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2019 Publications

 

Sharma D, De Falco L, Padavattan S, Rao C, Geifman-Shochat S, Liu CF, Davey CA. 

PARP1 exhibits enhanced association and catalytic efficiency with γH2A.X-nucleosome.

Nat Commun. 2019 Dec 17;10(1):5751. doi: 10.1038/s41467-019-13641-0.

 

 

Jaroensuk J, Wong YH, Zhong W, Liew CW, Maenpuen S, Sahili AE, Atichartpongkul S, Chionh YH, Nah Q, Thongdee N, McBee ME, Prestwich EG, DeMott MS, Chaiyen P, Mongkolsuk S, Dedon PC, Lescar J, Fuangthong M.

Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa.

RNA. 2019 Nov;25(11):1481-1496. doi: 10.1261/rna.066746.118. 

 

 

Xie Y, Sun J, Han X, Turšić-Wunder A, Toh JDW, Hong W, Gao YG, Miao Y.

Polarisome scaffolder Spa2-mediated macromolecular condensation of Aip5 for actin polymerization.

Nat Commun. 2019 Nov 7;10(1):5078. doi: 10.1038/s41467-019-13125-1.

 

 

Pan J, Qian X, Lattmann S, El Sahili A, Yeo TH, Jia H, Cressey T, Ludeke B, Noton S, Kalocsay M, Fearns R, Lescar J.

Structure of the human metapneumovirus polymerase phosphoprotein complex.

Nature. 2019 Nov 7. doi: 10.1038/s41586-019-1759-1. 

 

 

Winnerdy FR, Das P, Heddi B, Phan AT.

Solution structures of a G-quadruplex bound to linear- and cyclic-dinucleotides.

J Am Chem Soc. 2019 Oct 29. doi: 10.1021/jacs.9b05642.

 

 

Batchelor LK, De Falco L, von Erlach T, Sharma D, Adhireksan Z, Roethlisberger U, Davey CA, Dyson PJ.

Crosslinking allosteric sites on the nucleosome.

Angew Chem Int Ed Engl. 2019 Oct 28;58(44):15660-15664. doi: 10.1002/anie.201906423.

 

 

Qiao Z, Sun H, Ng JTY, Ma Q, Koh SH, Mu Y, Miao Y, Gao YG.

Structural and computational examination of the Arabidopsis profilin-poly-P complex reveals mechanistic details in profilin-regulated actin assembly.

J Biol Chem. 2019 Oct 25. pii: jbc.RA119.011307. doi: 10.1074/jbc.RA119.011307. 

 

 

Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C.

Backbone resonance assignment for the full length tRNA-(N1G37) methyltransferase of Pseudomonas aeruginosa. 

Biomol NMR Assign. 2019 Oct;13(2):327-332. doi: 10.1007/s12104-019-09900-2

 

 

Wang C, Ye F, Chang C, Liu X, Wang J, Wang J, Yan XF, Fu Q, Zhou J, Chen S, Gao YG, Zhang LH.

Agrobacteria reprogram virulence gene expression by controlled release of host-conjugated signals.

Proc Natl Acad Sci U S A. 2019 Oct 11. pii: 201903695. doi: 10.1073/pnas.1903695116.

 

 

El Sahili A, Soh TS, Schiltz J, Gharbi-Ayachi A, Seh CC, Shi PY, Lim SP, Lescar J.

NS5 from Dengue virus serotype 2 can adopt a conformation analogous to its ZIKV and JEV homologues.

J Virol. 2019 Oct 9. pii: JVI.01294-19. doi: 10.1128/JVI.01294-19.

 

 

Heddi B, Vee Cheong V, Schmitt E, Mechulam Y, Tuân Phan A.

Recognition of different base tetrads by RHAU: X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex.

J Struct Biol. 2019 Oct 3. pii: S1047-8477(19)30210-2. doi: 10.1016/j.jsb.2019.10.001.

 

 

Truong THA, Winnerdy FR, Phan AT.

An unprecedented knot-like G-quadruplex peripheral motif.

Angew Chem Int Ed Engl. 2019 Sep 23;58(39):13834-13839. doi: 10.1002/anie.201907740. 

 

 

Zhong W, Pasunooti KK, Balamkundu S, Wong YH, Nah Q, Gadi V, Gnanakalai S, Chionh YH, McBee ME, Gopal P, Lim SH, Olivier N, Buurman ET, Dick T, Liu CF, Lescar J, Dedon PC.

