National Cancer Institute - Cancer.gov

SAXS Facility: Publications

You can find a selection of our publications throughout the years below.

View our high impact publications

  • Stagno, J. R., Deme, J. C., Dwivedi, V., Lee, Y. T., Lee, H. K., Yu, P., Chen, S. Y., Fan, L., Degenhardt, M. F. S., Chari, R., Young, H. A., Lea, S. M. & Wang, Y. X. Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells. Nucleic Acids Res 53, doi:10.1093/nar/gkaf156 (2025).

  • Zhu, Y., Chaubey, B., Olsen, G. L. & Varani, G. Structure of Essential RNA Regulatory Elements in the West Nile Virus 3'-Terminal Stem Loop. J Mol Biol 436, 168767, doi:10.1016/j.jmb.2024.168767 (2024).
  • Zhang, Y., Xu, Z., Xiao, Y., Jiang, H., Zuo, X., Li, X. & Fang, X. Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST. Nat Commun 15, 4206, doi:10.1038/s41467-024-48478-9 (2024).
  • Skeparnias, I., Bou-Nader, C., Anastasakis, D. G., Fan, L., Wang, Y. X., Hafner, M. & Zhang, J. Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol, doi:10.1038/s41594-024-01340-4 (2024).
  • Lee, Y. T., Degenhardt, M. F. S., Skeparnias, I., Degenhardt, H. F., Bhandari, Y. R., Yu, P., Stagno, J. R., Fan, L., Zhang, J. & Wang, Y. X. The conformational space of RNase P RNA in solution. Nature, doi:10.1038/s41586-024-08336-6 (2024).
  • Kim, M., Le, M. T., Fan, L., Campbell, C., Sen, S., Capdevila, D. A., Stemmler, T. L. & Giedroc, D. P. Characterization of the Zinc Uptake Repressor (Zur) from Acinetobacter baumannii. Biochemistry-Us, doi:10.1021/acs.biochem.3c00679 (2024).
  • Degenhardt, M. F. S., Degenhardt, H. F., Bhandari, Y. R., Lee, Y. T., Ding, J., Yu, P., Heinz, W. F., Stagno, J. R., Schwieters, C. D., Watts, N. R., Wingfield, P. T., Rein, A., Zhang, J. & Wang, Y. X. Determining structures of RNA conformers using AFM and deep neural networks. Nature, doi:10.1038/s41586-024-07559-x (2024).
  • Caba, C., Black, M., Liu, Y., DaDalt, A. A., Mallare, J., Fan, L., Harding, R. J., Wang, Y., Vacratsis, P. O., Huang, R., Zhuang, Z. & Tong, Y. Autoinhibition of ubiquitin-specific protease 8: insights into domain interactions and mechanisms of regulation. J Biol Chem, 107727, doi:10.1016/j.jbc.2024.107727 (2024).

  • Xu, L., Xiao, Y., Zhang, J. & Fang, X. Structural insights into translation regulation by the THF-II riboswitch. Nucleic Acids Res 51, 952-965, doi:10.1093/nar/gkac1257 (2023).
  • Suddala, K. C., Yoo, J., Fan, L., Zuo, X., Wang, Y. X., Chung, H. S. & Zhang, J. Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble. Nat Commun 14, 5438, doi:10.1038/s41467-023-41155-3 (2023).
  • Shaw, G. X., Fan, L., Cherry, S., Shi, G., Tropea, J. E. & Ji, X. Structure of Helicobacter pylori dihydroneopterin aldolase suggests a fragment-based strategy for isozyme-specific inhibitor design. Curr Res Struct Biol 5, 100095, doi:10.1016/j.crstbi.2023.100095 (2023).
  • Olenginski, L. T., Attionu, S. K., Henninger, E. N., LeBlanc, R. M., Longhini, A. P. & Dayie, T. K. Hepatitis B Virus Epsilon (epsilon) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target. Viruses 15, doi:10.3390/v15091913 (2023).
  • Niu, X., Xu, Z., Zhang, Y., Zuo, X., Chen, C. & Fang, X. Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch. Nat Commun 14, 7394, doi:10.1038/s41467-023-43232-z (2023).
  • Lee, Y. T., Fan, L., Ding, J. & Wang, Y. X. Combining Biophysical Methods for Structure-Function Analyses of RNA in Solution. Methods Mol Biol 2568, 165-177, doi:10.1007/978-1-0716-2687-0_11 (2023).
  • Lee, H. K., Lee, Y. T., Fan, L., Wilt, H. M., Conrad, C. E., Yu, P., Zhang, J., Shi, G., Ji, X., Wang, Y. X. & Stagno, J. R. Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state. Structure 31, 848-859 e843, doi:10.1016/j.str.2023.05.003 (2023).
  •  Il Ahn, J., Zhang, L., Ravishankar, H., Fan, L., Kirsch, K., Zeng, Y., Meng, L., Park, J. E., Yun, H. Y., Ghirlando, R., Ma, B., Ball, D., Ku, B., Nussinov, R., Schmit, J. D., Heinz, W. F., Kim, S. J., Karpova, T., Wang, Y. X. & Lee, K. S. Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells. Commun Biol 6, 712, doi:10.1038/s42003-023-05067-8 (2023).
  • Escobar, C. A., Petersen, R. J., Tonelli, M., Fan, L. X., Wang, Y. X., Yan, J., Kennedy, S. G. & Butcher, S. E. Solution structure of poly(UG) RNA reveals a new fold that drives gene silencing. Biophysical Journal 122, 358a-358a (2023).
  • Escobar, C. A., Petersen, R. J., Tonelli, M., Fan, L., Henzler-Wildman, K. & Butcher, S. E. Solution structure of poly(UG) RNA. J Mol Biol, 168340, doi:10.1016/j.jmb.2023.168340 (2023).
  • Ding, J., Lee, Y. T., Bhandari, Y., Schwieters, C. D., Fan, L., Yu, P., Tarosov, S. G., Stagno, J. R., Ma, B., Nussinov, R., Rein, A., Zhang, J. & Wang, Y. X. Visualizing RNA conformational and architectural heterogeneity in solution. Nat Commun 14, 714, doi:10.1038/s41467-023-36184-x (2023).
  • Degenhardt, M. F. S., Degenhardt, H. F., Bhandari, Y. R., Lee, Y. T., Ding, J., Heinz, W. F., Stagno, J. R., Schwieters, C. D., Zhang, J. & Wang, Y. X. Determining structures of individual RNA conformers using atomic force microscopy images and deep neural networks. Res Sq, doi:10.21203/rs.3.rs-2798658/v1 (2023).
  • Chen, X., Wang, Y., Xu, Z., Cheng, M. L., Ma, Q. Q., Li, R. T., Wang, Z. J., Zhao, H., Zuo, X., Li, X. F., Fang, X. & Qin, C. F. Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1. Nat Commun 14, 1134, doi:10.1038/s41467-023-36838-w (2023).

