Publications

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2017

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB

Cell Stem Cell. 21(3):411. doi: 10.1016/j.stem.2017.08.008

Publication date: September 7, 2017

PMID: 28886368

RAC1 Missense Mutations in Developmental Disorders with Diverse Phenotypes.

Reijnders MRF, Ansor NM, Kousi M, Yue WW, Tan PL, Clarkson K, Clayton-Smith J, Corning K, Jones JR, Lam WWK, Mancini GMS, Marcelis C, Mohammed S, Pfundt R, Roifman M, Cohn R, Chitayat D, Millard TH, Katsanis N, Brunner HG, Banka S

Am. J. Hum. Genet.. 101(3):466-477. doi: 10.1016/j.ajhg.2017.08.007

Publication date: September 7, 2017

PMID: 28886345

Novel patient missense mutations in the HSD17B10 gene affect dehydrogenase and mitochondrial tRNA modification functions of the encoded protein.

Oerum S, Roovers M, Leichsenring M, Acquaviva-Bourdain C, Beermann F, Gemperle-Britschgi C, Fouilhoux A, Korwitz-Reichelt A, Bailey HJ, Droogmans L, Oppermann U, Sass JO, Yue WW

Biochim. Biophys. Acta. doi: 10.1016/j.bbadis.2017.09.002

Publication date: September 6, 2017

PMID: 28888424

A potent series targeting the malarial cGMP-dependent protein kinase clears infection and blocks transmission.

Baker DA, Stewart LB, Large JM, Bowyer PW, Ansell KH, Jiménez-Díaz MB, El Bakkouri M, Birchall K, Dechering KJ, Bouloc NS, Coombs PJ, Whalley D, Harding DJ, Smiljanic-Hurley E, Wheldon MC, Walker EM, Dessens JT, Lafuente MJ, Sanz LM, Gamo FJ, Ferrer SB, Hui R, Bousema T, Angulo-Barturén I, Merritt AT, Croft SL, Gutteridge WE, Kettleborough CA, Osborne SA

Nat Commun. 8(1):430. doi: 10.1038/s41467-017-00572-x

Publication date: September 5, 2017

PMID: 28874661

First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.

Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1706907114

Publication date: September 1, 2017

PMID: 28864533

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.

Lan X, Jörg DJ, Cavalli FMG, Richards LM, Nguyen LV, Vanner RJ, Guilhamon P, Lee L, Kushida MM, Pellacani D, Park NI, Coutinho FJ, Whetstone H, Selvadurai HJ, Che C, Luu B, Carles A, Moksa M, Rastegar N, Head R, Dolma S, Prinos P, Cusimano MD, Das S, Bernstein M, Arrowsmith CH, Mungall AJ, Moore RA, Ma Y, Gallo M, Lupien M, Pugh TJ, Taylor MD, Hirst M, Eaves CJ, Simons BD, Dirks PB

Nature. doi: 10.1038/nature23666

Publication date: August 30, 2017

PMID: 28854171

Role of remodeling and spacing factor 1 in histone H2A ubiquitination-mediated gene silencing.

Zhang Z, Jones AE, Wu W, Kim J, Kang Y, Bi X, Gu Y, Popov IK, Renfrow MB, Vassylyeva MN, Vassylyev DG, Giles KE, Chen D, Kumar A, Fan Y, Tong Y, Liu CF, An W, Chang C, Luo J, Chow LT, Wang H

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1711158114

Publication date: August 30, 2017

PMID: 28855339

Selective targeting of Bromodomains of the Bromodomain-PHD Fingers family impairs osteoclast differentiation.

Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UCT, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S

ACS Chem. Biol.. doi: 10.1021/acschembio.7b00481

Publication date: August 29, 2017

PMID: 28849908

TFG facilitates outer coat disassembly on COPII transport carriers to promote tethering and fusion with ER-Golgi intermediate compartments.

Hanna MG, Block S, Frankel EB, Hou F, Johnson A, Yuan L, Knight G, Moresco JJ, Yates JR, Ashton R, Schekman R, Tong Y, Audhya A

Proc. Natl. Acad. Sci. U.S.A.. doi: 10.1073/pnas.1709120114

Publication date: August 29, 2017

PMID: 28851831

Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities.

Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS

Structure. doi: 10.1016/j.str.2017.07.017

Publication date: August 28, 2017

PMID: 28890361

Tudor-domain protein PHF20L1 reads lysine methylated retinoblastoma tumour suppressor protein.

Carr SM, Munro S, Sagum CA, Fedorov O, Bedford MT, La Thangue NB

Cell Death Differ.. doi: 10.1038/cdd.2017.135

Publication date: August 25, 2017

PMID: 28841214

A novel image-based high throughput screening assay discovers therapeutic candidates for adult polyglucosan body disease.

