Publications

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2009

Prepublication data sharing.

Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP, Berglund L, Bobrow M, Bountra C, Brookes AJ, Cambon-Thomsen A, Carter NP, Chisholm RL, Contreras JL, Cooke RM, Crosby WL, Dewar K, Durbin R, Dyke SO, Ecker JR, El Emam K, Feuk L, Gabriel SB, Gallacher J, Gelbart WM, Granell A, Guarner F, Hubbard T, Jackson SA, Jennings JL, Joly Y, Jones SM, Kaye J, Kennedy KL, Knoppers BM, Kyrpides NC, Lowrance WW, Luo J, MacKay JJ, Martín-Rivera L, McCombie WR, McPherson JD, Miller L, Miller W, Moerman D, Mooser V, Morton CC, Ostell JM, Ouellette BF, Parkhill J, Raina PS, Rawlings C, Scherer SE, Scherer SW, Schofield PN, Sensen CW, Stodden VC, Sussman MR, Tanaka T, Thornton J, Tsunoda T, Valle D, Vuorio EI, Walker NM, Wallace S, Weinstock G, Whitman WB, Worley KC, Wu C, Wu J, Yu J

Nature. 461(7261):168-70. doi: 10.1038/461168a

Publication date: September 10, 2009

PMID: 19741685

Propionate analogues of zearalenone bind to Hsp90.

Ugele M, Sasse F, Knapp S, Fedorov O, Zubriene A, Matulis D, Maier ME

Chembiochem. 10(13):2203-12. doi: 10.1002/cbic.200900109

Publication date: September 4, 2009

PMID: 19637143

The case for open-access chemical biology. A strategy for pre-competitive medicinal chemistry to promote drug discovery.

Weigelt J

EMBO Rep.. 10(9):941-5. doi: 10.1038/embor.2009.193

Publication date: September 2, 2009

PMID: 19721463

Dissection of PIM serine/threonine kinases in FLT3-ITD-induced leukemogenesis reveals PIM1 as regulator of CXCL12-CXCR4-mediated homing and migration.

Grundler R, Brault L, Gasser C, Bullock AN, Dechow T, Woetzel S, Pogacic V, Villa A, Ehret S, Berridge G, Spoo A, Dierks C, Biondi A, Knapp S, Duyster J, Schwaller J

J. Exp. Med.. 206(9):1957-70. doi: 10.1084/jem.20082074

Publication date: August 31, 2009

PMID: 19687226

Evaluation of virtual screening as a tool for chemical genetic applications.

Campagna-Slater V, Schapira M

J Chem Inf Model. 49(9):2082-91. doi: 10.1021/ci900219u

Publication date: August 26, 2009

PMID: 19702241

Crystallographic structure of the tetratricopeptide repeat domain of Plasmodium falciparum FKBP35 and its molecular interaction with Hsp90 C-terminal pentapeptide.

Alag R, Bharatham N, Dong A, Hills T, Harikishore A, Widjaja AA, Shochat SG, Hui R, Yoon HS

Protein Sci.. 18(10):2115-24. doi: 10.1002/pro.226

Publication date: August 20, 2009

PMID: 19691130

Structural recognition of an optimized substrate for the ephrin family of receptor tyrosine kinases.

Davis TL, Walker JR, Allali-Hassani A, Parker SA, Turk BE, Dhe-Paganon S

FEBS J.. 276(16):4395-404. doi: 10.1111/j.1742-4658.2009.07147.x

Publication date: August 15, 2009

PMID: 19678838

Out of the box binding determines specificity of SH2 domain interaction.

Müller S, Knapp S

Structure. 17(8):1040-1. doi: 10.1016/j.str.2009.07.002

Publication date: August 12, 2009

PMID: 19679083

Crystal structure of human carbonic anhydrase-related protein VIII reveals the basis for catalytic silencing.

