17828-36. doi: 10.1074/jbc.M700917200

Publication date: June 15, 2007

PMID: 17405878

Glyoxylate and pyruvate are antagonistic effectors of the Escherichia coli IclR transcriptional regulator.

Lorca GL, Ezersky A, Lunin VV, Walker JR, Altamentova S, Evdokimova E, Vedadi M, Bochkarev A, Savchenko A

J. Biol. Chem.. 282(22):16476-91. doi: 10.1074/jbc.M610838200

Publication date: June 1, 2007

PMID: 17426033

Specificity profiling of Pak kinases allows identification of novel phosphorylation sites.

Rennefahrt UE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR

J. Biol. Chem.. 282(21):15667-78. doi: 10.1074/jbc.M700253200

Publication date: May 25, 2007

PMID: 17392278

Hexagonal close packing of nonionic surfactant micelles in water.

Zeng X, Liu Y, Impéror-Clerc M

J Phys Chem B. 111(19):5174-9. doi: 10.1021/jp0687955

Publication date: May 17, 2007

PMID: 17429992

Interaction of hydroxylated collagen IV with the von hippel-lindau tumor suppressor.

Grosfeld A, Stolze IP, Cockman ME, Pugh CW, Edelmann M, Kessler B, Bullock AN, Ratcliffe PJ, Masson N

J. Biol. Chem.. 282(18):13264-9. doi: 10.1074/jbc.M611648200

Publication date: May 4, 2007

PMID: 17339318

Structures of the human eIF4E homologous protein, h4EHP, in its m7GTP-bound and unliganded forms.

Rosettani P, Knapp S, Vismara MG, Rusconi L, Cameron AD

J. Mol. Biol.. 368(3):691-705. doi: 10.1016/j.jmb.2007.02.019

Publication date: May 4, 2007

PMID: 17368478

Protein-protein interaction site mapping using NMR-detected mutational scanning.

Baminger B, Ludwiczek ML, Kontaxis G, Knapp S, Konrat R

J. Biomol. NMR. 38(2):133-7. doi: 10.1007/s10858-007-9154-x

Publication date: April 20, 2007

PMID: 17447011

Structural and chemical profiling of the human cytosolic sulfotransferases.

Allali-Hassani A, Pan PW, Dombrovski L, Najmanovich R, Tempel W, Dong A, Loppnau P, Martin F, Thornton J, Thonton J, Edwards AM, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH

PLoS Biol.. 5(5):e97. doi: 10.1371/journal.pbio.0050097

Publication date: April 12, 2007

PMID: 17425406

Structural basis of allele variation of human thiopurine-S-methyltransferase.

Wu H, Horton JR, Battaile K, Allali-Hassani A, Martin F, Zeng H, Loppnau P, Vedadi M, Bochkarev A, Plotnikov AN, Cheng X

Proteins. 67(1):198-208. doi: 10.1002/prot.21272

Publication date: April 1, 2007

PMID: 17243178

Insights for the development of specific kinase inhibitors by targeted structural genomics.

Fedorov O, Sundström M, Marsden B, Knapp S

Drug Discov. Today. 12(9-10):365-72. doi: 10.1016/j.drudis.2007.03.006

Publication date: March 29, 2007

PMID: 17467572

Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin.

Schuetz A, Min J, Antoshenko T, Wang CL, Allali-Hassani A, Dong A, Loppnau P, Vedadi M, Bochkarev A, Sternglanz R, Plotnikov AN

Structure. 15(3):377-89. doi: 10.1016/j.str.2007.02.002

Publication date: March 16, 2007

PMID: 17355872

Structural and biochemical characterization of human orphan DHRS10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity.

Lukacik P, Keller B, Bunkoczi G, Kavanagh KL, Kavanagh K, Lee WH, Hwa Lee W, Adamski J, Oppermann U

Biochem. J.. 402(3):419-27. doi: 10.1042/BJ20061319

Publication date: March 15, 2007

PMID: 17067289

A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity.

Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP

J. Med. Chem.. 50(5):915-21. doi: 10.1021/jm060827p

Publication date: March 8, 2007

PMID: 17290979

Structure and regulation of the human Nek2 centrosomal kinase.

Rellos P, Ivins FJ, Baxter JE, Pike A, Nott TJ, Parkinson DM, Das S, Howell S, Fedorov O, Shen QY, Fry AM, Knapp S, Smerdon SJ

J. Biol. Chem.. 282(9):6833-42. doi: 10.1074/jbc.M609721200

Publication date: March 2, 2007

PMID: 17197699

Biochemical characterization of TASSELSEED 2, an essential plant short-chain dehydrogenase/reductase with broad spectrum activities.