Solemsky LJ, Khazanov N, Senderowitz H, Wang P, Minassian BA, Ferreira IM, Yue WW, Lossos A, Weil M, Kakhlon O

Biochem. J.. doi: 10.1042/BCJ20170469

Publication date: August 21, 2017

PMID: 28827282

Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle Intermediates.

Tarhonskaya H, Nowak RP, Johansson C, Szykowska A, Tumber A, Hancock RL, Lang P, Flashman E, Oppermann U, Schofield CJ, Kawamura A

J. Mol. Biol.. doi: 10.1016/j.jmb.2017.08.007

Publication date: August 18, 2017

PMID: 28827149

Characterization of a highly selective inhibitor of the Aurora kinases.

Ferguson FM, Doctor ZM, Chaikuad A, Sim T, Kim ND, Knapp S, Gray NS

Bioorg. Med. Chem. Lett.. doi: 10.1016/j.bmcl.2017.08.016

Publication date: August 10, 2017

PMID: 28818446

A statistical analysis on the performance of MMPBSA versus absolute binding free energy calculations: bromodomains as a case study.

Aldeghi M, Bodkin MJ, Knapp S, Biggin PC

J Chem Inf Model. doi: 10.1021/acs.jcim.7b00347

Publication date: August 8, 2017

PMID: 28786670

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations.

Couñago RM, Allerston CK, Savitsky P, Azevedo H, Godoi PH, Wells CI, Mascarello A, de Souza Gama FH, Massirer KB, Zuercher WJ, Guimarães CRW, Gileadi O

Sci Rep. 7(1):7501. doi: 10.1038/s41598-017-07755-y

Publication date: August 8, 2017

PMID: 28790404

Progress towards a public chemogenomic set for protein kinases and a call for contributions.

Drewry DH, Wells CI, Andrews DM, Angell R, Al-Ali H, Axtman AD, Capuzzi SJ, Elkins JM, Ettmayer P, Frederiksen M, Gileadi O, Gray N, Hooper A, Knapp S, Laufer S, Luecking U, Michaelides M, Müller S, Muratov E, Denny RA, Saikatendu KS, Treiber DK, Zuercher WJ, Willson TM

PLoS ONE. 12(8):e0181585. doi: 10.1371/journal.pone.0181585

Publication date: August 3, 2017

PMID: 28767711

(19) F NMR isotropic chemical shift for efficient screening of fluorinated fragments which are racemates and/or display multiple conformers.

Dalvit C, Knapp S

Magn Reson Chem. doi: 10.1002/mrc.4640

Publication date: August 1, 2017

PMID: 28762528

IDUA mutational profile and genotype-phenotype relationships in UK patients with Mucopolysaccharidosis I.

Ghosh A, Mercer J, Mackinnon S, Yue WW, Church H, Beesley CE, Broomfield A, Jones SA, Tylee K

Hum. Mutat.. doi: 10.1002/humu.23301

Publication date: July 28, 2017

PMID: 28752568

BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis.

Roberts TC, Etxaniz U, Dall'Agnese A, Wu SY, Chiang CM, Brennan PE, Wood MJA, Puri PL

Sci Rep. 7(1):6153. doi: 10.1038/s41598-017-06483-7

Publication date: July 21, 2017

PMID: 28733670

Design of a chemical probe for the Bromodomain and Plant Homeodomain Finger-containing (BRPF) family of proteins.

Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b00611

Publication date: July 17, 2017

PMID: 28714688

Global analysis of protein folding using massively parallel design, synthesis, and testing.

Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D

Science. 357(6347):168-175. doi: 10.1126/science.aan0693

Publication date: July 14, 2017

PMID: 28706065

NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin.

Melo-Hanchuk TD, Slepicka PF, Meirelles GV, Basei FL, Lovato DV, Granato DC, Pauletti BA, Domingues RR, Leme AFP, Pelegrini AL, Lenz G, Knapp S, Elkins JM, Kobarg J

Sci Rep. 7(1):5445. doi: 10.1038/s41598-017-05325-w

Publication date: July 14, 2017

PMID: 28710492

ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells.

Park NI, Guilhamon P, Desai K, McAdam RF, Langille E, O'Connor M, Lan X, Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB

Cell Stem Cell. doi: 10.1016/j.stem.2017.06.004

Publication date: July 11, 2017

PMID: 28712938

Alternative splicing promotes tumour aggressiveness and drug resistance in African American prostate cancer.

Wang BD, Ceniccola K, Hwang S, Andrawis R, Horvath A, Freedman JA, Olender J, Knapp S, Ching T, Garmire L, Patel V, Garcia-Blanco MA, Patierno SR, Lee NH

Nat Commun. 8:15921. doi: 10.1038/ncomms15921

Publication date: June 30, 2017

PMID: 28665395

Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.

