SAXS Core

点击翻译按钮获取中文摘要

The Core continues to serve the research communities and has made significant impact to science, as evidenced by the list of publications during this period of the report (see below). In the meantime, the first staff of the Core, Dr. Xianayng Fang, has accepted a faculty position offer in Tsinghua University in China and is scheduled to leave the position by the end of year 2014. Dr. Fang has made a great contribution to the community since he took over the responsibility of the Core. Dr. Lixin Fan has joined the Core on July 14. The Core technical transfer is taking place during this time until departure of Dr. Fang. The Core is in a procurement of an in-house small angle X-ray scattering instrument. We have done an extensive testing work using the instruments from two major vendors for the past year and have concluded that the Rigaku's BioSAXS-1000 offers the best sensitivity, reproducibility and applicability for the biological research. Currently, the purchase is being held up in the purchasing department waiting for an approval. Publications using the data generated from the CCR SAXS Core during the reporting period: 1. 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. 2. Chang FM, Coyne HJ, Cubillas C, Vinuesa P, Fang X, Ma Z, Ma D, Helmann JD, Garcia-de Los Santos A, Wang YX, Dann CE 3rd, Giedroc DP. Cu(I)-mediated Allosteric Switching in a Copper-sensing Operon Repressor (CsoR). J Biol Chem. 2014 Jul 4;289(27):19204-17. 3. 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. 4. Zhang J, Jones CP, Ferre-D'Amare AR. Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. Biochim Biophys Acta. 2014 Apr 24. doi: 10.1016/j.bbagrm.2014.04.014. 5. Warner KD, Homan P, Weeks KM, Smith AG, Abell C, Ferre-D'Amare 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. 6. Baird NJ, Ferre-D'Amare AR. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol. 2014;1103:211-25. 7. Lau MW, Ferre-D'Amare 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. 8. 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. 9. 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):16133-47. 10. 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. 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, 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. 12. 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. 13. 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. 14. 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. 15. Desai R, Kilburn D, Lee HT, Woodson SA. Increased ribozyme activity in crowded solutions. J Biol Chem. 2014 Jan 31;289(5):2972-7. 16. 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.