Picaud SS, Muniz JR, Kramm A, Pilka ES, Kochan G, Oppermann U, Yue WW

Proteins. 76(2):507-11. doi: 10.1002/prot.22411

Publication date: August 1, 2009

PMID: 19360879

Discovery and structural analysis of Eph receptor tyrosine kinase inhibitors.

Choi Y, Syeda F, Walker JR, Finerty PJ, Cuerrier D, Wojciechowski A, Liu Q, Dhe-Paganon S, Gray NS

Bioorg. Med. Chem. Lett.. 19(15):4467-70. doi: 10.1016/j.bmcl.2009.05.029

Publication date: August 1, 2009

PMID: 19553108

Identification and optimisation of a novel series of pyrimidine based cyclooxygenase-2 (COX-2) inhibitors. Utilisation of a biotransformation approach.

Beswick PJ, Blackaby AP, Bountra C, Brown T, Browning K, Campbell IB, Corfield J, Gleave RJ, Guntrip SB, Hall RM, Hindley S, Lambeth PF, Lucas F, Mathews N, Naylor A, Player H, Price HS, Sidebottom PJ, Taylor NL, Webb G, Wiseman J

Bioorg. Med. Chem. Lett.. 19(15):4509-14. doi: 10.1016/j.bmcl.2009.02.089

Publication date: August 1, 2009

PMID: 19523822

Identification of [4-[4-(methylsulfonyl)phenyl]-6-(trifluoromethyl)-2-pyrimidinyl] amines and ethers as potent and selective cyclooxygenase-2 inhibitors.

Swarbrick ME, Beswick PJ, Gleave RJ, Green RH, Bingham S, Bountra C, Carter MC, Chambers LJ, Chessell IP, Clayton NM, Collins SD, Corfield JA, Hartley CD, Kleanthous S, Lambeth PF, Lucas FS, Mathews N, Naylor A, Page LW, Payne JJ, Pegg NA, Price HS, Skidmore J, Stevens AJ, Stocker R, Stratton SC, Stuart AJ, Wiseman JO

Bioorg. Med. Chem. Lett.. 19(15):4504-8. doi: 10.1016/j.bmcl.2009.02.085

Publication date: August 1, 2009

PMID: 19520573

Structural determinants of G-protein alpha subunit selectivity by regulator of G-protein signaling 2 (RGS2).

Kimple AJ, Soundararajan M, Hutsell SQ, Roos AK, Urban DJ, Setola V, Temple BR, Roth BL, Knapp S, Willard FS, Siderovski DP

J. Biol. Chem.. 284(29):19402-11. doi: 10.1074/jbc.M109.024711

Publication date: July 17, 2009

PMID: 19478087

Crystal structure of human diphosphoinositol phosphatase 1.

Thorsell AG, Persson C, Gräslund S, Hammarström M, Busam RD, Hallberg BM

Proteins. 77(1):242-6. doi: 10.1002/prot.22489

Publication date: July 9, 2009

PMID: 19585659

Substrate recognition and hydrolysis by a fungal xyloglucan-specific family 12 hydrolase.

Powlowski J, Mahajan S, Schapira M, Master ER

Carbohydr. Res.. 344(10):1175-9. doi: 10.1016/j.carres.2009.04.020

Publication date: July 6, 2009

PMID: 19433323

Structural basis for different specificities of acyltransferases associated with the human cytosolic and mitochondrial fatty acid synthases.

Bunkoczi G, Misquitta S, Wu X, Lee WH, Rojkova A, Kochan G, Kavanagh KL, Oppermann U, Smith S

Chem. Biol.. 16(6):667-75. doi: 10.1016/j.chembiol.2009.04.011

Publication date: June 26, 2009

PMID: 19549604

Open access chemical and clinical probes to support drug discovery.

Edwards AM, Bountra C, Kerr DJ, Willson TM

Nat. Chem. Biol.. 5(7):436-40. doi: 10.1038/nchembio0709-436

Publication date: June 19, 2009

PMID: 19536100

Three-dimensional structure and enzymatic function of proapoptotic human p53-inducible quinone oxidoreductase PIG3.

