SAXS Core Facility: Publications


2017

  • Bhandari YR, Fan L, Fang X, Zaki GF, Stahlberg EA, Jiang W, Schwieters CD, Stagno JR, and Wang YX. (2017). Topological Structure Determination of RNA Using Small-Angle X-Ray Scattering. J Mol Biol. 429(23): 3635-3649.
  • Cantero-Camacho A, Fan A, Wang YX, and Gallego J. (2017). Three-dimensional structure of the 3'X-tail of hepatitis C virus RNA in monomeric and dimeric states. RNA 23(9): 1465-1476.
  • Fang X, Michnicka M, Zhang Y, Wang YX, and Nikonowicz EP. (2017). Capture and Release of tRNA by the T-Loop Receptor in the Function of the T-Box Riboswitch. Biochemistry 56(28): 3549-3558.
  • Houliston RS, Lemak A, Iqbal A, Ivanochko D, Duan S, Kaustov L, Ong MS, Fan L, Senisterra G, Brown PJ, Wang YX, and Arrowsmith CH. (2017). Conformational dynamics of the TTD-PHD histone reader module of UHRF1 reveals multiple histone binding states, allosteric regulation and druggability. J Biol Chem. 292(51):  20947-20959.
  • Lau MW, Trachman RJ 3rd, and Ferre-D'Amare AR. (2017). A divalent cation-dependent variant of the glmS ribozyme with stringent Ca2+ selectivity co-opts a preexisting nonspecific metal ion-binding site. RNA 23(3): 355-364.
  • O'Carroll IP, Thappeta Y, Fan L, Ramirez-Valdez EA, Smith S, Wang YX, and Rein A. (2017). Contributions of individual domains to function of the HIV-1 Rev response element. J Virol. [Epub ahead of print].
  • Sathiyamoorthy K, Vijayalakshmi J, Tirupati B, Fan L, and Saper MA. (2017). Structural analyses of the Haemophilus influenzae peptidoglycan synthase activator LpoA suggest multiple conformations in solution. J Biol Chem. 292(43): 17626-17642.
  • Song H, Fang X, Jin L, Shaw GX, Wang YX, and Ji X. (2017). The Functional Cycle of Rnt1p: Five Consecutive Steps of Double-Stranded RNA Processing by a Eukaryotic RNase III. Structure. 25(2): 353-363.
  • Stagno JR, Liu Y, Bhandari YR, Conrad CE, Panja S, Swain M, Fan L, Nelson G, Li C, Wendel DR, White TA, Coe JD, Wiedorn MO, Knoska J, Oberthuer D, Tuckey RA, Yu P, Dyba M, Tarasov SG, Weierstall U, Grant TD, Schwieters CD, Zhang J, Ferre-D'Amare AR, Fromme P, Draper DE, Liang M, Hunter MS, Boutet S, Tan K, Zuo X, Ji X, Barty A, Zatsepin NA, Chapman HN, Spence JC, Woodson SA,  and Wang YX. (2017). Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature. 541(7636): 242-246.
  • Warner KD, Sjekloca L, Song W, Filonov GS,Jaffrey SR, and Ferre-D'Amare AR. (2017). A homodimer interface without base pairs in an RNA mimic of red fluorescent protein. Nat Chem Biol. 13(11): 1195-1201.
  • Whitley MJ, Xi Z, Bartko JC, Jensen MR, Blackledge M, and Gronenborn AM. (2017). A Combined NMR and SAXS Analysis of the Partially Folded Cataract-Associated V75D gammaD-Crystallin. Biophys J. 112(6): 1135-1146.
  • Xi Z, Whitley MJ, and Gronenborn AM. (2017). Human betaB2-Crystallin Forms a Face-en-Face Dimer in Solution: An Integrated NMR and SAXS Study. Structure. 25(3): 496-505.