  • Xi, Z., Ilina, T. V., Guerrero, M., Fan, L., Sluis-Cremer, N., Wang, Y. X. & Ishima, R. Relative domain orientation of the L289K HIV-1 reverse transcriptase monomer. Protein Sci 31, e4307, doi:10.1002/pro.4307 (2022).
  • Truong, L., Kooshapur, H., Dey, S. K., Li, X., Tjandra, N., Jaffrey, S. R. & Ferre-D'Amare, A. R. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol 18, 191-198, doi:10.1038/s41589-021-00931-2 (2022).
  • Trachman, R. J., 3rd, Passalacqua, L. F. M. & Ferre-D'Amare, A. R. The bacterial yjdF riboswitch regulates translation through its tRNA-like fold. J Biol Chem 298, 101934, doi:10.1016/j.jbc.2022.101934 (2022).
  • Sun, Y. T. & Varani, G. Structure of the dengue virus RNA promoter. RNA 28, 1210-1223, doi:10.1261/rna.079197.122 (2022).
  • Sjekloca, L. & Ferre-D'Amare, A. R. Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNA (Phe) 4-demethylwyosine synthase Tyw1 in complex with FMN. MicroPubl Biol 2022, doi:10.17912/micropub.biology.000570 (2022).
  • Sharma, S., Pisignano, G., Merulla, J., Catapano, C. V. & Varani, G. A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript. Nucleic Acids Res 50, 11331-11343, doi:10.1093/nar/gkac875 (2022).
  • LeBlanc, R. M., Kasprzak, W. K., Longhini, A. P., Olenginski, L. T., Abulwerdi, F., Ginocchio, S., Shields, B., Nyman, J., Svirydava, M., Del Vecchio, C., Ivanic, J., Schneekloth, J. S., Jr., Shapiro, B. A., Dayie, T. K. & Le Grice, S. F. J. Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. J Biomol Struct Dyn 40, 9761-9773, doi:10.1080/07391102.2021.1934544 (2022).
  • Klein, B. J., Feigerle, J. T., Zhang, J., Ebmeier, C. C., Fan, L., Singh, R. K., Wang, W. W., Schmitt, L. R., Lee, T., Hansen, K. C., Liu, W. R., Wang, Y. X., Strahl, B. D., Anthony Weil, P. & Kutateladze, T. G. Taf2 mediates DNA binding of Taf14. Nat Commun 13, 3177, doi:10.1038/s41467-022-30937-w (2022).
  • Hu, Y., Wang, Y., Singh, J., Sun, R., Xu, L., Niu, X., Huang, K., Bai, G., Liu, G., Zuo, X., Chen, C., Qin, P. Z. & Fang, X. Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies. Acs Chem Biol 17, 2448-2460, doi:10.1021/acschembio.2c00199 (2022).
  • Fang, X., Gallego, J. & Wang, Y. X. Deriving RNA topological structure from SAXS. Methods Enzymol 677, 479-529, doi:10.1016/bs.mie.2022.08.037 (2022).
  • Endeward, B., Hu, Y., Bai, G., Liu, G., Prisner, T. F. & Fang, X. Long-range distance determination in fully deuterated RNA with pulsed EPR spectroscopy. Biophys J 121, 37-43, doi:10.1016/j.bpj.2021.12.007 (2022).
  • Castillo-Martinez, J., Fan, L., Szewczyk, M. P., Wang, Y. X. & Gallego, J. The low-resolution structural models of hepatitis C virus RNA subdomain 5BSL3.2 and its distal complex with domain 3'X point to conserved regulatory mechanisms within the Flaviviridae family. Nucleic Acids Res 50, 2287-2301, doi:10.1093/nar/gkac061 (2022).

  • Truong, L., Kooshapur, H., Dey, S. K., Li, X., Tjandra, N., Jaffrey, S. R. & Ferre-D'Amare, A. R. The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold. Nat Chem Biol, doi:10.1038/s41589-021-00931-2 (2021).
  • Trachman, R. J., 3rd & Ferre-D'Amare, A. R. An uncommon [K(+)(Mg(2+))2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch. RNA 27, 1257-1264, doi:10.1261/rna.078824.121 (2021).
  • Ramakrishnan, S., Stagno, J. R., Conrad, C. E., Ding, J., Yu, P., Bhandari, Y. R., Lee, Y. T., Pauly, G., Yefanov, O., Wiedorn, M. O., Knoska, J., Oberthur, D., White, T. A., Barty, A., Mariani, V., Li, C., Brehm, W., Heinz, W. F., Magidson, V., Lockett, S., Hunter, M. S., Boutet, S., Zatsepin, N. A., Zuo, X., Grant, T. D., Pandey, S., Schmidt, M., Spence, J. C. H., Chapman, H. N. & Wang, Y. X. Synchronous RNA conformational changes trigger ordered phase transitions in crystals. Nat Commun 12, 1762, doi:10.1038/s41467-021-21838-5 (2021).
  • Niu, X., Sun, R., Chen, Z., Yao, Y., Zuo, X., Chen, C. & Fang, X. Pseudoknot length modulates the folding, conformational dynamics, and robustness of Xrn1 resistance of flaviviral xrRNAs. Nat Commun 12, 6417, doi:10.1038/s41467-021-26616-x (2021).
  • Newman, J. D., Russell, M. M., Fan, L., Wang, Y. X., Gonzalez-Gutierrez, G. & van Kessel, J. C. The DNA binding domain of the Vibrio vulnificus SmcR transcription factor is flexible and binds diverse DNA sequences. Nucleic Acids Res 49, 5967-5984, doi:10.1093/nar/gkab387 (2021).
  • Ma, J. F., Cheng, X., Xu, Z. H., Zhang, Y. K., Valle, J., Fan, S. L., Zuo, X. B., Lasa, I. & Fang, X. Y. Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch. Embo J 40, doi:ARTN e107500 10.15252/embj.2020107500 (2021).
  • Hsu, S. D., Lee, Y. C., Mikula, K. M., Backlund, S. M., Tascon, I., Goldman, A. & Iwai, H. Tying up the Loose Ends: A Mathematically Knotted Protein. Front Chem 9, 663241, doi:10.3389/fchem.2021.663241 (2021).
  • Harding, R. J., Deme, J. C., Hevler, J. F., Tamara, S., Lemak, A., Cantle, J. P., Szewczyk, M. M., Begeja, N., Goss, S., Zuo, X., Loppnau, P., Seitova, A., Hutchinson, A., Fan, L., Truant, R., Schapira, M., Carroll, J. B., Heck, A. J. R., Lea, S. M. & Arrowsmith, C. H. Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1. Commun Biol 4, 1374, doi:10.1038/s42003-021-02895-4 (2021).
  • Fakhoury, J. N., Zhang, Y., Edmonds, K. A., Bringas, M., Luebke, J. L., Gonzalez-Gutierrez, G., Capdevila, D. A. & Giedroc, D. P. Functional asymmetry and chemical reactivity of CsoR family persulfide sensors. Nucleic Acids Res 49, 12556-12576, doi:10.1093/nar/gkab1040 (2021).