Porté S, Valencia E, Yakovtseva EA, Borràs E, Shafqat N, Debreczeny JE, Pike AC, Oppermann U, Farrés J, Fita I, Parés X

J. Biol. Chem.. 284(25):17194-205. doi: 10.1074/jbc.M109.001800

Publication date: June 19, 2009

PMID: 19349281

Crystal structures of human CDY proteins reveal a crotonase-like fold.

Wu H, Min J, Antoshenko T, Plotnikov AN

Proteins. 76(4):1054-61. doi: 10.1002/prot.22472

Publication date: June 10, 2009

PMID: 19507244

Large-scale structural biology of the human proteome.

Edwards A

Annu. Rev. Biochem.. 78:541-68. doi: 10.1146/annurev.biochem.78.070907.103305

Publication date: June 6, 2009

PMID: 19489729

Forward genetics in Toxoplasma gondii reveals a family of rhoptry kinases that mediates pathogenesis.

Sibley LD, Qiu W, Fentress S, Taylor SJ, Khan A, Hui R

Eukaryotic Cell. 8(8):1085-93. doi: 10.1128/EC.00107-09

Publication date: May 22, 2009

PMID: 19465561

Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.

Kochan G, Pilka ES, von Delft F, Oppermann U, Yue WW

J. Mol. Biol.. 388(5):997-1008. doi: 10.1016/j.jmb.2009.03.064

Publication date: May 22, 2009

PMID: 19345228

Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands.

Crowther GJ, Napuli AJ, Thomas AP, Chung DJ, Kovzun KV, Leibly DJ, Castaneda LJ, Bhandari J, Damman CJ, Hui R, Hol WG, Buckner FS, Verlinde CL, Zhang Z, Fan E, van Voorhis WC

J Biomol Screen. 14(6):700-7. doi: 10.1177/1087057109335749

Publication date: May 21, 2009

PMID: 19470714

Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.

Lehtiö L, Jemth AS, Collins R, Loseva O, Johansson A, Markova N, Hammarström M, Flores A, Holmberg-Schiavone L, Weigelt J, Helleday T, Schüler H, Karlberg T

J. Med. Chem.. 52(9):3108-11. doi: 10.1021/jm900052j

Publication date: May 14, 2009

PMID: 19354255

Girls homozygous for an IL-2-inducible T cell kinase mutation that leads to protein deficiency develop fatal EBV-associated lymphoproliferation.

Huck K, Feyen O, Niehues T, Rüschendorf F, Hübner N, Laws HJ, Telieps T, Knapp S, Wacker HH, Meindl A, Jumaa H, Borkhardt A

J. Clin. Invest.. 119(5):1350-8. doi: 10.1172/JCI37901

Publication date: May 9, 2009

PMID: 19425169

The DEXD/H-box RNA helicase DDX19 is regulated by an {alpha}-helical switch.

Collins R, Karlberg T, Lehtiö L, Schütz P, van den Berg S, Dahlgren LG, Hammarström M, Weigelt J, Schüler H

J. Biol. Chem.. 284(16):10296-300. doi: 10.1074/jbc.C900018200

Publication date: April 17, 2009

PMID: 19244245

Specificity of Campylobacter jejuni adhesin PEB3 for phosphates and structural differences among its ligand complexes.

Min T, Vedadi M, Watson DC, Wasney GA, Munger C, Cygler M, Matte A, Young NM

Biochemistry. 48(14):3057-67. doi: 10.1021/bi802195d

Publication date: April 14, 2009

PMID: 19236052

Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii.

Qiu W, Wernimont A, Tang K, Taylor S, Lunin V, Schapira M, Fentress S, Hui R, Sibley LD

EMBO J.. 28(7):969-79. doi: 10.1038/emboj.2009.24

Publication date: April 8, 2009

PMID: 19197235

In situ proteolysis to generate crystals for structure determination: an update.