Wu X, Knapp S, Stamp A, Stammers DK, Jörnvall H, Dellaporta SL, Oppermann U

FEBS J.. 274(5):1172-82. doi: 10.1111/j.1742-4658.2007.05642.x

Publication date: February 15, 2007

PMID: 17298439

Crystal Structures of the p21-activated kinases PAK4, PAK5, and PAK6 reveal catalytic domain plasticity of active group II PAKs.

Eswaran J, Lee WH, Debreczeni JE, Filippakopoulos P, Turnbull A, Fedorov O, Deacon SW, Peterson JR, Knapp S

Structure. 15(2):201-13. doi: 10.1016/j.str.2007.01.001

Publication date: February 13, 2007

PMID: 17292838

The crystal structures of human calpains 1 and 9 imply diverse mechanisms of action and auto-inhibition.

Davis TL, Walker JR, Finerty PJ, Mackenzie F, Newman EM, Dhe-Paganon S

J. Mol. Biol.. 366(1):216-29. doi: 10.1016/j.jmb.2006.11.037

Publication date: February 9, 2007

PMID: 17157313

Crystal structure of human inosine triphosphatase. Substrate binding and implication of the inosine triphosphatase deficiency mutation P32T.

Stenmark P, Kursula P, Flodin S, Gräslund S, Landry R, Nordlund P, Schüler H

J. Biol. Chem.. 282(5):3182-7. doi: 10.1074/jbc.M609838200

Publication date: February 2, 2007

PMID: 17138556

Reversible sequestration of active site cysteines in a 2Fe-2S-bridged dimer provides a mechanism for glutaredoxin 2 regulation in human mitochondria.

Johansson C, Kavanagh KL, Gileadi O, Oppermann U

J. Biol. Chem.. 282(5):3077-82. doi: 10.1074/jbc.M608179200

Publication date: February 2, 2007

PMID: 17121859

SDR-type human hydroxysteroid dehydrogenases involved in steroid hormone activation.

Wu X, Lukacik P, Kavanagh KL, Oppermann U

Mol. Cell. Endocrinol.. 265-266:71-6. doi: 10.1016/j.mce.2006.12.006

Publication date: January 17, 2007

PMID: 17234335

Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.

Najmanovich RJ, Allali-Hassani A, Morris RJ, Dombrovsky L, Pan PW, Vedadi M, Plotnikov AN, Edwards A, Arrowsmith C, Thornton JM

Bioinformatics. 23(2):e104-9. doi: 10.1093/bioinformatics/btl292

Publication date: January 15, 2007

PMID: 17237076

Resonance assignment of the RGS domain of human RGS10.

Fedorov OY, Higman VA, Schmieder P, Leidert M, Diehl A, Elkins J, Soundararajan M, Oschkinat H, Ball LJ

J. Biomol. NMR. 38(2):191. doi: 10.1007/s10858-006-9111-0

Publication date: December 19, 2006

PMID: 17180548

Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).

Avvakumov GV, Walker JR, Xue S, Finerty PJ, Mackenzie F, Newman EM, Dhe-Paganon S

J. Biol. Chem.. 281(49):38061-70. doi: 10.1074/jbc.M606704200

Publication date: December 8, 2006

PMID: 17035239

Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms.

Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R

Mol. Biochem. Parasitol.. 151(1):100-10. doi: 10.1016/j.molbiopara.2006.10.011

Publication date: November 13, 2006

PMID: 17125854

Screening for ligands using a generic and high-throughput light-scattering-based assay.

Senisterra GA, Markin E, Yamazaki K, Hui R, Vedadi M, Awrey DE

J Biomol Screen. 11(8):940-8. doi: 10.1177/1087057106294699

Publication date: November 7, 2006

PMID: 17092916

Structure of human protein kinase C eta (PKCeta) C2 domain and identification of phosphorylation sites.

Littler DR, Walker JR, She YM, Finerty PJ, Newman EM, Dhe-Paganon S

Biochem. Biophys. Res. Commun.. 349(4):1182-9. doi: 10.1016/j.bbrc.2006.08.160

Publication date: November 3, 2006

PMID: 16973127

Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination.

Vedadi M, Niesen FH, Allali-Hassani A, Fedorov OY, Finerty PJ, Wasney GA, Yeung R, Arrowsmith C, Ball LJ, Berglund H, Hui R, Marsden BD, Nordlund P, Sundstrom M, Weigelt J, Edwards AM

Proc. Natl. Acad. Sci. U.S.A.. 103(43):15835-40. doi: 10.1073/pnas.0605224103

Publication date: October 24, 2006

PMID: 17035505

Type 1 11beta-hydroxysteroid dehydrogenase as universal drug target in metabolic diseases?

Oppermann U

Endocr Metab Immune Disord Drug Targets. 6(3):259-69.

Publication date: October 5, 2006

PMID: 17017977