Publications

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2009

Structure of the pseudokinase VRK3 reveals a degraded catalytic site, a highly conserved kinase fold, and a putative regulatory binding site.

Scheeff ED, Eswaran J, Bunkoczi G, Knapp S, Manning G

Structure. 17(1):128-38. doi: 10.1016/j.str.2008.10.018

Publication date: January 14, 2009

PMID: 19141289

2008

Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis.

Artz JD, Dunford JE, Arrowood MJ, Dong A, Chruszcz M, Kavanagh KL, Minor W, Russell RG, Ebetino FH, Oppermann U, Hui R

Chem. Biol.. 15(12):1296-306. doi: 10.1016/j.chembiol.2008.10.017

Publication date: December 22, 2008

PMID: 19101474

Extremely tight binding of a ruthenium complex to glycogen synthase kinase 3.

Atilla-Gokcumen GE, Pagano N, Streu C, Maksimoska J, Filippakopoulos P, Knapp S, Meggers E

Chembiochem. 9(18):2933-6. doi: 10.1002/cbic.200800489

Publication date: December 15, 2008

PMID: 19035373

Inhibitor scaffolds for 2-oxoglutarate-dependent histone lysine demethylases.

Rose NR, Ng SS, Mecinović J, Liénard BM, Bello SH, Sun Z, McDonough MA, Oppermann U, Schofield CJ

J. Med. Chem.. 51(22):7053-6. doi: 10.1021/jm800936s

Publication date: November 27, 2008

PMID: 18942826

Structural basis for parasite-specific functions of the divergent profilin of Plasmodium falciparum.

Kursula I, Kursula P, Ganter M, Panjikar S, Matuschewski K, Schüler H

Structure. 16(11):1638-48. doi: 10.1016/j.str.2008.09.008

Publication date: November 12, 2008

PMID: 19000816

Structural insights into the inhibited states of the Mer receptor tyrosine kinase.

Huang X, Finerty P, Walker JR, Butler-Cole C, Vedadi M, Schapira M, Parker SA, Turk BE, Thompson DA, Dhe-Paganon S

J. Struct. Biol.. 165(2):88-96. doi: 10.1016/j.jsb.2008.10.003

Publication date: November 5, 2008

PMID: 19028587

Building skeletally diverse architectures on the Indoline Scaffold: the discovery of a chemical probe of focal adhesion kinase signaling networks.

Prakesch M, Bijian K, Campagna-Slater V, Quevillon S, Joseph R, Wei CQ, Sesmilo E, Reayi A, Poondra RR, Barnes ML, Leek DM, Xu B, Lougheed C, Schapira M, Alaoui-Jamali M, Arya P

Bioorg. Med. Chem.. 16(21):9596-602. doi: 10.1016/j.bmc.2008.09.025

Publication date: November 1, 2008

PMID: 18835181

Structural and kinetic differences between human and Aspergillus fumigatus D-glucosamine-6-phosphate N-acetyltransferase.

Hurtado-Guerrero R, Raimi OG, Min J, Zeng H, Vallius L, Shepherd S, Ibrahim AF, Wu H, Plotnikov AN, van Aalten DM

Biochem. J.. 415(2):217-23. doi: 10.1042/BJ20081000

Publication date: October 15, 2008

PMID: 18601654

Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

Avvakumov GV, Walker JR, Xue S, Li Y, Duan S, Bronner C, Arrowsmith CH, Dhe-Paganon S

Nature. 455(7214):822-5. doi: 10.1038/nature07273

Publication date: October 9, 2008

PMID: 18772889

A pilot project to generate affinity reagents to human proteins.

Uhlen M, Gräslund S, Sundström M

Nat. Methods. 5(10):854-5. doi: 10.1038/nmeth1008-854

Publication date: October 1, 2008

PMID: 18825127

Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

Eydoux C, Spinelli S, Davis TL, Walker JR, Seitova A, Dhe-Paganon S, De Caro A, Cambillau C, Carrière F

Biochemistry. 47(36):9553-64. doi: 10.1021/bi8005576

Publication date: September 9, 2008

PMID: 18702514

Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation.

Filippakopoulos P, Kofler M, Hantschel O, Gish GD, Grebien F, Salah E, Neudecker P, Kay LE, Turk BE, Superti-Furga G, Pawson T, Knapp S

Cell. 134(5):793-803. doi: 10.1016/j.cell.2008.07.047

Publication date: September 5, 2008

PMID: 18775312

Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10.

Wu X, Oppermann M, Berndt KD, Bergman T, Jörnvall H, Knapp S, Oppermann U

Biochem. Biophys. Res. Commun.. 373(4):482-7. doi: 10.1016/j.bbrc.2008.06.030

Publication date: September 5, 2008

PMID: 18571501

Linear motif atlas for phosphorylation-dependent signaling.