  • Zhang, Y., Edmonds, K. A., Raines, D. J., Murphy, B. A., Wu, H., Guo, C., Nolan, E. M., VanNieuwenhze, M. S., Duhme-Klair, A. K. & Giedroc, D. P. The Pneumococcal Iron Uptake Protein A (PiuA) Specifically Recognizes Tetradentate Fe(III)bis- and Mono-Catechol Complexes. J Mol Biol 432, 5390-5410, doi:10.1016/j.jmb.2020.08.005 (2020).
  • Wang, Y., Kathiresan, V., Chen, Y. Y., Hu, Y. P., Jiang, W., Bai, G. C., Liu, G. Q., Qin, P. Z. & Fang, X. Y. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 11, 9655-9664, doi:10.1039/d0sc01717e (2020).
  • Wang, Y., Chen, Y. Y., Hu, Y. P. & Fang, X. Y. Site-specific covalent labeling of large RNAs with nanoparticles empowered by expanded genetic alphabet transcription. P Natl Acad Sci USA 117, 22823-22832, doi:10.1073/pnas.2005217117 (2020).
  • Tauber, M., Kreuz, S., Lemak, A., Mandal, P., Yerkesh, Z., Veluchamy, A., Al-Gashgari, B., Aljahani, A., Cortes-Medina, L. V., Azhibek, D., Fan, L., Ong, M. S., Duan, S., Houliston, S., Arrowsmith, C. H. & Fischle, W. Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1. Nucleic Acids Res 48(14), 7728-7747, doi:10.1093/nar/gkaa520 (2020).
  • Song, H., Dharmasena, M. N., Wang, C., Shaw, G. X., Cherry, S., Tropea, J. E., Jin, D. J. & Ji, X. Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. Febs J 287, 1865-1885, doi:10.1111/febs.15120 (2020).
  • Shin, J. H., Sulpizio, A. G., Kelley, A., Alvarez, L., Murphy, S. G., Fan, L., Cava, F., Mao, Y., Saper, M. A. & Dorr, T. Structural basis of peptidoglycan endopeptidase regulation. Proc Natl Acad Sci U S A 117, 11692-11702, doi:10.1073/pnas.2001661117 (2020).
  • Ray, A., Edmonds, K. A., Palmer, L. D., Skaar, E. P. & Giedroc, D. P. Staphylococcus aureus glucose-induced biofilm accessory protein A (GbaA) is a monothiol-dependent electrophile sensor. Biochemistry-Us 59, 2882-2895, doi:10.1021/acs.biochem.0c00347 (2020).
  • O'Carroll, I. P., Fan, L., Kroupa, T., McShane, E. K., Theodore, C., Yates, E. A., Kondrup, B., Ding, J., Martin, T. S., Rein, A. & Wang, Y. X. Structural Mimicry Drives HIV-1 Rev-Mediated HERV-K Expression. J Mol Biol 432, 166711, doi:10.1016/j.jmb.2020.11.010 (2020).
  • Niu, X., Liu, Q., Xu, Z., Chen, Z., Xu, L., Xu, L., Li, J. & Fang, X. Molecular mechanisms underlying the extreme mechanical anisotropy of the flaviviral exoribonuclease-resistant RNAs (xrRNAs). Nat Commun 11, 5496, doi:10.1038/s41467-020-19260-4 (2020).
  • Majumder, P., Zhang, Y. C., Iglesias, M., Fan, L. X., Kelley, J. A., Andrews, C., Patel, N., Stagno, J. R., Oh, B. C., Furtmuller, G. J., Lai, C. C., Wang, Y. X., Brandacher, G., Raimondi, G. & Schneider, J. P. Multiphase Assembly of Small Molecule Microcrystalline Peptide Hydrogel Allows Immunomodulatory Combination Therapy for Long-Term Heart Transplant Survival. Small 16, 2002791, doi:10.1002/smll.202002791 (2020).
  • Jeng, S. S., Trachman, R. J., 3rd, Weissenboek, F., Troung, L., Link, K., Jepsen, M. B., Knutson, J., Andersen, E., Ferre-D'Amare, A. R. & Unrau, P. J. Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET. RNA, doi:10.1261/rna.078220.120 (2020).
  • Jaynes, J. M., Sable, R., Ronzetti, M., Bautista, W., Knotts, Z., Abisoye-Ogunniyan, A., Li, D., Calvo, R., Dashnyam, M., Singh, A., Guerin, T., White, J., Ravichandran, S., Kumar, P., Talsania, K., Chen, V., Ghebremedhin, A., Karanam, B., Bin Salam, A., Amin, R., Odzorig, T., Aiken, T., Nguyen, V., Bian, Y., Zarif, J. C., de Groot, A. E., Mehta, M., Fan, L., Hu, X., Simeonov, A., Pate, N., Abu-Asab, M., Ferrer, M., Southall, N., Ock, C. Y., Zhao, Y., Lopez, H., Kozlov, S., de Val, N., Yates, C. C., Baljinnyam, B., Marugan, J. & Rudloff, U. Mannose receptor (CD206) activation in tumor-associated macrophages enhances adaptive and innate antitumor immune responses. Sci Transl Med 12, doi:10.1126/scitranslmed.aax6337 (2020).
  • Hauseman, Z. J., Harvey, E. P., Newman, C. E., Wales, T. E., Bucci, J. C., Mintseris, J., Schweppe, D. K., David, L., Fan, L., Cohen, D. T., Herce, H. D., Mourtada, R., Ben-Nun, Y., Bloch, N. B., Hansen, S. B., Wu, H., Gygi, S. P., Engen, J. R. & Walensky, L. D. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Mol Cell 79, 68-83 e67, doi:10.1016/j.molcel.2020.05.029 (2020).
  • Chen, M. R., Pan, H., Sun, L. F., Shi, P., Zhang, Y. K., Li, L., Huang, Y. X., Chen, J. H., Jiang, P., Fang, X. Y., Wu, C. Y. & Chen, Z. C. Structure and regulation of human epithelial cell transforming 2 protein. P Natl Acad Sci USA 117, 1027-1035, doi:10.1073/pnas.1913054117 (2020).