Wernimont A, Edwards A

PLoS ONE. 4(4):e5094. doi: 10.1371/journal.pone.0005094

Publication date: April 7, 2009

PMID: 19352432

HD-PTP is a catalytically inactive tyrosine phosphatase due to a conserved divergence in its phosphatase domain.

Gingras MC, Zhang YL, Kharitidi D, Barr AJ, Knapp S, Tremblay ML, Pause A

PLoS ONE. 4(4):e5105. doi: 10.1371/journal.pone.0005105

Publication date: April 2, 2009

PMID: 19340315

Novel mutations in ACVR1 result in atypical features in two fibrodysplasia ossificans progressiva patients.

Petrie KA, Lee WH, Bullock AN, Pointon JJ, Smith R, Russell RG, Brown MA, Wordsworth BP, Triffitt JT

PLoS ONE. 4(3):e5005. doi: 10.1371/journal.pone.0005005

Publication date: March 30, 2009

PMID: 19330033

Short-term glucocorticoid treatment increases insulin secretion in islets derived from lean mice through multiple pathways and mechanisms.

Hult M, Ortsäter H, Schuster G, Graedler F, Beckers J, Adamski J, Ploner A, Jörnvall H, Bergsten P, Oppermann U

Mol. Cell. Endocrinol.. 301(1-2):109-16. doi: 10.1016/j.mce.2008.09.038

Publication date: March 25, 2009

PMID: 18984029

Structure of dystrophia myotonica protein kinase.

Elkins JM, Amos A, Niesen FH, Pike AC, Fedorov O, Knapp S

Protein Sci.. 18(4):782-91. doi: 10.1002/pro.82

Publication date: March 25, 2009

PMID: 19309729

Structure-activity relationships of human AKR-type oxidoreductases involved in bile acid synthesis: AKR1D1 and AKR1C4.

Lee WH, Lukacik P, Guo K, Ugochukwu E, Kavanagh KL, Marsden B, Oppermann U

Mol. Cell. Endocrinol.. 301(1-2):199-204. doi: 10.1016/j.mce.2008.09.042

Publication date: March 25, 2009

PMID: 19013211

Analysis of the substrate-binding site of human carbonyl reductases CBR1 and CBR3 by site-directed mutagenesis.

El-Hawari Y, Favia AD, Pilka ES, Kisiela M, Oppermann U, Martin HJ, Maser E

Chem. Biol. Interact.. 178(1-3):234-41. doi: 10.1016/j.cbi.2008.11.004

Publication date: March 16, 2009

PMID: 19061875

The human short-chain dehydrogenase/reductase (SDR) superfamily: a bioinformatics summary.

Bray JE, Marsden BD, Oppermann U

Chem. Biol. Interact.. 178(1-3):99-109. doi: 10.1016/j.cbi.2008.10.058

Publication date: March 16, 2009

PMID: 19061874

The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative.

Persson B, Kallberg Y, Bray JE, Bruford E, Dellaporta SL, Favia AD, Duarte RG, Jörnvall H, Kavanagh KL, Kedishvili N, Kisiela M, Maser E, Mindnich R, Orchard S, Penning TM, Thornton JM, Adamski J, Oppermann U

Chem. Biol. Interact.. 178(1-3):94-8. doi: 10.1016/j.cbi.2008.10.040

Publication date: March 16, 2009

PMID: 19027726

Crystal structure of human eIF5A1: insight into functional similarity of human eIF5A1 and eIF5A2.

Tong Y, Park I, Hong BS, Nedyalkova L, Tempel W, Park HW

Proteins. 75(4):1040-5. doi: 10.1002/prot.22378

Publication date: March 13, 2009

PMID: 19280598

Kinase domain insertions define distinct roles of CLK kinases in SR protein phosphorylation.

Bullock AN, Das S, Debreczeni JE, Rellos P, Fedorov O, Niesen FH, Guo K, Papagrigoriou E, Amos AL, Cho S, Turk BE, Ghosh G, Knapp S

Structure. 17(3):352-62. doi: 10.1016/j.str.2008.12.023

Publication date: March 11, 2009

PMID: 19278650

Discovery of indoline-based, natural-product-like compounds as probes of focal adhesion kinase signaling pathways.