Xiong Y, Li F, Babault N, Wu H, Dong A, Zeng H, Chen X, Arrowsmith CH, Brown PJ, Liu J, Vedadi M, Jin J

Bioorg. Med. Chem.. doi: 10.1016/j.bmc.2017.06.021

Publication date: June 19, 2017

PMID: 28662962

Readers, writers and erasers of N(6)-methylated adenosine modification.

Wu B, Li L, Huang Y, Ma J, Min J

Curr. Opin. Struct. Biol.. 47:67-76. doi: 10.1016/j.sbi.2017.05.011

Publication date: June 15, 2017

PMID: 28624569

Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment.

Aquino B, Couñago RM, Verza N, Ferreira LM, Massirer KB, Gileadi O, Arruda P

Front Plant Sci. 8:852. doi: 10.3389/fpls.2017.00852

Publication date: June 13, 2017

PMID: 28603531

Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.

Chaikuad A, Filippakopoulos P, Marcsisin SR, Picaud S, Schröder M, Sekine S, Ichijo H, Engen JR, Takeda K, Knapp S

Structure. doi: 10.1016/j.str.2017.05.020

Publication date: June 10, 2017

PMID: 28648608

Generation and validation of intracellular ubiquitin variant inhibitors for USP7 and USP10.

Zhang W, Sartori MA, Makhnevych T, Federowicz KE, Dong X, Liu L, Nim S, Dong A, Yang J, Li Y, Haddad D, Ernst A, Heerding D, Tong Y, Moffat J, Sidhu SS

J. Mol. Biol.. doi: 10.1016/j.jmb.2017.05.025

Publication date: June 3, 2017

PMID: 28587923

A trust approach for sharing research reagents.

Edwards A, Morgan M, Al Chawaf A, Andrusiak K, Charney R, Cynader Z, ElDessouki A, Lee Y, Moeser A, Stern S, Zuercher WJ

Sci Transl Med. 9(392):. doi: 10.1126/scitranslmed.aai9055

Publication date: May 31, 2017

PMID: 28566431

Oxalyl Boronates Enable Modular Synthesis of Bioactive Imidazoles.

Lee CF, Holownia A, Bennett JM, Elkins JM, St Denis JD, Adachi S, Yudin AK

Angew. Chem. Int. Ed. Engl.. 56(22):6264-6267. doi: 10.1002/anie.201611006

Publication date: May 22, 2017

PMID: 28267269

The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats.

Pascoal CC, Islam Z, Adamoski D, Ferreira IM, Righetto RD, Bettini J, Portugal RV, Yue WW, Gonzalez A, Dias SMG, Ambrosio ALB

J. Biol. Chem.. doi: 10.1074/jbc.M117.787291

Publication date: May 19, 2017

PMID: 28526749

Protein destabilization and loss of protein-protein interaction are fundamental mechanisms in cblA-type methylmalonic aciduria.

Plessl T, Bürer C, Lutz S, Yue WW, Baumgartner MR, Froese DS

Hum. Mutat.. doi: 10.1002/humu.23251

Publication date: May 12, 2017

PMID: 28497574

A specific and covalent JNK-1 ligand selected from an encoded self-assembling chemical library.

Zimmermann G, Rieder U, Bajic D, Vanetti S, Chaikuad A, Knapp S, Scheuermann J, Mattarella M, Neri D

Chemistry. doi: 10.1002/chem.201701644

Publication date: May 9, 2017

PMID: 28485044

In Vivo Biotinylation of Antigens in E. coli.

Gräslund S, Savitsky P, Müller-Knapp S

Methods Mol. Biol.. 1586:337-344. doi: 10.1007/978-1-4939-6887-9_22

Publication date: May 5, 2017

PMID: 28470616

N- and C-Terminal Truncations to Enhance Protein Solubility and Crystallization: Predicting Protein Domain Boundaries with Bioinformatics Tools.

Cooper CDO, Marsden BD

Methods Mol. Biol.. 1586:11-31. doi: 10.1007/978-1-4939-6887-9_2

Publication date: May 5, 2017

PMID: 28470596

Recombinant Protein Expression in E. coli : A Historical Perspective.

Gileadi O

Methods Mol. Biol.. 1586:3-10. doi: 10.1007/978-1-4939-6887-9_1

Publication date: May 5, 2017

PMID: 28470595

Hyperactive locomotion in a Drosophila model is a functional readout for the synaptic abnormalities underlying fragile X syndrome.