Miller ML, Jensen LJ, Diella F, Jørgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R

Sci Signal. 1(35):ra2. doi: 10.1126/scisignal.1159433

Publication date: September 4, 2008

PMID: 18765831

The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site.

Trésaugues L, Stenmark P, Schüler H, Flodin S, Welin M, Nyman T, Hammarström M, Moche M, Gräslund S, Nordlund P

Proteins. 73(4):1047-52. doi: 10.1002/prot.22198

Publication date: September 4, 2008

PMID: 18767156

Structural and functional characterization of human Iba proteins.

Schulze JO, Quedenau C, Roske Y, Adam T, Schüler H, Behlke J, Turnbull AP, Sievert V, Scheich C, Mueller U, Heinemann U, Büssow K

FEBS J.. 275(18):4627-40. doi: 10.1111/j.1742-4658.2008.06605.x

Publication date: September 1, 2008

PMID: 18699778

FKBP family proteins: immunophilins with versatile biological functions.

Kang CB, Hong Y, Dhe-Paganon S, Yoon HS

Neurosignals. 16(4):318-25. doi: 10.1159/000123041

Publication date: July 18, 2008

PMID: 18635947

UnPAKing the class differences among p21-activated kinases.

Eswaran J, Soundararajan M, Kumar R, Knapp S

Trends Biochem. Sci.. 33(8):394-403. doi: 10.1016/j.tibs.2008.06.002

Publication date: July 17, 2008

PMID: 18639460

The structure of the PP2A regulatory subunit B56 gamma: the remaining piece of the PP2A jigsaw puzzle.

Magnusdottir A, Stenmark P, Flodin S, Nyman T, Kotenyova T, Gräslund S, Ogg D, Nordlund P

Proteins. 74(1):212-21. doi: 10.1002/prot.22150

Publication date: July 12, 2008

PMID: 18618707

The structure of P-TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation.

Baumli S, Lolli G, Lowe ED, Troiani S, Rusconi L, Bullock AN, Debreczeni JE, Knapp S, Johnson LN

EMBO J.. 27(13):1907-18. doi: 10.1038/emboj.2008.121

Publication date: July 9, 2008

PMID: 18566585

Actin/myosin-based gliding motility in apicomplexan parasites.

Matuschewski K, Schüler H

Subcell. Biochem.. 47:110-20.

Publication date: July 1, 2008

PMID: 18512346

Structural analysis of CYP2R1 in complex with vitamin D3.

Strushkevich N, Usanov SA, Plotnikov AN, Jones G, Park HW

J. Mol. Biol.. 380(1):95-106. doi: 10.1016/j.jmb.2008.03.065

Publication date: June 27, 2008

PMID: 18511070

Autoregulation by the juxtamembrane region of the human ephrin receptor tyrosine kinase A3 (EphA3).

Davis TL, Walker JR, Loppnau P, Butler-Cole C, Allali-Hassani A, Dhe-Paganon S

Structure. 16(6):873-84. doi: 10.1016/j.str.2008.03.008

Publication date: June 13, 2008

PMID: 18547520

High throughput crystallography at SGC Toronto: an overview.

Bochkarev A, Tempel W

Methods Mol. Biol.. 426:515-21. doi: 10.1007/978-1-60327-058-8_34

Publication date: June 11, 2008

PMID: 18542887

High throughput production of recombinant human proteins for crystallography.

Gileadi O, Burgess-Brown NA, Colebrook SM, Berridge G, Savitsky P, Smee CE, Loppnau P, Johansson C, Salah E, Pantic NH

Methods Mol. Biol.. 426:221-46. doi: 10.1007/978-1-60327-058-8_14

Publication date: June 11, 2008

PMID: 18542867

Crystal structure of human spermine synthase: implications of substrate binding and catalytic mechanism.

Wu H, Min J, Zeng H, McCloskey DE, Ikeguchi Y, Loppnau P, Michael AJ, Pegg AE, Plotnikov AN

J. Biol. Chem.. 283(23):16135-46. doi: 10.1074/jbc.M710323200

Publication date: June 6, 2008

PMID: 18367445

A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research.

Nady N, Min J, Kareta MS, Chédin F, Arrowsmith CH

Trends Biochem. Sci.. 33(7):305-13. doi: 10.1016/j.tibs.2008.04.014

Publication date: June 4, 2008

PMID: 18538573

Structural and biophysical characterization of human myo-inositol oxygenase.

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

J. Biol. Chem.. 283(22):15209-16. doi: 10.1074/jbc.M800348200

Publication date: May 30, 2008

PMID: 18364358

Zinc binding catalytic domain of human tankyrase 1.

