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Structural Biophysics Laboratory (SBL)
SAXS Core Facility

SAXS Core Facility Publication list

---2008 - 2011---

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

  2. Wang, J., Zuo, X., Yu, P., Byeon, I. J., Jung, J., Wang, X., Dyba, M., Seifert, S., Schwieters, C. D., Q in, J., Gronenborn, A. M., and Wang, Y. X. (2009) Determination of multicomponent protein structures in solution using global orientation and shape restraints, J. Am. Chem. Soc. 131, 10507-10515.

  3. Wang, J., Zuo, X., Yu, P., Xu, H., Starich, M. R., Tiede, D. M., Shapiro, B. A., Schwieters, C. D., and Wang, Y. X. (2009) 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.

  4. 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., and Qin, J. (2009) Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase, J. Biol. Chem. 284, 5836-5844.

  5. Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, Weissman AM Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78, Mol Cell. 2009 Jun 26; 34(6):674-85. doi: 10.1016/j.molcel.2009.05.010

  6. 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., and Wang, Y. X. (2010) 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.

  7. Wang YX, Zuo X, Wang J, Yu P, Butcher SE. Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering (2010). , Methods, 52(2):180-91.

  8. Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, Tyers M, Forman-Kay JD. (2010) 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. This article was highlighted by Faculty of 1000:

  9. Schwieters CD, Suh JY, Grishaev A, Ghirlando R, Takayama Y, Clore GM.(2010) 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. i>J Am Chem Soc. 132,13026-45. This article was highlighted by Faculty of 1000:

  10. Grishaev A, Guo L, Irving T, Bax A.(2010) Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling. J Am Chem Soc. 132, 15484-6.

  11. Liao JC, Lam R, Brazda V, Duan S, Ravichandran M, Ma J, Xiao T, Tempel W, Zuo X, Wang YX, Chirgadze NY, Arrowsmith CH. (2011) Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53 Structure.19,418-29.

  12. Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S. (2011) Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem. 286, 24300-11

  13. Datta SA, Zuo X, Clark PK, Campbell SJ, Wang YX, Rein A. (2011) Properties of Murine Leukemia Virus Gag Protein: Differences from HIV-1 Gag J Virol. 85, 12733-41

  14. Takayama Y, Schwieters CD, Grishaev A, Ghirlando R, Clore GM.(2011) 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 , 424–27

  15. ---2012---

  16. Giladi M, Sasson Y, Fang X., Hiller R, Buki T, Wang YX, Hirsch JA, Khananshvili D. Common Common Ca(2+)-Driven Interdomain Module Governs Eukaryotic NCX Regulation PLoS One, 2012, 7(6):e39985.

  17. Avvakumov G, Walker J, Xue S, Allali-Hassani A, Asinas A, Nair U, Fang X., Zuo X., Wang YX, Wilkinson K, Dhe-Paganon S (2012). Two ZnF-UBP domains in isopeptidase T (USP5), Biochemistry, 51(6):1188-98.

  18. Chen B, Zuo X, Wang YX, Dayie TK. Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy, Nucleic Acids Res, 2012, 40(7):3117-30.

  19. Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE. Structure of the yeast U2/U6 snRNA complex. RNA, 2012, 18(4):673-83.

  20. Giladi M, Friedberg I, Fang X., Hiller R, Wang YX , Khananshvili D. G503 is obligatory for coupling of regulatory domains in NCX proteins Biochemistry. 2012, 51:7313-20.

  21. 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. 2012, 134, 14686-14689

  22. Sharla Wood, Adrian R. Ferré-D’Amaré, and David Rueda; Allosteric Tertiary Interactions Preorganize the c-di-GMP Riboswitch and Accelerate Ligand Binding; ACS Chem. Biol., 2012, 7 (5), pp 920–927

  23. Alexander Grishaev, Sample Preparation, Data Collection, and Preliminary Data Analysis in Biomolecular Solution X-Ray Scattering; Current Protocols in Protein Science, 2012, DOI: 10.1002/0471140864.ps1714s70

  24. A. Maltsev, A. Grishaev, A. Bax “Monomeric α-synuclein binds Congo Red micelles in a disordered manner”, Biochemistry (2012) 51, 631-642.