Poondra RR, Kumar NN, Bijian K, Prakesch M, Campagna-Slater V, Reayi A, Reddy PT, Choudhry A, Barnes ML, Leek DM, Daroszewska M, Lougheed C, Xu B, Schapira M, Alaoui-Jamali MA, Arya P

J Comb Chem. 11(2):303-9. doi: 10.1021/cc8001525

Publication date: March 9, 2009

PMID: 19146410

Structural basis and specificity of human otubain 1-mediated deubiquitination.

Edelmann MJ, Iphöfer A, Akutsu M, Altun M, di Gleria K, Kramer HB, Fiebiger E, Dhe-Paganon S, Kessler BM

Biochem. J.. 418(2):379-90. doi: 10.1042/BJ20081318

Publication date: March 1, 2009

PMID: 18954305

Structure and function of histone methylation binding proteins.

Adams-Cioaba MA, Min J

Biochem. Cell Biol.. 87(1):93-105. doi: 10.1139/O08-129

Publication date: February 24, 2009

PMID: 19234526

The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta.

Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, Liu S, Zhang R, Tiefenbach J, Lajoie G, Plotnikov AN, Botchkarev A, Krause HM, Edwards A

PLoS Biol.. 7(2):e43. doi: 10.1371/journal.pbio.1000043

Publication date: February 24, 2009

PMID: 19243223

Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

Guo Y, Nady N, Qi C, Allali-Hassani A, Zhu H, Pan P, Adams-Cioaba MA, Amaya MF, Dong A, Vedadi M, Schapira M, Read RJ, Arrowsmith CH, Min J

Nucleic Acids Res.. 37(7):2204-10. doi: 10.1093/nar/gkp086

Publication date: February 20, 2009

PMID: 19233876

An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene.

Tempel W, Wu H, Dombrovsky L, Zeng H, Loppnau P, Zhu H, Plotnikov AN, Bochkarev A

Proteins. 74(3):789-93. doi: 10.1002/prot.22299

Publication date: February 15, 2009

PMID: 19089949

Distinguishing between calpain heterodimerization and homodimerization.

Ravulapalli R, Campbell RL, Gauthier SY, Dhe-Paganon S, Davies PL

FEBS J.. 276(4):973-82. doi: 10.1111/j.1742-4658.2008.06833.x

Publication date: February 14, 2009

PMID: 19215300

Structure of the human RECQ1 helicase reveals a putative strand-separation pin.

Pike AC, Shrestha B, Popuri V, Burgess-Brown N, Muzzolini L, Costantini S, Vindigni A, Gileadi O

Proc. Natl. Acad. Sci. U.S.A.. 106(4):1039-44. doi: 10.1073/pnas.0806908106

Publication date: January 27, 2009

PMID: 19151156

Large-scale structural analysis of the classical human protein tyrosine phosphatome.

Barr AJ, Ugochukwu E, Lee WH, King ON, Filippakopoulos P, Alfano I, Savitsky P, Burgess-Brown NA, Müller S, Knapp S

Cell. 136(2):352-63. doi: 10.1016/j.cell.2008.11.038

Publication date: January 23, 2009

PMID: 19167335

Targeting group II PAKs in cancer and metastasis.

Eswaran J, Soundararajan M, Knapp S

Cancer Metastasis Rev.. 28(1-2):209-17. doi: 10.1007/s10555-008-9181-4

Publication date: January 23, 2009

PMID: 19160016

Discovery of a potent and selective inhibitor for human carbonyl reductase 1 from propionate scanning applied to the macrolide zearalenone.

Zimmermann TJ, Niesen FH, Pilka ES, Knapp S, Oppermann U, Maier ME

Bioorg. Med. Chem.. 17(2):530-6. doi: 10.1016/j.bmc.2008.11.076

Publication date: January 15, 2009

PMID: 19097799

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