Thienopyrimidinone derivatives that inhibit bacterial tRNA (Guanine37-N1)-methyltransferase (TrmD) by restructuring the active site with a tyrosine-flipping mechanism. 

J Med Chem. 2019 Sep 12;62(17):7788-7805. doi: 10.1021/acs.jmedchem.9b00582. 

 

 

Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC.

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.

Nucleic Acids Res. 2019 Sep 2. pii: gkz751. doi: 10.1093/nar/gkz751.

 

 

Gallart-Palau X, Tan LM, Serra A, Gao Y, Ho HH, Richards AM, Kandiah N, Chen CP, Kalaria RN, Sze SK.

Degenerative protein modifications in the aging vasculature and central nervous system: A problem shared is not always halved. 

Ageing Res Rev. 2019 Aug;53:100909. doi: 10.1016/j.arr.2019.100909. 

 

 

Zhong W, Guo J, Cui L, Chionh YH, Li K, El Sahili A, Cai Q, Yuan M, Michels PAM, Fothergill-Gilmore LA, Walkinshaw MD, Mu Y, Lescar J, Dedon PC.

Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in Mycobacterium tuberculosis. 

J Mol Biol. 2019 Aug 2. pii: S0022-2836(19)30484-X. doi: 10.1016/j.jmb.2019.07.033. 

 

 

Kamariah N, Huber RG, Nartey W, Bhushan S, Bond PJ, Grüber G.

Structure and subunit arrangement of mycobacterial F1FO ATP synthase and novel features of the unique mycobacterial subunit δ. 

J Struct Biol. 2019 Aug 1;207(2):199-208. doi: 10.1016/j.jsb.2019.05.008. 

 

 

Yong HY, Zheng J, Ho VCY, Nguyen MT, Fink K, Griffin PR, Luo D.

Structure-guided design of immunomodulatory RNAs specifically targeting the cytoplasmic viral RNA sensor RIG-I. 

FEBS Lett. 2019 Aug 1. doi: 10.1002/1873-3468.13564. 

 

 

Deng Y, Wu T, Wang M, Shi S, Yuan G, Li X, Chong H, Wu B, Zheng P.

Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level.

Nat Commun. 2019 Jun 24;10(1):2775. doi: 10.1038/s41467-019-10696-x.

 

 

Sun T, Mirzoev A, Minhas V, Korolev N, Lyubartsev AP, Nordenskiöld L.

A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.

Nucleic Acids Res. 2019 Jun 20;47(11):5550-5562. doi: 10.1093/nar/gkz377.

 

 

Hemu X, El Sahili A, Hu S, Wong K, Chen Y, Wong YH, Zhang X, Serra A, Goh BC, Darwis DA, Chen MW, Sze SK, Liu CF, Lescar J, Tam JP.

Structural determinants for peptide-bond formation by asparaginyl ligases.

Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11737-11746. doi: 10.1073/pnas.1818568116. 

 

 

Dai L, Lin J, Said AB, Yau YH, Shochat SG, Ruiz-Carrillo D, Sun K, Chandrasekaran R, Sze SK, Lescar J, Cheung PC4.

Pellino1 specifically binds to phospho-Thr18 of p53 and is recruited to sites of DNA damage. Biochem Biophys Res Commun. 2019 Jun 4;513(3):714-720. doi: 10.1016/j.bbrc.2019.03.095. 

 

 

Bogdanović N, Trifunović D, Sielaff H, Westphal L, Bhushan S, Müller V, Grüber G.

The structural features of Acetobacterium woodii F-ATP synthase reveal the importance of the unique subunit γ-loop in Na+ translocation and ATP synthesis. 

FEBS J. 2019 May;286(10):1894-1907. doi: 10.1111/febs.14793.

 

Ahmed SM, Ramani PD, Wong SQR, Zhao X, Ivanyi-Nagy R, Leong TC, Chua C, Li Z, Hentze H, Tan IB, Yan J, DasGupta R, Dröge P.

The chromatin structuring protein HMGA2 influences human subtelomere stability and cancer chemosensitivity. 

PLoS One. 2019 May 8;14(5):e0215696. doi: 10.1371/journal.pone.0215696. eCollection 2019.

 

 

Law YS, Utt A, Tan YB, Zheng J, Wang S, Chen MW, Griffin PR, Merits A, Luo D.

Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase

Proc Natl Acad Sci U S A. 2019 May 7;116(19):9558-9567. doi: 10.1073/pnas.1900656116. 