2019

  • Zhao, Y., Zhang, Y., Huang, J., Wang, S., Yi, L., Zhang, X., Xu, M., Fang, X. & Liu, J. The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus. Proteins 87, 257-264, doi:10.1002/prot.25647 (2019).
  • Zhang, Y., Zhang, Y., Liu, Z. Y., Cheng, M. L., Ma, J., Wang, Y., Qin, C. F. & Fang, X. Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution. EMBO Rep 20, e47016, doi:10.15252/embr.201847016 (2019).
  • Yonkunas, M. J. & Baird, N. J. A highly ordered, nonprotective MALAT1 ENE structure is adopted prior to triplex formation. RNA 25, 975-984, doi:10.1261/rna.069906.118 (2019).
  • Song, H. & Ji, X. The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X. Nat Commun 10, 3085-3093, doi:10.1038/s41467-019-11083-2 (2019).
  • Song, H., Dharmasena, M. N., Wang, C., Shaw, G. X., Cherry, S., Tropea, J. E., Jin, D. J. & Ji, X. Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori. Febs J 287, 1865-1885, doi:10.1111/febs.15120 (2019).
  • Martin, J. E., Le, M. T., Bhattarai, N., Capdevila, D. A., Shen, J. C., Winkler, M. E. & Giedroc, D. P. A Mn-sensing riboswitch activates expression of a Mn2+/Ca2+ ATPase transporter in Streptococcus. Nucleic Acids Research 47, 6885-6899, doi:10.1093/nar/gkz494 (2019).
  • Li, S., Su, Z., Lehmann, J., Stamatopoulou, V., Giarimoglou, N., Henderson, F. E., Fan, L., Pintilie, G. D., Zhang, K., Chen, M., Ludtke, S. J., Wang, Y. X., Stathopoulos, C., Chiu, W. & Zhang, J. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol 26, 1094-1105, doi:10.1038/s41594-019-0326-7 (2019).
  • Kim, T.-S., Zhang, L., Il Ahn, J., Meng, L., Chen, Y., Lee, E., Bang, J. K., Lim, J. M., Ghirlando, R., Fan, L., Wang, Y.-X., Kim, B. Y., Park, J.-E. & Lee, K. S. Molecular architecture of a cylindrical self-assembly at human centrosomes. Nat Commun 10, 1151-1166, doi:10.1038/s41467-019-08838-2 (2019).
  • Kim, S. K., Whitley, M. J., Krzysiak, T. C., Hinck, C. S., Taylor, A. B., Zwieb, C., Byeon, C. H., Zhou, X., Mendoza, V., Lopez-Casillas, F., Furey, W. & Hinck, A. P. Structural Adaptation in Its Orphan Domain Engenders Betaglycan with an Alternate Mode of Growth Factor Binding Relative to Endoglin. Structure 27, 1427-1442 e1424, doi:10.1016/j.str.2019.06.010 (2019).
  • Kaustov, L., Lemak, A., Wu, H., Faini, M., Fan, L., Fang, X., Zeng, H., Duan, S., Allali-Hassani, A., Li, F., Wei, Y., Vedadi, M., Aebersold, R., Wang, Y., Houliston, S. & Arrowsmith, C. H. The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions. Nucleic Acids Res 47, 9433-9447, doi:10.1093/nar/gkz697 (2019).
  • Jordan, M. R., Wang, J. F., Weiss, A., Skaar, E. P., Capdevila, D. A. & Giedroc, D. P. Mechanistic Insights into the Metal-Dependent Activation of Zn-II-Dependent Metallochaperones. Inorg Chem 58, 13661-13672, doi:10.1021/acs.inorgchem.9b01173 (2019).
  • Harding, R. J., Loppnau, P., Ackloo, S., Lemak, A., Hutchinson, A., Hunt, B., Holehouse, A. S., Ho, J. C., Fan, L., Toledo-Sherman, L., Seitova, A. & Arrowsmith, C. H. Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems. J Biol Chem 294, 6986-7001, doi:10.1074/jbc.RA118.007204 (2019).
  • Cao, B., Lu, T. W., Martinez Fiesco, J. A., Tomasini, M., Fan, L., Simon, S. M., Taylor, S. S. & Zhang, P. Structures of the PKA RIalpha Holoenzyme with the FLHCC Driver J-PKAcalpha or Wild-Type PKAcalpha. Structure 27, 816-828 e814, doi:10.1016/j.str.2019.03.001 (2019).
  • Bofill-De Ros, X., Kasprzak, W. K., Bhandari, Y., Fan, L., Cavanaugh, Q., Jiang, M., Dai, L., Yang, A., Shao, T. J., Shapiro, B. A., Wang, Y. X. & Gu, S. Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires. Cell Rep 26, 447-459 e444, doi:10.1016/j.celrep.2018.12.054 (2019).