2016

  • Altieri AS, Ladner JE, Li Z, Robinson H, Sallman ZF, Marino JP, and Kelman Z. (2016). A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic Acids Res. 44(20): 10015.
  • Bhandari YR, Jiang W, Stahlberg EA, Stagno JR, and Wang YX. (2016). Modeling RNA topological structures using small angle X-ray scattering. Methods. 103: 18-24.
  • Borgia A, Zheng W, Buholzer K, Borgia MB, Schuler A, Hofmann H, Soranno A, Nettels D, Gast K, Grishaev A, Best RB, and Schuler B. (2016). Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods. J Am Chem Soc. 138(36): 11714-11726.
  • Deshmukh L, Schwieters CD, Grishaev A, and Clore GM. (2016). Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering. Chemphyschem. 17(11): 1548-1552.
  • Jung D, Kang Y, Kim MY, Ma RW, and  Bhandari P. (2016). Zero-Inflated Poisson Modeling of Fall Risk Factors in Community-Dwelling Older Adults. West J Nurs Res. 38(2): 231-247.
  • LaRochelle JR, Fodor M, Xu X, Durzynska I, Fan L, Stams T, Chan HM, LaMarche MJ, Chopra R, Wang P,  Fortin PD, Acker MG, and Blacklow SC. (2016). Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2. Biochemistry. 55(15): 2269-2277.
  • Venditti V,  Egner TK, and Clore GM. (2016). 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(11): 6305-6322.
  • Zheng W, Borgia A, Buholzer K, Grishaev A, Schuler B, and Best RB. (2016). Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment. J Am Chem Soc. 138(36): 11702-11713.

2015

  • Ithychanda SS, Fang X, Mohan ML, Zhu L, Tirupula KC, Prasad SV, Wang YX, Karnik S, and Qin JA. (2015). A mechanism of global shape-dependent recognition and phosphorylation of filamin by protein kinase A.  J Biol Chem. 290(13):8527-8538.
  • Gruschus JM, Jiang Z, Yap TL, Hill SA, Grishaev A, Piszczek G, Sidransky E, and Lee JC. (2015). Dissociation of glucocerebrosidase in solution by its co-factor, saposin C. Biochem Biophys Res Commun. 457(4):561-566.
  • Venditti V, Tugarinov V, Schwieters C, Grishaev A, and Clore GM. (2015). Large scale interdomain rearrangement triggered by suppression of us-ms dynamics in the Escherichia coli Enzyme I. Nature Commun. 6: 5960.
  • Venditti V, Schwieters CD, Grishaev A, and Clore GM. (2015). 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(37): 11565-70.
  • Fang X, Stagno JR, Bhandari YR, Zuo X, and Wang YX. (2015). Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. Curr Opin Struct Biol. 30: 147-160.
  • Kakar S, Fang X, Lubkowska L, Zhou YN, Shaw GX, Wang YX, Jin DJ, Kashlev M, and Ji X. (2015). Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES. J Biol Chem. 290(39): 23656-69.
  • Jones CP and Ferré-D’Amaré AR. (2015). Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains , Nature Struct Mol Biol.  22: 679-685.
  • Jones CP and Ferré-D'Amaré AR. (2015). RNA quaternary structure and global symmetry. Trends Biochem Sci. 40(4): 211-20.
  • Dick RA, Datta SA, Nanda H, Fang X, Wen Y, Barros M, Wang YX, Rein A, and Vogt VM. (2015). Hydrodynamic and Membrane Binding Properties of Purified Rous Sarcoma Virus Gag Protein. J Virol. 89(20): 10371-82.
  • Zhang Q, Fan L, Hou F, Dong A, Wang YX, and Tong Y. (2015). New Insights into the RNA-Binding and E3 Ubiquitin Ligase Activities of Roquins. Sci Rep.  5: 15660.