  25. Wang, X-Y, Wang, J, Zuo, X (2012). Top-down Approach to Determine Global Structures of RNAs in Solution Using NMR and Small-angle X-ray Scattering Measurements, Chapter of book ”RNA 3D Structure Analysis and Prediction”, Volume 27 of the series Nucleic Acids and Molecular Biology pp 335-359, E. Westhof and N. Leontis (Eds).

  26. ---2013---

  27. Fang X, Wang J, O'Carroll IP, Mitchell M, Zuo X, Wang Y, Yu P, Liu Y, Rausch JW, Dyba MA, Kjems J, Schwieters CD, Seifert S, Winans RE, Watts NR, Stahl SJ, Wingfield PT, Byrd RA, Le Grice SF, Rein A, Wang YX An unusual topological structure of the HIV-1 Rev response element. Cell. 2013 Oct 24;155(3):594-605.

  28. Lau MW, Ferré-D'Amaré AR An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol. 2013 Dec;9(12):805-10.

  29. Deshmukh L, Schwieters CD, Grishaev A, Ghirlando R, Baber JL, Clore GM. Structure and dynamics of full-length HIV-1 capsid protein in solution. J Am Chem Soc. 2013 Oct 30;135(43):16

  30. Clore GM, Venditti V. Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Trends Biochem Sci. 2013 Oct;38(10):515-30.

  31. Ha JH, Eo Y, Grishaev A, Guo M, Smith JA, Sintim HO, Kim EH, Cheong HK, Bentley WE, Ryu KS. 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. 2013 Oct 16;135(41):15526-35.

  32. Lakomek NA, Kaufman JD, Stahl SJ, Louis JM, Grishaev A, Wingfield PT, Bax A. Internal dynamics of the homotrimeric HIV-1 viral coat protein gp41 on multiple time scales. Angew Chem Int Ed Engl. 2013 Apr 2;52(14):3911-5.

  33. Baird, N.J., & Ferré-D'Amaré, A.R. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches RNA 19, 167-176 (2013).

  34. Kristof Nolan, Chandramohan Kattamuri, David M. Luedeke, Xiaodi Deng, Amrita Jagpal, Fuming Zhang, Robert J. Linhardt, Alan P. Kenny, Aaron M. Zorn, Thomas B. Thompson; Structure of Protein Related to Dan and Cerberus: Insights into the Mechanism of Bone Morphogenetic Protein Antagonism, Structure, 21(8), 1417-1429 (2013). DOI: 10.1016/j.str.2013.06.005

  35. Xiaodi Deng, Jamie Morris, Catherine Chaton, Gunnar F. Schröder, W. Sean Davidson, and Thomas B. Thompson; Small-angle X-ray Scattering of Apolipoprotein A-IV Reveals the Importance of Its Termini for Structural Stability; J. Biol. Chem., 2013, 288(7), 4854-4866.

  36. ---2014---

  37. Chang FM, Coyne HJ, Cubillas C, Vinuesa P, Fang X, Ma Z, Ma D, Helmann JD, García-de Los Santos A, Wang YX, Dann CE 3rd, Giedroc DP. Allosteric Switching in a Copper-sensing Operon Repressor (CsoR). J Biol Chem. 2014 Jul 4; 289(27):19204-17.

  38. Alexander Lemak, Bin Wu, Adelinda Yee, Scott Houliston, Hsiau-Wei Lee, Aleksandras Gutmanas, Xianyang Fang, Maite Garcia, Anthony Semesi, Yun-Xing Wang, James H. Prestegard, and Cheryl H. Arrowsmith; Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data, Structure, 2014, 22, 1862–1874.

  39. Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., and Ferre-D'Amare, A.R. Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature structural & molecular biology. 2014, 21, 658-663.

  40. Zhang J, Jones CP, Ferré-D'Amaré AR. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim. Biophys. Acta 1839, 1020-1029 (2014).

  41. Warner KD, Homan P, Weeks KM, Smith AG, Abell C, Ferré-D'Amaré AR. Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol. 2014 May 22;21(5):591-5.