2018

  • Zhao, Y., Zhang, Y., Huang, J., Wang, S., Yi, L., Zhang, X., Xu, M., Fang, X. & Liu, J. The effect of phosphate ion on the ssDNA binding mode of MoSub1, a Sub1/PC4 homolog from rice blast fungus. Proteins 87, 257-264, doi:10.1002/prot.25647 (2018).
  • Wang, Y., Jiang, J., Gao, Y., Sun, Y., Dai, J., Wu, Y., Qu, D., Ma, G. & Fang, X. Staphylococcus epidermidis small basic protein (Sbp) forms amyloid fibrils, consistent with its function as a scaffolding protein in biofilms. J Biol Chem 293, 14296-14311, doi:10.1074/jbc.RA118.002448 (2018).
  • Glauninger, H., Zhang, Y., Higgins, K. A., Jacobs, A. D., Martin, J. E., Fu, Y., Coyne Rd, H. J., Bruce, K. E., Maroney, M. J., Clemmer, D. E., Capdevila, D. A. & Giedroc, D. P. Metal-dependent allosteric activation and inhibition on the same molecular scaffold: the copper sensor CopY from Streptococcus pneumoniae. Chem Sci 9, 105-118, doi:10.1039/c7sc04396a (2018).
  • Dong, Y., Mu, Y., Xie, Y., Zhang, Y., Han, Y., Zhou, Y., Wang, W., Liu, Z., Wu, M., Wang, H., Pan, M., Xu, N., Xu, C. Q., Yang, M., Fan, S., Deng, H., Tan, T., Liu, X., Liu, L., Li, J., Wang, J., Fang, X. & Feng, Y. Structural basis of ubiquitin modification by the Legionella effector SdeA. Nature 557, 674-678, doi:10.1038/s41586-018-0146-7 (2018).
  • Debnath, S., Kosek, D., Tagad, H. D., Durell, S. R., Appella, D. H., Acevedo, R., Grishaev, A., Dyda, F., Appella, E. & Mazur, S. J. A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity. J Biol Chem 293, 7993-8008, doi:10.1074/jbc.RA117.001213 (2018).
  • Debiec, K. T., Whitley, M. J., Koharudin, L. M. I., Chong, L. T. & Gronenborn, A. M. Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. Biophys J 114, 839-855, doi:10.1016/j.bpj.2018.01.001 (2018).
  • Capdevila, D. A., Huerta, F., Edmonds, K. A., Le, M. T., Wu, H. & Giedroc, D. P. Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator. Elife 7, e37268-37298, doi:10.7554/eLife.37268 (2018).

2017

  • Zehr, E., Szyk, A., Piszczek, G., Szczesna, E., Zuo, X. & Roll-Mecak, A. Katanin spiral and ring structures shed light on power stroke for microtubule severing. Nat Struct Mol Biol 24, 717-725, doi:10.1038/nsmb.3448 (2017).
  • Xi, Z., Whitley, M. J. & Gronenborn, A. M. Human betaB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study. Structure 25, 496-505, doi:10.1016/j.str.2017.02.001 (2017).
  • Whitley, M. J., Xi, Z., Bartko, J. C., Jensen, M. R., Blackledge, M. & Gronenborn, A. M. A Combined NMR and SAXS Analysis of the Partially Folded Cataract-Associated V75D gammaD-Crystallin. Biophys J 112, 1135-1146, doi:10.1016/j.bpj.2017.02.010 (2017).
  • Warner, K. D., Sjekloca, L., Song, W., Filonov, G. S., Jaffrey, S. R. & Ferre-D'Amare, A. R. A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol 13, 1195-1201, doi:10.1038/nchembio.2475 (2017).
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  • Stagno, J. R., Liu, Y., Bhandari, Y. R., Conrad, C. E., Panja, S., Swain, M., Fan, L., Nelson, G., Li, C., Wendel, D. R., White, T. A., Coe, J. D., Wiedorn, M. O., Knoska, J., Oberthuer, D., Tuckey, R. A., Yu, P., Dyba, M., Tarasov, S. G., Weierstall, U., Grant, T. D., Schwieters, C. D., Zhang, J., Ferre-D'Amare, A. R., Fromme, P., Draper, D. E., Liang, M., Hunter, M. S., Boutet, S., Tan, K., Zuo, X., Ji, X., Barty, A., Zatsepin, N. A., Chapman, H. N., Spence, J. C., Woodson, S. A. & Wang, Y. X. Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 541, 242-246, doi:10.1038/nature20599 (2017).
  • Song, H., Fang, X., Jin, L., Shaw, G. X., Wang, Y. X. & Ji, X. The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III. Structure 25, 353-363, doi:10.1016/j.str.2016.12.013 (2017).
  • Sathiyamoorthy, K., Vijayalakshmi, J., Tirupati, B., Fan, L. & Saper, M. A. Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. J Biol Chem 292, 17626-17642, doi:10.1074/jbc.M117.804997 (2017).
  • Roy, S., Lammert, H., Hayes, R. L., Chen, B., LeBlanc, R., Dayie, T. K., Onuchic, J. N. & Sanbonmatsu, K. Y. A magnesium-induced triplex pre-organizes the SAM-II riboswitch. PLoS Comput Biol 13, e1005406, doi:10.1371/journal.pcbi.1005406 (2017).
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  • Lau, M. W., Trachman, R. J., 3rd & Ferre-D'Amare, A. R. A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a preexisting nonspecific metal ion-binding site. RNA 23, 355-364, doi:10.1261/rna.059824.116 (2017).
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  • Fang, X., Michnicka, M., Zhang, Y., Wang, Y. X. & Nikonowicz, E. P. Capture and Release of tRNA by the T-Loop Receptor in the Function of the T-Box Riboswitch. Biochemistry-Us 56, 3549-3558, doi:10.1021/acs.biochem.7b00284 (2017).
  • Cantero-Camacho, A., Fan, L., Wang, Y. X. & Gallego, J. Three-dimensional structure of the 3'X-tail of hepatitis C virus RNA in monomeric and dimeric states. RNA 23, 1465-1476, doi:10.1261/rna.060632.117 (2017).
  • Bhandari, Y. R., Fan, L., Fang, X., Zaki, G. F., Stahlberg, E. A., Jiang, W., Schwieters, C. D., Stagno, J. R. & Wang, Y. X. Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering. J Mol Biol 429, 3635-3649, doi:10.1016/j.jmb.2017.09.006 (2017).