2014

  • 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, and Giedroc DP. (2014). Allosteric Switching in a Copper-sensing Operon Repressor (CsoR). J Biol Chem. 289(27): 19204-17.
  • Lemak A, Wu B, Yee A, Houliston S, Lee H-W, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, and Arrowsmith CH. (2014). Structural Characterization of a Flexible Two-Domain Protein in Solution Using Small Angle X-Ray Scattering and NMR Data. Structure.  22: 862–1874.
  • Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, and Ferre-D'Amare AR. (2014). Structural basis for activity of highly efficient RNA mimics of green fluorescent protein. Nature Struct Mol Biol. 21: 658-663.
  • Zhang J, Jones CP, and Ferré-D'Amaré AR. (2014). Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta. 1839: 1020-1029.
  • Warner KD, Homan P, Weeks KM, Smith AG, Abell C, and Ferré-D'Amaré AR. (2014). Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem Biol. 21(5): 591-5.
  • Baird NJ, and Ferré-D'Amaré AR. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). (2014). Methods Mol Biol. 1103: 211-25.
  • Schwieters CD, and Clore GM. Using small angle solution scattering data in Xplor-NIH structure calculations. (2014). Prog Nucl Magn Reson Spectrosc. 80: 1-11.
  • Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, and Dyda F. (2014). Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica. Cell. 158(2): 353-67.
  • Das R, Liang YH, Mariano J, Li J, Huang T, King A, Tarasov SG, Weissman AM, Ji X, and Byrd RA. (2013). Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 32(18): 2504-16.
  • Jones CP, and Ferré‐D'Amaré AR. (2014). Crystal structure of ac‐di‐AMP riboswitch reveals an internally pseudo‐dimeric RNA. EMBO J. 33: 2692.
  • Desai R, Kilburn D, Lee HT, and Woodson SA. (2014). Increased ribozyme activity in crowded solutions. J Biol Chem. 289(5): 2972-7.
  • Luo Y, Chen B, Zhou J, Sintim HO, and Dayie TK. (2014). 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(3): 384-90.
  • Peng Y, Curtis JE, Fang X, and Woodsond SA. (2014). Structural model of an mRNA in complex with the bacterial chaperone Hfq. Proc Natl Acad Sci U S A. 111: 17134-17139.
  • Schwieters CD, and Clore GM. (2014). Using small angle solution scattering data in Xplor-NIH structure calculations. Progr Nucl Magn Reson Spectroscopy. 80: 1-11.
  • Gill ML, and Byrd RA. (2014). Dynamic activation of apoptosis: conformational ensembles of cIAP1 are linked to a spring-loaded mechanism. Nature Struct Mol Biol. 21: 1022–1023.

2013

  • 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, and Wang YX. (2013). An unusual topological structure of the HIV-1 Rev response element. Cell. 155(3): 594-605.
  • Lau MW, and Ferré-D'Amaré AR. (2013). An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol. 9(12): 805-10.
  • Deshmukh L, Schwieters CD, Grishaev A, Ghirlando R, Baber JL, and Clore GM. (2013). Structure and dynamics of full-length HIV-1 capsid protein in solution. J Am Chem Soc.  135(43): 16.
  • Clore GM, and Venditti V. (2013). Structure, dynamics and biophysics of the cytoplasmic protein-protein complexes of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Trends Biochem Sci. 38(10): 515-30.
  • Ha JH, Eo Y, Grishaev A, Guo M, Smith JA, Sintim HO, Kim EH, Cheong HK, Bentley WE, and Ryu KS. (2013). 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(41): 15526-35.
  • Lakomek NA, Kaufman JD, Stahl SJ, Louis JM, Grishaev A, Wingfield PT, and Bax A. (2013). Internal dynamics of the homotrimeric HIV-1 viral coat protein gp41 on multiple time scales. Angew Chem Int Ed Engl. 52(14): 3911-5.
  • Baird NJ, and Ferré-D'Amaré AR. (2013). Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 19: 167-176.
  • Nolan K, Kattamuri C, Luedeke DM, Deng X, Jagpal A, Zhang F, Robert J. inhardt RJ, Kenny AP, Zorn AM, and Thompson TB. (2013). Structure of Protein Related to Dan and Cerberus: Insights into the Mechanism of Bone Morphogenetic Protein Antagonism. Structure. 21(8): 1417-1429 (2013).
  • Deng X, Morris J, Chaton C, Schröder GF, Davidson WS, and Thompson TB. (2013). Small-angle X-ray Scattering of Apolipoprotein A-IV Reveals the Importance of Its Termini for Structural Stability. J Biol Chem. 288(7): 4854-4866.

