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Structural basis of a small molecule targeting RNA for a specific splicing correction.

Campagne S, Boigner S, Rüdisser S, Moursy A, Gillioz L, Knörlein A, Hall J, Ratni H, Cléry A, Allain FH.

Nat Chem Biol. 2019 Oct 21. doi: 10.1038/s41589-019-0384-5. [Epub ahead of print]


Editorial overview: Protein-nucleic acid interactions - cryo-EM, what else?

Allain FH, Jinek M.

Curr Opin Struct Biol. 2019 Oct 18. pii: S0959-440X(19)30106-X. doi: 10.1016/ [Epub ahead of print] No abstract available.


Recent advances in understanding bacterial and archaeoeukaryotic primases.

Bergsch J, Allain FH, Lipps G.

Curr Opin Struct Biol. 2019 Oct 1;59:159-167. doi: 10.1016/ [Epub ahead of print] Review.


Systematic mapping of protein-metabolite interactions in central metabolism of Escherichia coli.

Diether M, Nikolaev Y, Allain FH, Sauer U.

Mol Syst Biol. 2019 Aug;15(8):e9008. doi: 10.15252/msb.20199008.


Publisher Correction: Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Sep;16(9):932. doi: 10.1038/s41592-019-0546-0.


Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis.

Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FH.

Nat Methods. 2019 Aug;16(8):743-749. doi: 10.1038/s41592-019-0495-7. Epub 2019 Jul 29. Erratum in: Nat Methods. 2019 Sep;16(9):932.


Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes.

Leitner A, Dorn G, Allain FH.

Cold Spring Harb Perspect Biol. 2019 Jul 1;11(7). pii: a032359. doi: 10.1101/cshperspect.a032359. Review.


A Step-by-Step Guide to Study Protein-RNA Interactions.

Cléry A, Gillioz L, Nguyen CKX, Allain FH.

Chimia (Aarau). 2019 May 29;73(6):406-414. doi: 10.2533/chimia.2019.406.


Specific inhibition of splicing factor activity by decoy RNA oligonucleotides.

Denichenko P, Mogilevsky M, Cléry A, Welte T, Biran J, Shimshon O, Barnabas GD, Danan-Gotthold M, Kumar S, Yavin E, Levanon EY, Allain FH, Geiger T, Levkowitz G, Karni R.

Nat Commun. 2019 Apr 8;10(1):1590. doi: 10.1038/s41467-019-09523-0.


Distinct G protein-coupled receptor phosphorylation motifs modulate arrestin affinity and activation and global conformation.

Mayer D, Damberger FF, Samarasimhareddy M, Feldmueller M, Vuckovic Z, Flock T, Bauer B, Mutt E, Zosel F, Allain FHT, Standfuss J, Schertler GFX, Deupi X, Sommer ME, Hurevich M, Friedler A, Veprintsev DB.

Nat Commun. 2019 Mar 19;10(1):1261. doi: 10.1038/s41467-019-09204-y.


SAM68 interaction with U1A modulates U1 snRNP recruitment and regulates mTor pre-mRNA splicing.

Subramania S, Gagné LM, Campagne S, Fort V, O'Sullivan J, Mocaer K, Feldmüller M, Masson JY, Allain FHT, Hussein SM, Huot MÉ.

Nucleic Acids Res. 2019 May 7;47(8):4181-4197. doi: 10.1093/nar/gkz099.


MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans.

Sendoel A, Subasic D, Ducoli L, Keller M, Michel E, Kohler I, Singh KD, Zheng X, Brümmer A, Imig J, Kishore S, Wu Y, Kanitz A, Kaech A, Mittal N, Matia-González AM, Gerber AP, Zavolan M, Aebersold R, Hall J, Allain FH, Hengartner MO.

Cell Death Differ. 2019 Oct;26(10):2157-2178. doi: 10.1038/s41418-019-0291-z. Epub 2019 Feb 6.


Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM.

Ripin N, Boudet J, Duszczyk MM, Hinniger A, Faller M, Krepl M, Gadi A, Schneider RJ, Šponer J, Meisner-Kober NC, Allain FH.

Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):2935-2944. doi: 10.1073/pnas.1808696116. Epub 2019 Feb 4.


Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein-RNA Complexes.

Campagne S, Krepl M, Sponer J, Allain FH.

Methods Enzymol. 2019;614:393-422. doi: 10.1016/bs.mie.2018.09.002. Epub 2018 Dec 10.


A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template.

Boudet J, Devillier JC, Wiegand T, Salmon L, Meier BH, Lipps G, Allain FH.

Cell. 2019 Jan 10;176(1-2):154-166.e13. doi: 10.1016/j.cell.2018.11.031. Epub 2018 Dec 27.


The Solution Structure of FUS Bound to RNA Reveals a Bipartite Mode of RNA Recognition with Both Sequence and Shape Specificity.

Loughlin FE, Lukavsky PJ, Kazeeva T, Reber S, Hock EM, Colombo M, Von Schroetter C, Pauli P, Cléry A, Mühlemann O, Polymenidou M, Ruepp MD, Allain FH.

Mol Cell. 2019 Feb 7;73(3):490-504.e6. doi: 10.1016/j.molcel.2018.11.012. Epub 2018 Dec 20.


Molecular basis for disassembly of an importin:ribosomal protein complex by the escortin Tsr2.

Schütz S, Michel E, Damberger FF, Oplová M, Peña C, Leitner A, Aebersold R, Allain FH, Panse VG.

Nat Commun. 2018 Sep 10;9(1):3669. doi: 10.1038/s41467-018-06160-x.


Control of the polyamine biosynthesis pathway by G2-quadruplexes.

Lightfoot HL, Hagen T, Cléry A, Allain FH, Hall J.

Elife. 2018 Jul 31;7. pii: e36362. doi: 10.7554/eLife.36362.


Segmental isotope labelling and solid-state NMR of a 12 × 59 kDa motor protein: identification of structural variability.

Wiegand T, Cadalbert R, von Schroetter C, Allain FH, Meier BH.

J Biomol NMR. 2018 Aug;71(4):237-245. doi: 10.1007/s10858-018-0196-z. Epub 2018 Jun 12.


Structural Flexibility Enables Alternative Maturation, ARGONAUTE Sorting and Activities of miR168, a Global Gene Silencing Regulator in Plants.

Iki T, Cléry A, Bologna NG, Sarazin A, Brosnan CA, Pumplin N, Allain FHT, Voinnet O.

Mol Plant. 2018 Aug 6;11(8):1008-1023. doi: 10.1016/j.molp.2018.05.006. Epub 2018 May 24.


rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences.

Sellier C, Cerro-Herreros E, Blatter M, Freyermuth F, Gaucherot A, Ruffenach F, Sarkar P, Puymirat J, Udd B, Day JW, Meola G, Bassez G, Fujimura H, Takahashi MP, Schoser B, Furling D, Artero R, Allain FHT, Llamusi B, Charlet-Berguerand N.

Nat Commun. 2018 May 22;9(1):2009. doi: 10.1038/s41467-018-04370-x.


An Integrated Cell-Free Assay to Study Translation Regulation by Small Bacterial Noncoding RNAs.

Michel E, Duss O, Allain FH.

Methods Mol Biol. 2018;1737:177-195. doi: 10.1007/978-1-4939-7634-8_11.


Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains.

Masliah G, Maris C, König SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FH.

EMBO J. 2018 Mar 15;37(6). pii: e97089. doi: 10.15252/embj.201797089. Epub 2018 Feb 15.


Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.

Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FH, Luisi BF, Urlaub H, Bläsi U.

Nucleic Acids Res. 2018 Feb 16;46(3):1470-1485. doi: 10.1093/nar/gkx1245.


Binding to SMN2 pre-mRNA-protein complex elicits specificity for small molecule splicing modifiers.