2016

  • Zheng, W., Borgia, A., Buholzer, K., Grishaev, A., Schuler, B. & Best, R. B. Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J Am Chem Soc 138, 11702-11713, doi:10.1021/jacs.6b05443 (2016).
  • Venditti, V., Egner, T. K. & Clore, G. M. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering. Chem Rev 116, 6305-6322, doi:10.1021/acs.chemrev.5b00592 (2016).
  • Lau, M. W., Trachman, R. J. & Ferre-D'Amare, A. R. A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a pre-existing non-specific metal ion binding site. RNA 23, 355-364, doi:10.1261/rna.059824.116 (2016).
  • LaRochelle, J. R., Fodor, M., Xu, X., Durzynska, I., Fan, L., Stams, T., Chan, H. M., LaMarche, M. J., Chopra, R., Wang, P., Fortin, P. D., Acker, M. G. & Blacklow, S. C. Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2. Biochemistry-Us 55, 2269-2277, doi:10.1021/acs.biochem.5b01287 (2016).
  • Deshmukh, L., Schwieters, C. D., Grishaev, A. & Clore, G. M. Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering. Chemphyschem 17, 1548-1552, doi:10.1002/cphc.201600212 (2016).
  • Cornilescu, G., Didychuk, A. L., Rodgers, M. L., Michael, L. A., Burke, J. E., Montemayor, E. J., Hoskins, A. A. & Butcher, S. E. Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA. J Mol Biol 428, 777-789, doi:10.1016/j.jmb.2015.11.026 (2016).
  • Borgia, A., Zheng, W., Buholzer, K., Borgia, M. B., Schuler, A., Hofmann, H., Soranno, A., Nettels, D., Gast, K., Grishaev, A., Best, R. B. & Schuler, B. Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc 138, 11714-11726, doi:10.1021/jacs.6b05917 (2016).
  • Bhandari, Y. R., Jiang, W., Stahlberg, E. A., Stagno, J. R. & Wang, Y. X. Modeling RNA topological structures using small angle X-ray scattering. Methods 103, 18-24, doi:10.1016/j.ymeth.2016.04.015 (2016).
  • Altieri, A. S., Ladner, J. E., Li, Z., Robinson, H., Sallman, Z. F., Marino, J. P. & Kelman, Z. A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic Acids Res 44, 6232-6241, doi:10.1093/nar/gkw824 (2016).

2015

  • Zhang, Q., Fan, L., Hou, F., Dong, A., Wang, Y. X. & Tong, Y. New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins. Sci Rep 5, 15660, doi:10.1038/srep15660 (2015).
  • Walker, R. G., Angerman, E. B., Kattamuri, C., Lee, Y. S., Lee, S. J. & Thompson, T. B. Alternative binding modes identified for growth and differentiation factor-associated serum protein (GASP) family antagonism of myostatin. J Biol Chem 290, 7506-7516, doi:10.1074/jbc.M114.624130 (2015).
  • Venditti, V., Tugarinov, V., Schwieters, C. D., Grishaev, A. & Clore, G. M. Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I. Nat Commun 6, 5960, doi:10.1038/ncomms6960 (2015).
  • Venditti, V., Schwieters, C. D., Grishaev, A. & Clore, G. M. Dynamic equilibrium between closed and partially closed states of the bacterial Enzyme I unveiled by solution NMR and X-ray scattering. Proc Natl Acad Sci U S A 112, 11565-11570, doi:10.1073/pnas.1515366112 (2015).
  • Kakar, S., Fang, X., Lubkowska, L., Zhou, Y. N., Shaw, G. X., Wang, Y. X., Jin, D. J., Kashlev, M. & Ji, X. Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES. J Biol Chem 290, 23656-23669, doi:10.1074/jbc.M114.618801 (2015).
  • Jones, C. P. & Ferre-D'Amare, A. R. RNA quaternary structure and global symmetry. Trends Biochem Sci 40, 211-220, doi:10.1016/j.tibs.2015.02.004 (2015).
  • Jones, C. P. & Ferre-D'Amare, A. R. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nat Struct Mol Biol 22, 679-685, doi:10.1038/nsmb.3073 (2015).
  • Ithychanda, S. S., Fang, X., Mohan, M. L., Zhu, L., Tirupula, K. C., Naga Prasad, S. V., Wang, Y. X., Karnik, S. S. & Qin, J. A mechanism of global shape-dependent recognition and phosphorylation of filamin by protein kinase A. J Biol Chem 290, 8527-8538, doi:10.1074/jbc.M114.633446 (2015).
  • Gruschus, J. M., Jiang, Z., Yap, T. L., Hill, S. A., Grishaev, A., Piszczek, G., Sidransky, E. & Lee, J. C. Dissociation of glucocerebrosidase dimer in solution by its co-factor, saposin C. Biochem Biophys Res Commun 457, 561-566, doi:10.1016/j.bbrc.2015.01.024 (2015).
  • Fang, X., Stagno, J. R., Bhandari, Y. R., Zuo, X. & Wang, Y. X. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. Curr Opin Struct Biol 30, 147-160, doi:10.1016/j.sbi.2015.02.010 (2015).
  • Dick, R. A., Datta, S. A., Nanda, H., Fang, X., Wen, Y., Barros, M., Wang, Y. X., Rein, A. & Vogt, V. M. Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein. J Virol 89, 10371-10382, doi:10.1128/JVI.01628-15 (2015).
  • Deng, X., Walker, R. G., Morris, J., Davidson, W. S. & Thompson, T. B. Role of Conserved Proline Residues in Human Apolipoprotein A-IV Structure and Function. J Biol Chem 290, 10689-10702, doi:10.1074/jbc.M115.637058 (2015).
  • Datta, S. A., Clark, P. K., Fan, L., Ma, B., Harvin, D. P., Sowder, R. C., 2nd, Nussinov, R., Wang, Y. X. & Rein, A. Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly. J Virol 90, 1773-1787, doi:10.1128/JVI.02061-15 (2015).
  • Au, H. H., Cornilescu, G., Mouzakis, K. D., Ren, Q., Burke, J. E., Lee, S., Butcher, S. E. & Jan, E. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci U S A 112, E6446-6455, doi:10.1073/pnas.1512088112 (2015).