2012

  • Giladi M, Sasson Y, Fang X, Hiller R, Buki T, Wang YX, Hirsch JA, and Khananshvili D. (2012). Common Common Ca(2+)-Driven Interdomain Module Governs Eukaryotic NCX Regulation. PLoS One. 7(6): e39985.
  • Avvakumov G, Walker J, Xue S, Allali-Hassani A, Asinas A, Nair U, Fang X, Zuo X, Wang YX, Wilkinson K, and Dhe-Paganon S. (2012). Two ZnF-UBP domains in isopeptidase T (USP5). Biochemistry. 51(6): 1188-98.
  • Chen B, Zuo X, Wang YX, and Dayie TK. (2012). Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy. Nucleic Acids Res. 40(7): 3117-30.
  • Burke JE, Sashital DG, Zuo X, Wang YX, and Butcher SE. (2012). Structure of the yeast U2/U6 snRNA complex. RNA.18(4): 673-83.
  • Giladi M, Friedberg I, Fang X, Hiller R, Wang YX, and Khananshvili D. (2012). G503 is obligatory for coupling of regulatory domains in NCX proteins. Biochemistry. 51: 7313-20.
  • Grishaev A, Anthis NJ, and Clore GM. (2012). 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.
  • Wood S, Ferré-D’Amaré AR, and Rueda D. (2012). Allosteric Tertiary Interactions Preorganize the c-di-GMP Riboswitch and Accelerate Ligand Binding. ACS Chem Biol. 7(5): 920-927.
  • Grishaev A. (2012). Sample Preparation, Data Collection, and Preliminary Data Analysis in Biomolecular Solution X-Ray Scattering. Curr Protoc Protein Sci. Chapter 17: Unit 17.
  • Maltsev A, Grishaev A, and Bax A. (2012). Monomeric α-synuclein binds Congo Red micelles in a disordered manner. Biochemistry. 51: 631-642.
  • Wang X-Y, Wang J, and Zuo X. (2012). Top-down Approach to Determine Global Structures of RNAs in Solution Using NMR and Small-angle X-ray Scattering Measurements, in RNA 3D Structure Analysis and Prediction, Vol. 27, Nucleic Acids and Molecular Biology, pp. 335-359, E. Westhof and N. Leontis (Eds).

2008 - 2011

  • Takayama Y, Schwieters CD, Grishaev A, Ghirlando R, and 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.
  • Datta SA, Zuo X, Clark PK, Campbell SJ, Wang YX, and Rein A. (2011). Properties of Murine Leukemia Virus Gag Protein: Differences from HIV-1 Gag. J Virol. 85: 12733-41.
  • 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, and Dhe-Paganon S. (2011). Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem. 286: 24300-11.
  • Liao JC, Lam R, Brazda V, Duan S, Ravichandran M, Ma J, Xiao T, Tempel W, Zuo X, Wang YX, Chirgadze NY, and Arrowsmith CH. (2011). Interferon-inducible protein 16: insight into the interaction with tumor suppressor p53. Structure.19: 418-29.
  • Grishaev A, Guo L, Irving T, and 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.
  • Schwieters CD, Suh JY, Grishaev A, Ghirlando R, Takayama Y, and 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. J Am Chem Soc. 132: 13026-45. This article was highlighted by Faculty of 1000.
  • Mittag T, Marsh J, Grishaev A, Orlicky S, Lin H, Sicheri F, Tyers M, and 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.
  • Wang YX, Zuo X, Wang J, Yu P, and Butcher SE. (2010). Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods. 52(2): 180-91.
  • Zuo X, Wang J, Yu P, Eyler D, Xu H, Starich MR, Tiede DM, Simon AE, Kasprzak W, Schwieters CD, Shapiro BA, and Wang YX. (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.
  • Das R, Mariano J, Tsai YC, Kalathur RC, Kostova Z, Li J, Tarasov SG, McFeeters RL, Altieri AS, Ji X, Byrd RA, and Weissman AM. (2009). Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Mol Cell. 34(6): 674-85.
  • Yang Y, Wang X, Hawkins CA, Chen K, Vaynberg J, Mao X, Tu Y, Zuo X, Wang J, Wang YX, 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.
  • Wang J, Zuo X, Yu P, Xu H, Starich MR, Tiede DM, Shapiro BA, Schwieters CD, and Wang YX. (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.
  • Wang J, Zuo X, Yu P, Byeon IJ, Jung J, Wang X, Dyba M, Seifert S, Schwieters CD, Qin J, Gronenborn AM and Wang, YX. (2009). Determination of multicomponent protein structures in solution using global orientation and shape restraints. J Am Chem Soc. 131: 10507-10515.
  • Zuo X, Wang J, Foster TR, Schwieters CD, Tiede DM, Butcher SE, and Wang YX. (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.