Sivaramakrishnan M, McCarthy KD, Campagne S, Huber S, Meier S, Augustin A, Heckel T, Meistermann H, Hug MN, Birrer P, Moursy A, Khawaja S, Schmucki R, Berntenis N, Giroud N, Golling S, Tzouros M, Banfai B, Duran-Pacheco G, Lamerz J, Hsiu Liu Y, Luebbers T, Ratni H, Ebeling M, Cléry A, Paushkin S, Krainer AR, Allain FH, Metzger F.

Nat Commun. 2017 Nov 14;8(1):1476. doi: 10.1038/s41467-017-01559-4.


Spin labelling for integrative structure modelling: a case study of the polypyrimidine-tract binding protein 1 domains in complexes with short RNAs.

Gmeiner C, Dorn G, Allain FHT, Jeschke G, Yulikov M.

Phys Chem Chem Phys. 2017 Oct 25;19(41):28360-28380. doi: 10.1039/c7cp05822e.


Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination.

Diarra Dit Konté N, Krepl M, Damberger FF, Ripin N, Duss O, Šponer J, Allain FH.

Nat Commun. 2017 Sep 21;8(1):654. doi: 10.1038/s41467-017-00631-3.


Orthogonal Tyrosine and Cysteine Site-Directed Spin Labeling for Dipolar Pulse EPR Spectroscopy on Proteins.

Gmeiner C, Klose D, Mileo E, Belle V, Marque SRA, Dorn G, Allain FHT, Guigliarelli B, Jeschke G, Yulikov M.

J Phys Chem Lett. 2017 Oct 5;8(19):4852-4857. doi: 10.1021/acs.jpclett.7b02220. Epub 2017 Sep 22.


Functional and dynamic polymerization of the ALS-linked protein TDP-43 antagonizes its pathologic aggregation.

Afroz T, Hock EM, Ernst P, Foglieni C, Jambeau M, Gilhespy LAB, Laferriere F, Maniecka Z, Plückthun A, Mittl P, Paganetti P, Allain FHT, Polymenidou M.

Nat Commun. 2017 Jun 29;8(1):45. doi: 10.1038/s41467-017-00062-0.


A Secondary Structural Element in a Wide Range of Fucosylated Glycoepitopes.

Aeschbacher T, Zierke M, Smieško M, Collot M, Mallet JM, Ernst B, Allain FH, Schubert M.

Chemistry. 2017 Aug 25;23(48):11598-11610. doi: 10.1002/chem.201701866. Epub 2017 Aug 3.


Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7.

Beusch I, Barraud P, Moursy A, Cléry A, Allain FH.

Elife. 2017 Jun 26;6. pii: e25736. doi: 10.7554/eLife.25736.


Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.

Krepl M, Blatter M, Cléry A, Damberger FF, Allain FHT, Sponer J.

Nucleic Acids Res. 2017 Jul 27;45(13):8046-8063. doi: 10.1093/nar/gkx418.


Structural modeling of protein-RNA complexes using crosslinking of segmentally isotope-labeled RNA and MS/MS.

Dorn G, Leitner A, Boudet J, Campagne S, von Schroetter C, Moursy A, Aebersold R, Allain FH.

Nat Methods. 2017 May;14(5):487-490. doi: 10.1038/nmeth.4235. Epub 2017 Mar 27.


Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs.

Samatanga B, Cléry A, Barraud P, Allain FH, Jelesarov I.

Nucleic Acids Res. 2017 Jun 2;45(10):6037-6050. doi: 10.1093/nar/gkx136.


switchSENSE: A new technology to study protein-RNA interactions.

Cléry A, Sohier TJM, Welte T, Langer A, Allain FHT.

Methods. 2017 Apr 15;118-119:137-145. doi: 10.1016/j.ymeth.2017.03.004. Epub 2017 Mar 9.


Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins.

Barandun J, Damberger FF, Delley CL, Laederach J, Allain FH, Weber-Ban E.

BMC Struct Biol. 2017 Feb 1;17(1):1. doi: 10.1186/s12900-017-0072-1.


Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria.

Bergé M, Campagne S, Mignolet J, Holden S, Théraulaz L, Manley S, Allain FH, Viollier PH.

