Publications | Structural Genomics Consortium

Gräslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schütz A, Heinemann U, Yokoyama S, Büssow K, Gunsalus KC

Nat. Methods. 5(2):135-46. doi: 10.1038/nmeth.f.202

Publication date: February 1, 2008

PMID: 18235434

Structure and function of sedoheptulose-7-phosphate isomerase, a critical enzyme for lipopolysaccharide biosynthesis and a target for antibiotic adjuvants.

Taylor PL, Blakely KM, de Leon GP, Walker JR, McArthur F, Evdokimova E, Zhang K, Valvano MA, Wright GD, Junop MS

J. Biol. Chem.. 283(5):2835-45. doi: 10.1074/jbc.M706163200

Publication date: February 1, 2008

PMID: 18056714

Codon optimization can improve expression of human genes in Escherichia coli: A multi-gene study.

Burgess-Brown NA, Sharma S, Sobott F, Loenarz C, Oppermann U, Gileadi O

Protein Expr. Purif.. 59(1):94-102. doi: 10.1016/j.pep.2008.01.008

Publication date: January 26, 2008

PMID: 18289875

First crystallographic models of human TBC domains in the context of a family-wide structural analysis.

Tempel W, Tong Y, Dimov S, Bochkarev A, Park H

Proteins. 71(1):497-502. doi: 10.1002/prot.21885

Publication date: January 12, 2008

PMID: 18186464

Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture.

Eswaran J, Bernad A, Ligos JM, Guinea B, Debreczeni JE, Sobott F, Parker SA, Najmanovich R, Turk BE, Knapp S

Structure. 16(1):115-24. doi: 10.1016/j.str.2007.10.026

Publication date: January 11, 2008

PMID: 18184589

SALMON: solvent accessibility, ligand binding, and mapping of ligand orientation by NMR spectroscopy.

Ludwig C, Michiels PJ, Wu X, Kavanagh KL, Pilka E, Jansson A, Oppermann U, Günther UL

J. Med. Chem.. 51(1):1-3. doi: 10.1021/jm701020f

Publication date: January 10, 2008

PMID: 18062662

Structure-function analysis of the filamentous actin binding domain of the neuronal scaffolding protein spinophilin.

Schüler H, Peti W

FEBS J.. 275(1):59-68. doi: 10.1111/j.1742-4658.2007.06171.x

Publication date: January 1, 2008

PMID: 18028445

Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain.

Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M

J. Biol. Chem.. 282(51):37215-24. doi: 10.1074/jbc.M703800200

Publication date: December 21, 2007

PMID: 17916560

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