Kashima R, Redmond PL, Ghatpande P, Roy S, Kornberg TB, Hanke T, Knapp S, Lagna G, Hata A

Sci Signal. 10(477):. doi: 10.1126/scisignal.aai8133

Publication date: May 2, 2017

PMID: 28465421

Histone lysine methyltransferase structure activity relationships that allow for segregation of G9a inhibition and anti-Plasmodium activity.

Sundriyal S, Chen PB, Lubin AS, Lueg GA, Li F, White AJP, Malmquist NA, Vedadi M, Scherf A, Fuchter MJ

Medchemcomm. 8(5):1069-1092. doi: 10.1039/c7md00052a

Publication date: May 1, 2017

PMID: 29308121

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.

Pearce NM, Krojer T, Bradley AR, Collins P, Nowak RP, Talon R, Marsden BD, Kelm S, Shi J, Deane CM, von Delft F

Nat Commun. 8:15123. doi: 10.1038/ncomms15123

Publication date: April 24, 2017

PMID: 28436492

Global survey of the immunomodulatory potential of common drugs.

Vladimer GI, Snijder B, Krall N, Bigenzahn JW, Huber KVM, Lardeau CH, Sanjiv K, Ringler A, Berglund UW, Sabler M, de la Fuente OL, Knöbl P, Kubicek S, Helleday T, Jäger U, Superti-Furga G

Nat. Chem. Biol.. doi: 10.1038/nchembio.2360

Publication date: April 24, 2017

PMID: 28437395

The RNF168 paralog RNF169 defines a new class of ubiquitylated-histone reader involved in the response to DNA damage.

Kitevski-LeBlanc J, Fradet-Turcotte A, Kukic P, Wilson MD, Portella G, Yuwen T, Panier S, Duan S, Canny MD, van Ingen H, Arrowsmith CH, Rubinstein JL, Vendruscolo M, Durocher D, Kay LE

Elife. 6:. doi: 10.7554/eLife.23872

Publication date: April 13, 2017

PMID: 28406400

Benzo-isoquinoline-diones As Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains.

Bouché L, Christ CD, Siegel S, Fernández-Montalván AE, Holton SJ, Fedorov O, Ter Laak A, Sugawara T, Stöckigt D, Tallant C, Bennett JM, Monteiro OP, Díaz-Sáez L, Siejka P, Meier J, Puetter V, Weiske J, Müller S, Huber KV, Hartung IV, Haendler B

J. Med. Chem.. doi: 10.1021/acs.jmedchem.7b00306

Publication date: April 12, 2017

PMID: 28402630

Highly selective inhibition of histone demethylases by de novo macrocyclic peptides.

Kawamura A, Münzel M, Kojima T, Yapp C, Bhushan B, Goto Y, Tumber A, Katoh T, King ON, Passioura T, Walport LJ, Hatch SB, Madden S, Müller S, Brennan PE, Chowdhury R, Hopkinson RJ, Suga H, Schofield CJ

Nat Commun. 8:14773. doi: 10.1038/ncomms14773

Publication date: April 6, 2017

PMID: 28382930

Molecular basis for the methylation specificity of ATXR5 for histone H3.

Bergamin E, Sarvan S, Malette J, Eram MS, Yeung S, Mongeon V, Joshi M, Brunzelle JS, Michaels SD, Blais A, Vedadi M, Couture JF

Nucleic Acids Res.. doi: 10.1093/nar/gkx224

Publication date: April 5, 2017

PMID: 28383693

Structure-based design of highly selective inhibitors of the CREB binding protein bromodomain.

Denny RA, Flick AC, Coe JW, Langille J, Basak A, Liu S, Stock IA, Sahasrabudhe P, Bonin PD, Hay DA, Brennan PE, Pletcher MT, Jones LH, Chekler EL

J. Med. Chem.. doi: 10.1021/acs.jmedchem.6b01839

Publication date: April 4, 2017

PMID: 28375629

MOB1 mediated phospho-recognition in the core mammalian Hippo pathway.

Couzens AL, Xiong S, Knight JD, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, Gingras AC

Mol. Cell Proteomics. doi: 10.1074/mcp.M116.065490

Publication date: April 3, 2017

PMID: 28373298

Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites.

Pearce NM, Bradley AR, Krojer T, Marsden BD, Deane CM, von Delft F

Struct Dyn. 4(3):032104. doi: 10.1063/1.4974176

Publication date: March 28, 2017

PMID: 28345007

Bilayer-Mediated Structural Transitions Control Mechanosensitivity of the TREK-2 K2P Channel.

Aryal P, Jarerattanachat V, Clausen MV, Schewe M, McClenaghan C, Argent L, Conrad LJ, Dong YY, Pike AC, Carpenter EP, Baukrowitz T, Sansom MS, Tucker SJ

Structure. doi: 10.1016/j.str.2017.03.006

Publication date: March 24, 2017

PMID: 28392258

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