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Yi Xue, Ph.D. - Publications

Affiliations: 
2016- School of Life Sciences Tsinghua National University, Beijing, Beijing Shi, China 
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Zhao S, Li X, Wen Z, Zou M, Yu G, Liu X, Mao J, Zhang L, Xue Y, Fu R, Wang S. Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy. Iscience. 25: 105322. PMID 36325062 DOI: 10.1016/j.isci.2022.105322  0.339
2022 Han G, Xue Y. Rational design of hairpin RNA excited states reveals multi-step transitions. Nature Communications. 13: 1523. PMID 35314698 DOI: 10.1038/s41467-022-29194-8  0.335
2021 Cao J, Xue Y. Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures. Nucleic Acids Research. 49: 4294-4307. PMID 33849076 DOI: 10.1093/nar/gkab250  0.3
2021 Wang Y, Han G, Jiang X, Yuwen T, Xue Y. Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states. Nature Communications. 12: 1595. PMID 33707433 DOI: 10.1038/s41467-021-21840-x  0.301
2019 Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically C- and N-Labeled DNA. Biochemistry. PMID 30950607 DOI: 10.1021/Acs.Biochem.9B00027  0.762
2018 Kimsey IJ, Szymanski ES, Zahurancik WJ, Shakya A, Xue Y, Chu CC, Sathyamoorthy B, Suo Z, Al-Hashimi HM. Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature. 554: 195-201. PMID 29420478 DOI: 10.1038/Nature25487  0.65
2017 Kurauskas V, Izmailov SA, Rogacheva ON, Hessel A, Ayala I, Woodhouse J, Shilova A, Xue Y, Yuwen T, Coquelle N, Colletier JP, Skrynnikov NR, Schanda P. Slow conformational exchange and overall rocking motion in ubiquitin protein crystals. Nature Communications. 8: 145. PMID 28747759 DOI: 10.1038/S41467-017-00165-8  0.387
2017 Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Research. PMID 28369571 DOI: 10.1093/Nar/Gkx186  0.698
2016 Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. Journal of Molecular Biology. PMID 27452365 DOI: 10.1016/J.Jmb.2016.07.013  0.622
2016 Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM. Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nature Communications. 7: ncomms11768. PMID 27292179 DOI: 10.1038/Ncomms11768  0.63
2016 Merriman DK, Xue Y, Yang S, Kimsey IJ, Shakya A, Clay MC, Al-Hashimi HM. Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes Over a Broad Range of Timescales. Biochemistry. PMID 27232530 DOI: 10.1021/Acs.Biochem.6B00285  0.708
2016 Yuwen T, Xue Y, Skrynnikov NR. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 2. The model of encounter complex involving the double mutant of the c-Crk N-SH3 domain and peptide Sos. Biochemistry. PMID 26910732 DOI: 10.1021/Acs.Biochem.5B01283  0.348
2015 Ren A, Xue Y, Peselis A, Serganov A, Al-Hashimi HM, Patel DJ. Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch. Cell Reports. 13: 1800-1813. PMID 26655897 DOI: 10.1016/J.Celrep.2015.10.062  0.655
2015 Shakya A, Dougherty CA, Xue Y, Al-Hashimi HM, Banaszak Holl MM. Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release. Biomacromolecules. PMID 26595195 DOI: 10.1021/Acs.Biomac.5B01280  0.785
2015 Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, ... ... Xue Y, et al. Engineering a Therapeutic Lectin by Uncoupling Mitogenicity from Antiviral Activity. Cell. 163: 746-58. PMID 26496612 DOI: 10.1016/J.Cell.2015.09.056  0.733
2015 Ma P, Xue Y, Coquelle N, Haller JD, Yuwen T, Ayala I, Mikhailovskii O, Willbold D, Colletier JP, Skrynnikov NR, Schanda P. Observing the overall rocking motion of a protein in a crystal. Nature Communications. 6: 8361. PMID 26436197 DOI: 10.1038/Ncomms9361  0.302
2015 Xue Y, Kellogg D, Kimsey IJ, Sathyamoorthy B, Stein ZW, McBrairty M, Al-Hashimi HM. Characterizing RNA Excited States Using NMR Relaxation Dispersion. Methods in Enzymology. 558: 39-73. PMID 26068737 DOI: 10.1016/Bs.Mie.2015.02.002  0.752