 

 

Ero R, Kumar V, Su W, Gao YG

Ribosome protection by ABC-F proteins-molecular mechanism and potential drug design. 

Protein Sci. 2019 Apr;28(4):684-693

 


 

Shimada M, Chen WY, Nakadai T, Onikubo T, Guermah M, Rhodes D, Roeder RG.

Gene-Specific H1 Eviction through a Transcriptional Activator→p300→NAP1→H1 Pathway

Mol Cell. 2019 Apr 18;74(2):268-283.e5. doi: 10.1016/j.molcel.2019.02.016. 

 

 

Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C.

Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N1G37) methyltransferase.

Biomol NMR Assign. 2019 Apr;13(1):49-53. doi: 10.1007/s12104-018-9849-9.

 

 

Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A.

A tail-based mechanism drives nucleosome demethylation by the LSD2/NPAC multimeric complex.

Cell Rep. 2019 Apr 9;27(2):387-399.e7. doi: 10.1016/j.celrep.2019.03.061.

 

 

Kesy J, Patil KM, Kumar SR, Shu Z, Yong HY, Zimmermann L, Ong AAL, Toh DK, Krishna MS, Yang L, Decout JL, Luo D, Prabakaran M, Chen G, Kierzek E. 

A short chemically modified dsRNA-binding PNA (dbPNA) inhibits influenza viral replication by targeting viral RNA panhandle structure. 

Bioconjug Chem. 2019 Mar 20;30(3):931-943. doi: 10.1021/acs.bioconjchem.9b00039. Epub 2019 Feb 15.

 

 

Del Rio D, Beucher B, Lavigne M, Wehbi A, Gonzalez Dopeso-Reyes I, Saggio I, Kremer EJ.

CAV-2 vector development and gene transfer in the central and peripheral nervous systems 

Front Mol Neurosci. 2019 Mar 29;12:71. doi: 10.3389/fnmol.2019.00071. eCollection 2019.

 

 

Zhong W, Koay A, Ngo A, Li Y, Nah Q, Wong YH, Chionh YH, Ng HQ, Koh-Stenta X, Poulsen A, Foo K, McBee M, Choong ML, El Sahili A, Kang C, Matter A, Lescar J, Hill J, Dedon P.

Targeting the bacterial epitranscriptome for antibiotic development: Discovery of novel tRNA-(N1G37) methyltransferase (TrmD) inhibitors. 

ACS Infect Dis. 2019 Mar 8;5(3):326-335. doi: 10.1021/acsinfecdis.8b00275. 

 

 

Rhodes D.

Aaron Klug (1926-2018).

Nat Struct Mol Biol. 2019 Feb;26(2):85-86. doi: 10.1038/s41594-018-0183-9.

 

 

Gu Y, Wong YH, Liew CW, Chan CEZ, Murali TM, Yap J, Too CT, Purushotorman K, Hamidinia M, El Sahili A, Goh ATH, Teo RZC, Wood KJ, Hanson BJ, Gascoigne NRJ, Lescar J, Vathsala A, MacAry PA.

Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01.

Nat Commun. 2019 Feb 21;10(1):893. doi: 10.1038/s41467-019-08790-1. 

 

 

Konarzewska P, Wang Y, Han GS, Goh KJ, Gao YG, Carman GM, Xue C.

Phosphatidylserine synthesis is essential for viability of the human fungal pathogen Cryptococcus neoformans

J Biol Chem. 2019 Feb 15;294(7):2329-2339. doi: 10.1074/jbc.RA118.006738. 

 

 

Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT.

A minimal sequence for left-handed G-quadruplex formation. 

Angew Chem Int Ed Engl. 2019 Feb 18;58(8):2331-2335

 

 

Badolo A, Burt F, Daniel S, Fearns R, Gudo ES, Kielian M, Lescar J, Shi Y, von Brunn A, Weiss SR, Hilgenfeld R.

Third Tofo advanced study week on emerging and re-emerging viruses, 2018. 

Antiviral Res. 2019 Feb;162:142-150. doi: 10.1016/j.antiviral.2018.12.015.

 

 

Zheng S, Kusnadi A, Choi JE, Vuong BQ, Rhodes D, Chaudhuri J.

NME proteins regulate class switch recombination.

FEBS Lett. 2019 Jan;593(1):80-87. doi: 10.1002/1873-3468.13290. Epub 2018 Nov 23.