2014

  • Zhang, J., Jones, C. P. & Ferre-D'Amare, A. R. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta 1839, 1020-1029, doi:10.1016/j.bbagrm.2014.04.014 (2014).
  • Warner, K. D., Homan, P., Weeks, K. M., Smith, A. G., Abell, C. & Ferre-D'Amare, A. R. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol 21, 591-595, doi:10.1016/j.chembiol.2014.03.007 (2014).
  • Warner, K. D., Chen, M. C., Song, W., Strack, R. L., Thorn, A., Jaffrey, S. R. & Ferre-D'Amare, A. R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nat Struct Mol Biol 21, 658-663, doi:10.1038/nsmb.2865 (2014).
  • Schwieters, C. D. & Clore, G. M. Using small angle solution scattering data in Xplor-NIH structure calculations. Prog Nucl Magn Reson Spectrosc 80, 1-11, doi:10.1016/j.pnmrs.2014.03.001 (2014).
  • Peng, Y., Curtis, J. E., Fang, X. & Woodson, S. A. Structural model of an mRNA in complex with the bacterial chaperone Hfq. Proc Natl Acad Sci U S A 111, 17134-17139, doi:10.1073/pnas.1410114111 (2014).
  • Luo, Y., Chen, B., Zhou, J., Sintim, H. O. & Dayie, T. K. E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs. Mol Biosyst 10, 384-390, doi:10.1039/c3mb70467j (2014).
  • Lemak, A., Wu, B., Yee, A., Houliston, S., Lee, H. W., Gutmanas, A., Fang, X., Garcia, M., Semesi, A., Wang, Y. X., Prestegard, J. H. & Arrowsmith, C. H. Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data. Structure 22, 1862-1874, doi:10.1016/j.str.2014.09.013 (2014).
  • Jones, C. P. & Ferre-D'Amare, A. R. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA. Embo J 33, 2692-2703, doi:10.15252/embj.201489209 (2014).
  • Hickman, A. B., Ewis, H. E., Li, X., Knapp, J. A., Laver, T., Doss, A. L., Tolun, G., Steven, A. C., Grishaev, A., Bax, A., Atkinson, P. W., Craig, N. L. & Dyda, F. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. Cell 158, 353-367, doi:10.1016/j.cell.2014.05.037 (2014).
  • Gill, M. L. & Byrd, R. A. Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism. Nat Struct Mol Biol 21, 1022-1023, doi:10.1038/nsmb.2925 (2014).
  • Desai, R., Kilburn, D., Lee, H. T. & Woodson, S. A. Increased ribozyme activity in crowded solutions. J Biol Chem 289, 2972-2977, doi:10.1074/jbc.M113.527861 (2014).
  • Chang, F. M., Coyne, H. J., Cubillas, C., Vinuesa, P., Fang, X., Ma, Z., Ma, D., Helmann, J. D., Garcia-de los Santos, A., Wang, Y. X., Dann, C. E., 3rd & Giedroc, D. P. Cu(I)-mediated allosteric switching in a copper-sensing operon repressor (CsoR). J Biol Chem 289, 19204-19217, doi:10.1074/jbc.M114.556704 (2014).
  • Baird, N. J. & Ferre-D'Amare, A. R. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 1103, 211-225, doi:10.1007/978-1-62703-730-3_16 (2014).

2013

  • Nolan, K., Kattamuri, C., Luedeke, D. M., Deng, X., Jagpal, A., Zhang, F., Linhardt, R. J., Kenny, A. P., Zorn, A. M. & Thompson, T. B. Structure of protein related to Dan and Cerberus: insights into the mechanism of bone morphogenetic protein antagonism. Structure 21, 1417-1429, doi:10.1016/j.str.2013.06.005 (2013).
  • Lau, M. W. & Ferre-D'Amare, A. R. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol 9, 805-810, doi:10.1038/nchembio.1360 (2013).
  • Lakomek, N. A., Kaufman, J. D., Stahl, S. J., Louis, J. M., Grishaev, A., Wingfield, P. T. & Bax, A. Internal dynamics of the homotrimeric HIV-1 viral coat protein gp41 on multiple time scales. Angew Chem Int Ed Engl 52, 3911-3915, doi:10.1002/anie.201207266 (2013).
  • Ha, J. H., Eo, Y., Grishaev, A., Guo, M., Smith, J. A., Sintim, H. O., Kim, E. H., Cheong, H. K., Bentley, W. E. & Ryu, K. S. Crystal structures of the LsrR proteins complexed with phospho-AI-2 and two signal-interrupting analogues reveal distinct mechanisms for ligand recognition. J Am Chem Soc 135, 15526-15535, doi:10.1021/ja407068v (2013).
  • Fang, X., Wang, J., O'Carroll, I. P., Mitchell, M., Zuo, X., Wang, Y., Yu, P., Liu, Y., Rausch, J. W., Dyba, M. A., Kjems, J., Schwieters, C. D., Seifert, S., Winans, R. E., Watts, N. R., Stahl, S. J., Wingfield, P. T., Byrd, R. A., Le Grice, S. F., Rein, A. & Wang, Y. X. An unusual topological structure of the HIV-1 Rev response element. Cell 155, 594-605, doi:10.1016/j.cell.2013.10.008 (2013).
  • Deshmukh, L., Schwieters, C. D., Grishaev, A., Ghirlando, R., Baber, J. L. & Clore, G. M. Structure and dynamics of full-length HIV-1 capsid protein in solution. J Am Chem Soc 135, 16133-16147, doi:10.1021/ja406246z (2013).
  • Deng, X., Morris, J., Chaton, C., Schroder, G. F., Davidson, W. S. & Thompson, T. B. Small-angle X-ray scattering of apolipoprotein A-IV reveals the importance of its termini for structural stability. J Biol Chem 288, 4854-4866, doi:10.1074/jbc.M112.436709 (2013).
  • Das, R., Liang, Y. H., Mariano, J., Li, J., Huang, T., King, A., Tarasov, S. G., Weissman, A. M., Ji, X. & Byrd, R. A. Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. Embo J 32, 2504-2516, doi:10.1038/emboj.2013.174 (2013).
  • Clore, G. M. & Venditti, V. Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Trends Biochem Sci 38, 515-530, doi:10.1016/j.tibs.2013.08.003 (2013).
  • Baird, N. J. & Ferre-D'Amare, A. R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19, 167-176, doi:10.1261/rna.036269.112 (2013).