Lehtiö L, Collins R, van den Berg S, Johansson A, Dahlgren LG, Hammarström M, Helleday T, Holmberg-Schiavone L, Karlberg T, Weigelt J

J. Mol. Biol.. 379(1):136-45. doi: 10.1016/j.jmb.2008.03.058

Publication date: May 23, 2008

PMID: 18436240

The crystal structure of human WD40 repeat-containing peptidylprolyl isomerase (PPWD1).

Davis TL, Walker JR, Ouyang H, MacKenzie F, Butler-Cole C, Newman EM, Eisenmesser EZ, Dhe-Paganon S

FEBS J.. 275(9):2283-95. doi: 10.1111/j.1742-4658.2008.06381.x

Publication date: May 1, 2008

PMID: 18397323

Application of high-throughput isothermal denaturation to assess protein stability and screen for ligands.

Senisterra GA, Soo Hong B, Park HW, Vedadi M

J Biomol Screen. 13(5):337-42. doi: 10.1177/1087057108317825

Publication date: April 30, 2008

PMID: 18448703

Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity.

Schuetz A, Min J, Allali-Hassani A, Schapira M, Shuen M, Loppnau P, Mazitschek R, Kwiatkowski NP, Lewis TA, Maglathin RL, McLean TH, Bochkarev A, Plotnikov AN, Vedadi M, Arrowsmith CH

J. Biol. Chem.. 283(17):11355-63. doi: 10.1074/jbc.M707362200

Publication date: April 25, 2008

PMID: 18285338

Similar biological activities of two isostructural ruthenium and osmium complexes.

Maksimoska J, Williams DS, Atilla-Gokcumen GE, Smalley KS, Carroll PJ, Webster RD, Filippakopoulos P, Knapp S, Herlyn M, Meggers E

Chemistry. 14(16):4816-22. doi: 10.1002/chem.200800294

Publication date: April 22, 2008

PMID: 18425743

Crystal structure of the methyltransferase domain of human TARBP1.

Wu H, Min J, Zeng H, Plotnikov AN

Proteins. 72(1):519-25. doi: 10.1002/prot.22065

Publication date: April 17, 2008

PMID: 18412263

Structure-activity relationships among the nitrogen containing bisphosphonates in clinical use and other analogues: time-dependent inhibition of human farnesyl pyrophosphate synthase.

Dunford JE, Kwaasi AA, Rogers MJ, Barnett BL, Ebetino FH, Russell RG, Oppermann U, Kavanagh KL

J. Med. Chem.. 51(7):2187-95. doi: 10.1021/jm7015733

Publication date: April 10, 2008

PMID: 18327899

Baculovirus expression vector system: an emerging host for high-throughput eukaryotic protein expression.

Shrestha B, Smee C, Gileadi O

Methods Mol. Biol.. 439:269-89. doi: 10.1007/978-1-59745-188-8_19

Publication date: March 29, 2008

PMID: 18370110

Role of short-chain hydroxyacyl CoA dehydrogenases in SCHAD deficiency.

Filling C, Keller B, Hirschberg D, Marschall HU, Jörnvall H, Bennett MJ, Oppermann U

Biochem. Biophys. Res. Commun.. 368(1):6-11. doi: 10.1016/j.bbrc.2007.10.188

Publication date: March 28, 2008

PMID: 18036338

Structural genomics and drug discovery: all in the family.

Weigelt J, McBroom-Cerajewski LD, Schapira M, Zhao Y, Arrowsmith CH, Arrowmsmith CH

Curr Opin Chem Biol. 12(1):32-9. doi: 10.1016/j.cbpa.2008.01.045

Publication date: March 7, 2008

PMID: 18282486

Doing more than just the structure-structural genomics in kinase drug discovery.

Marsden BD, Knapp S

Curr Opin Chem Biol. 12(1):40-5. doi: 10.1016/j.cbpa.2008.01.042

Publication date: February 29, 2008

PMID: 18267130

Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites.

Pike AC, Rellos P, Niesen FH, Turnbull A, Oliver AW, Parker SA, Turk BE, Pearl LH, Knapp S

EMBO J.. 27(4):704-14. doi: 10.1038/emboj.2008.8

Publication date: February 20, 2008

PMID: 18239682

Ligand supplementation as a method to increase soluble heterologous protein production.

Hozjan V, Guo K, Wu X, Oppermann U

Expert Rev Proteomics. 5(1):137-43. doi: 10.1586/14789450.5.1.137

Publication date: February 20, 2008

PMID: 18282129

Bermuda Principles meet structural biology.

Edwards A

Nat. Struct. Mol. Biol.. 15(2):116. doi: 10.1038/nsmb0208-116

Publication date: February 6, 2008

PMID: 18250626

Protein production and purification.

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

2007

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

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