Elife. 2016 Dec 23;5. pii: e20640. doi: 10.7554/eLife.20640.


Role of the PFXFATG[G/Y] Motif in the Activation of SdrG, a Response Regulator Involved in the Alphaproteobacterial General Stress Response.

Campagne S, Dintner S, Gottschlich L, Thibault M, Bortfeld-Miller M, Kaczmarczyk A, Francez-Charlot A, Allain FH, Vorholt JA.

Structure. 2016 Aug 2;24(8):1237-1247. doi: 10.1016/j.str.2016.05.015. Epub 2016 Jul 7.


Structural basis for sulfation-dependent self-glycan recognition by the human immune-inhibitory receptor Siglec-8.

Pröpster JM, Yang F, Rabbani S, Ernst B, Allain FH, Schubert M.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4170-9. doi: 10.1073/pnas.1602214113. Epub 2016 Jun 29.


Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs.

Krepl M, Cléry A, Blatter M, Allain FH, Sponer J.

Nucleic Acids Res. 2016 Jul 27;44(13):6452-70. doi: 10.1093/nar/gkw438. Epub 2016 May 18.


Systematic Identification of Protein-Metabolite Interactions in Complex Metabolite Mixtures by Ligand-Detected Nuclear Magnetic Resonance Spectroscopy.

Nikolaev YV, Kochanowski K, Link H, Sauer U, Allain FH.

Biochemistry. 2016 May 10;55(18):2590-600. doi: 10.1021/acs.biochem.5b01291. Epub 2016 Apr 25.


Cut and paste RNA for nuclear magnetic resonance, paramagnetic resonance enhancement, and electron paramagnetic resonance structural studies.

Duss O, Diarra Dit Konté N, Allain FH.

Methods Enzymol. 2015;565:537-62. doi: 10.1016/bs.mie.2015.05.029. Epub 2015 Jun 22.


Selective amino acid segmental labeling of multi-domain proteins.

Michel E, Allain FH.

Methods Enzymol. 2015;565:389-422. doi: 10.1016/bs.mie.2015.05.028. Epub 2015 Jun 18.


SRSF1-Regulated Alternative Splicing in Breast Cancer.

Anczuków O, Akerman M, Cléry A, Wu J, Shen C, Shirole NH, Raimer A, Sun S, Jensen MA, Hua Y, Allain FH, Krainer AR.

Mol Cell. 2015 Oct 1;60(1):105-17. doi: 10.1016/j.molcel.2015.09.005.


Evidence for cooperative tandem binding of hnRNP C RRMs in mRNA processing.

Cieniková Z, Jayne S, Damberger FF, Allain FH, Maris C.

RNA. 2015 Nov;21(11):1931-42. doi: 10.1261/rna.052373.115. Epub 2015 Sep 14.


Preface. Structures of Large RNA Molecules and Their Complexes.

Allain FHT, Woodson SA.

Methods Enzymol. 2015;558:xix-xxi. doi: 10.1016/S0076-6879(15)00322-5. No abstract available.


Combining NMR and EPR to Determine Structures of Large RNAs and Protein-RNA Complexes in Solution.

Duss O, Yulikov M, Allain FHT, Jeschke G.

Methods Enzymol. 2015;558:279-331. doi: 10.1016/bs.mie.2015.02.005. Epub 2015 Mar 26.


One, Two, Three, Four! How Multiple RRMs Read the Genome Sequence.

Afroz T, Cienikova Z, Cléry A, Allain FHT.

Methods Enzymol. 2015;558:235-278. doi: 10.1016/bs.mie.2015.01.015. Epub 2015 Mar 12.


The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FH.

J Mol Biol. 2015 Sep 25;427(19):3001-22. doi: 10.1016/j.jmb.2015.05.020. Epub 2015 Jun 5.


Structures to complement the archaeo-eukaryotic primases catalytic cycle description: What's next?

Boudet J, Devillier JC, Allain FH, Lipps G.

Comput Struct Biotechnol J. 2015 May 2;13:339-51. doi: 10.1016/j.csbj.2015.04.006. eCollection 2015. Review.

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