2012

  • Wood, S., Ferre-D'Amare, A. R. & Rueda, D. Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. Acs Chem Biol 7, 920-927, doi:10.1021/cb300014u (2012).
  • Wang, X.-Y., Wang, J. & Zuo, X. in RNA 3D Structure Analysis and Prediction  Nucleic Acids and Molecular Biology (ed E. Westhof and N. Leontis)  335-359 (2012).
  • Maltsev, A. S., Grishaev, A. & Bax, A. Monomeric alpha-synuclein binds Congo Red micelles in a disordered manner. Biochemistry-Us 51, 631-642, doi:10.1021/bi201435d (2012).
  • Grishaev, A., Anthis, N. J. & Clore, G. M. Contrast-matched small-angle X-ray scattering from a heavy-atom-labeled protein in structure determination: application to a lead-substituted calmodulin-peptide complex. J Am Chem Soc 134, 14686-14689, doi:10.1021/ja306359z (2012).
  • Grishaev, A. Sample preparation, data collection, and preliminary data analysis in biomolecular solution X-ray scattering. Curr Protoc Protein Sci Chapter 17, Unit17 14, doi:10.1002/0471140864.ps1714s70 (2012).
  • Giladi, M., Sasson, Y., Fang, X., Hiller, R., Buki, T., Wang, Y. X., Hirsch, J. A. & Khananshvili, D. A common Ca2+-driven interdomain module governs eukaryotic NCX regulation. Plos One 7, e39985, doi:10.1371/journal.pone.0039985 (2012).
  • Giladi, M., Friedberg, I., Fang, X., Hiller, R., Wang, Y. X. & Khananshvili, D. G503 is obligatory for coupling of regulatory domains in NCX proteins. Biochemistry-Us 51, 7313-7320, doi:10.1021/bi300739z (2012).
  • Chen, B., Zuo, X., Wang, Y. X. & Dayie, T. K. Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy. Nucleic Acids Res 40, 3117-3130, doi:10.1093/nar/gkr1154 (2012).
  • Burke, J. E., Sashital, D. G., Zuo, X., Wang, Y. X. & Butcher, S. E. Structure of the yeast U2/U6 snRNA complex. RNA 18, 673-683, doi:10.1261/rna.031138.111 (2012).
  • Burke, J. E. & Butcher, S. E. Nucleic acid structure characterization by small angle X-ray scattering (SAXS). Curr Protoc Nucleic Acid Chem Chapter 7, Unit7 18, doi:10.1002/0471142700.nc0718s51 (2012).
  • Avvakumov, G. V., Walker, J. R., Xue, S., Allali-Hassani, A., Asinas, A., Nair, U. B., Fang, X., Zuo, X., Wang, Y. X., Wilkinson, K. D. & Dhe-Paganon, S. Two ZnF-UBP domains in isopeptidase T (USP5). Biochemistry-Us 51, 1188-1198, doi:10.1021/bi200854q (2012).

2011

  • Takayama, Y., Schwieters, C. D., Grishaev, A., Ghirlando, R. & Clore, G. M. Combined use of residual dipolar couplings and solution X-ray scattering to rapidly probe rigid-body conformational transitions in a non-phosphorylatable active-site mutant of the 128 kDa enzyme I dimer. J Am Chem Soc 133, 424-427, doi:10.1021/ja109866w (2011).
  • Nady, N., Lemak, A., Walker, J. R., Avvakumov, G. V., Kareta, M. S., Achour, M., Xue, S., Duan, S., Allali-Hassani, A., Zuo, X., Wang, Y. X., Bronner, C., Chedin, F., Arrowsmith, C. H. & Dhe-Paganon, S. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem 286, 24300-24311, doi:10.1074/jbc.M111.234104 (2011).
  • Liao, J. C., Lam, R., Brazda, V., Duan, S., Ravichandran, M., Ma, J., Xiao, T., Tempel, W., Zuo, X., Wang, Y. X., Chirgadze, N. Y. & Arrowsmith, C. H. Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53. Structure 19, 418-429, doi:10.1016/j.str.2010.12.015 (2011).
  • Datta, S. A., Zuo, X., Clark, P. K., Campbell, S. J., Wang, Y. X. & Rein, A. Solution properties of murine leukemia virus gag protein: differences from HIV-1 gag. J Virol 85, 12733-12741, doi:10.1128/JVI.05889-11 (2011).

2010

  • Zuo, X., Wang, J., Yu, P., Eyler, D., Xu, H., Starich, M. R., Tiede, D. M., Simon, A. E., Kasprzak, W., Schwieters, C. D., Shapiro, B. A. & Wang, Y. X. Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proc Natl Acad Sci U S A 107, 1385-1390, doi:10.1073/pnas.0908140107 (2010).
  • Wang, Y. X., Zuo, X., Wang, J., Yu, P. & Butcher, S. E. Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods 52, 180-191, doi:10.1016/j.ymeth.2010.06.009 (2010).
  • Schwieters, C. D., Suh, J. Y., Grishaev, A., Ghirlando, R., Takayama, Y. & Clore, G. M. Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering. J Am Chem Soc 132, 13026-13045, doi:10.1021/ja105485b (2010).
  • Mittag, T., Marsh, J., Grishaev, A., Orlicky, S., Lin, H., Sicheri, F., Tyers, M. & Forman-Kay, J. D. Structure/function implications in a dynamic complex of the intrinsically disordered Sic1 with the Cdc4 subunit of an SCF ubiquitin ligase. Structure 18, 494-506, doi:10.1016/j.str.2010.01.020 (2010).
  • Grishaev, A., Guo, L., Irving, T. & Bax, A. Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling. J Am Chem Soc 132, 15484-15486, doi:10.1021/ja106173n (2010).

2009

  • Yang, Y., Wang, X., Hawkins, C. A., Chen, K., Vaynberg, J., Mao, X., Tu, Y., Zuo, X., Wang, J., Wang, Y. X., Wu, C., Tjandra, N. & Qin, J. Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase. J Biol Chem 284, 5836-5844, doi:10.1074/jbc.M805319200 (2009).
  • Wang, J., Zuo, X., Yu, P., Xu, H., Starich, M. R., Tiede, D. M., Shapiro, B. A., Schwieters, C. D. & Wang, Y. X. A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol 393, 717-734, doi:10.1016/j.jmb.2009.08.001 (2009).
  • Wang, J., Zuo, X., Yu, P., Byeon, I. J., Jung, J., Wang, X., Dyba, M., Seifert, S., Schwieters, C. D., Qin, J., Gronenborn, A. M. & Wang, Y. X. Determination of multicomponent protein structures in solution using global orientation and shape restraints. J Am Chem Soc 131, 10507-10515, doi:10.1021/ja902528f (2009).
  • Das, R., Mariano, J., Tsai, Y. C., Kalathur, R. C., Kostova, Z., Li, J., Tarasov, S. G., McFeeters, R. L., Altieri, A. S., Ji, X., Byrd, R. A. & Weissman, A. M. Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Mol Cell 34, 674-685, doi:10.1016/j.molcel.2009.05.010 (2009).

2008

  • Zuo, X., Wang, J., Foster, T. R., Schwieters, C. D., Tiede, D. M., Butcher, S. E. & Wang, Y. X. Global molecular structure and interfaces: refining an RNA:RNA complex structure using solution X-ray scattering data. J Am Chem Soc 130, 3292-3293, doi:10.1021/ja7114508 (2008).