2014 Xue Y, Yuwen T, Zhu F, Skrynnikov NR. Role of electrostatic interactions in binding of peptides and intrinsically disordered proteins to their folded targets. 1. NMR and MD characterization of the complex between the c-Crk N-SH3 domain and the peptide Sos. Biochemistry. 53: 6473-95. PMID 25207671 DOI: 10.1021/Bi500904F  0.39
2014 del Amo JM, Agarwal V, Sarkar R, Porter J, Asami S, Rübbelke M, Fink U, Xue Y, Lange OF, Reif B. Site-specific analysis of heteronuclear Overhauser effects in microcrystalline proteins. Journal of Biomolecular Nmr. 59: 241-9. PMID 24989039 DOI: 10.1007/S10858-014-9843-1  0.316
2014 Xue Y, Skrynnikov NR. Ensemble MD simulations restrained via crystallographic data: accurate structure leads to accurate dynamics. Protein Science : a Publication of the Protein Society. 23: 488-507. PMID 24452989 DOI: 10.1002/Pro.2433  0.38
2012 Xue Y, Ward JM, Yuwen T, Podkorytov IS, Skrynnikov NR. Microsecond time-scale conformational exchange in proteins: using long molecular dynamics trajectory to simulate NMR relaxation dispersion data. Journal of the American Chemical Society. 134: 2555-62. PMID 22206299 DOI: 10.1021/Ja206442C  0.423
2011 Xue Y, Skrynnikov NR. Motion of a disordered polypeptide chain as studied by paramagnetic relaxation enhancements, 15N relaxation, and molecular dynamics simulations: how fast is segmental diffusion in denatured ubiquitin? Journal of the American Chemical Society. 133: 14614-28. PMID 21819149 DOI: 10.1021/Ja201605C  0.403
2010 Chevelkov V, Xue Y, Linser R, Skrynnikov NR, Reif B. Comparison of solid-state dipolar couplings and solution relaxation data provides insight into protein backbone dynamics. Journal of the American Chemical Society. 132: 5015-7. PMID 20297847 DOI: 10.1021/Ja100645K  0.427
2010 Chevelkov V, Xue Y, Rao DK, Forman-Kay JD, Skrynnikov NR. 15N H/D-SOLEXSY experiment for accurate measurement of amide solvent exchange rates: application to denatured drkN SH3. Journal of Biomolecular Nmr. 46: 227-44. PMID 20195703 DOI: 10.1007/S10858-010-9398-8  0.388
2009 Mo H, Harwood J, Zhang S, Xue Y, Santini R, Raftery D. R: A quantitative measure of NMR signal receiving efficiency. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 200: 239-44. PMID 19647457 DOI: 10.1016/J.Jmr.2009.07.004  0.316
2009 Xu J, Xue Y, Skrynnikov NR. Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent. Journal of Biomolecular Nmr. 45: 57-72. PMID 19582374 DOI: 10.1007/S10858-009-9336-9  0.347
2009 Xue Y, Podkorytov IS, Rao DK, Benjamin N, Sun H, Skrynnikov NR. Paramagnetic relaxation enhancements in unfolded proteins: theory and application to drkN SH3 domain. Protein Science : a Publication of the Protein Society. 18: 1401-24. PMID 19544584 DOI: 10.1002/Pro.153  0.362
2008 Agarwal V, Xue Y, Reif B, Skrynnikov NR. Protein side-chain dynamics as observed by solution- and solid-state NMR spectroscopy: a similarity revealed. Journal of the American Chemical Society. 130: 16611-21. PMID 19049457 DOI: 10.1021/Ja804275P  0.427
2007 Chevelkov V, Zhuravleva AV, Xue Y, Reif B, Skrynnikov NR. Combined analysis of (15)N relaxation data from solid- and solution-state NMR spectroscopy. Journal of the American Chemical Society. 129: 12594-5. PMID 17902660 DOI: 10.1021/Ja073234S  0.415
2007 Xue Y, Pavlova MS, Ryabov YE, Reif B, Skrynnikov NR. Methyl rotation barriers in proteins from 2H relaxation data. Implications for protein structure. Journal of the American Chemical Society. 129: 6827-38. PMID 17488010 DOI: 10.1021/Ja0702061  0.368
2006 Reif B, Xue Y, Agarwal V, Pavlova MS, Hologne M, Diehl A, Ryabov YE, Skrynnikov NR. Protein side-chain dynamics observed by solution- and solid-state NMR: comparative analysis of methyl 2H relaxation data. Journal of the American Chemical Society. 128: 12354-5. PMID 16984151 DOI: 10.1021/Ja062808A  0.425
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