  42. Baird NJ, Ferré-D'Amaré AR. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol. 2014;1103: 211-25.

  43. Schwieters CD, Clore GM. Using small angle solution scattering data in Xplor-NIH structure calculations. Prog Nucl Magn Reson Spectrosc. 2014 Jul;80:1-11.

  44. Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F. Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica. Cell. 2014 Jul 17;158(2):353-67.

  45. Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, Byrd RA. Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 2013 Sep 11;32(18):2504-16.

  46. CP Jones, AR Ferré‐D'Amaré, Crystal structure of ac‐di‐AMP riboswitch reveals an internally pseudo‐dimeric RNA, The EMBO Journal, 2014, 33, 2692

  47. Desai R, Kilburn D, Lee HT, Woodson SA. Increased ribozyme activity in crowded solutions. J Biol Chem. 2014 Jan 31;289(5):2972-7.

  48. Luo Y, Chen B, Zhou J, Sintim HO, Dayie TK. 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. 2014 Mar 4;10(3):384-90.

  49. Yi Peng, Joseph E. Curtis, Xianyang Fang, and Sarah A. Woodsond, Structural model of an mRNA in complex with the bacterial chaperone Hfq, PNAS, 111, 17134-17139 (2014)

  50. Schwieters, C.D. & Clore, G.M. (2014) Using small angle solution scattering data in Xplor-NIH structure calculations. Progr. Nucl. Magn. Reson. Spectroscopy 80, 1-11

  51. Michelle L Gill & R Andrew Byrd Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism. Nature Structural & Molecular Biology 21, 1022–1023 (2014)

  52. ---2015---

  53. Ithychanda SS, Fang X, Mohan ML, Zhu L, Tirupula KC, Prasad SV, Wang YX, Karnik S, Qin J A mechanism of global shape-dependent recognition and phosphorylation of filamin by protein kinase A, J BIOL CHEM Feb 9 (2015)

  54. J. Gruschus, J. Jiang, T. Yap, S. Hill, A. Grishaev, G. Piszczek, E. Sidransky, J. Lee. “Dissociation of Glucocerebrosidase in solution by its co-factor, Saposin C” Biochem. Biophys. Res. Commun. (2015), 457, 561-566.

  55. V. Venditti, V. Tugarinov, C. Schwieters, A. Grishaev, M. Clore. “Large scale interdomain rearrangement triggered by suppression of us-ms dynamics in the Escherichia coli Enzyme I” Nature Commun. (2015), 6, 5960.

  56. Venditti V, Schwieters CD, Grishaev A, Clore GM. 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. 2015 Sep 15;112(37):11565-70

  57. Xianyang Fang, Jason R Stagno, Yuba R Bhandari, Xiaobing Zuo, Yun-Xing Wang. Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures, Current Opinion in Structural Biology.(2015), 30,147–160

  58. Kakar S, Fang X, Lubkowska L, Zhou YN, Shaw GX, Wang YX, Jin DJ, 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. 2015 Sep 25;290(39):23656-69

  59. Ithychanda SS, Fang X, Mohan ML, Zhu L, Tirupula KC, Naga Prasad SV, Wang YX, Karnik SS, Qin J. A mechanism of global shape-dependent recognition and phosphorylation of filamin by protein kinase A. J Biol Chem. 2015 Mar 27;290(13):8527-38.

  60. Christopher P Jones & Adrian R Ferré-D’Amaré, Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains , Nature Structural & Molecular Biology (2015), 22, 679–685

  61. Jones CP, Ferré-D'Amaré AR. RNA quaternary structure and global symmetry. Trends Biochem Sci. 2015 Apr; 40(4):211-20.

  62. Dick RA, Datta SA, Nanda H, Fang X, Wen Y, Barros M, Wang YX, Rein A, Vogt VM. Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein. J Virol. 2015 Oct 15;89(20):10371-82

  63. Qi Zhang, Lixin Fan, Feng Hou, Aiping Dong, Yun-Xing Wang &Yufeng Tong. Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins, Scientific Reports( 2015 Oct) 22;5:15660