SAXS Core

《核心》继续为研究界服务，并对科学产生了重大影响，报告这一时期的出版物清单证明了这一点（见下文）。与此同时，核心的第一位员工方宪勇博士已经接受了中国清华大学的教职，并计划于2014年底离开该职位。方博士接手Core以来，为社区做出了巨大贡献。范立新博士于7月14日加入Core。核心技术转移在这段时间内进行，直到方博士离开。核心是在采购一个内部小角度x射线散射仪器。在过去的一年里，我们使用两家主要供应商的仪器进行了广泛的测试工作，并得出结论，理学的BioSAXS-1000为生物学研究提供了最佳的灵敏度、可重复性和适用性。目前，采购被搁置在采购部门等待批准。在报告期内使用CCR SAXS核心生成的数据的出版物：方欣，王军，O'Carroll IP, Mitchell M，左旭，王勇，于平，刘勇，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，王永新。HIV-1 Rev反应元件的不寻常拓扑结构。Cell. 2013, 10(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。铜敏感操纵子抑制因子（CsoR）中Cu(I)介导的变构开关。生物化学学报，2014;29(7):1294 - 1294。3. Warner， K.D, Chen， M.C, Song， W., Strack， R.L, Thorn， A., Jaffrey， S.R和Ferre-D'Amare, a.r。高效RNA模拟绿色荧光蛋白活性的结构基础。自然结构与分子生物学。2014, 21, 658-663。4. 张杰，Jones CP, Ferre-D'Amare AR.基于小角x射线散射和量热法的核开关全局分析。生物化学生物物理学报2014年4月24日。doi: 10.1016 / j.bbagrm.2014.04.014。5. 张晓东，张晓东，张晓东，张晓东，等。基于dna片段的生物rna药物发现：铅片段特异性结合和重组TPP核糖开关。化学与生物学报。2014年5月22日；21(5):591-5。6. Baird NJ, Ferre-D'Amare AR.小角x射线散射（SAXS）分析核开关结构和配体结合。方法：中华医学杂志。2014;1103:211-25。7. 一种体外进化的glmS核酶具有野生型折叠，但失去了辅酶依赖性。化学学报，2013;9(12):805-10。8. Schwieters CD, Clore GM.在Xplor-NIH结构计算中使用小角度溶液散射数据。核磁共振波谱学报，2014,31(1):1-11。9. 陈建军，陈建军，陈建军，陈建军，等。HIV-1全长衣壳蛋白在溶液中的结构和动力学研究。生物化学学报，2013,30(3):563 - 567。10. 郭志强，王志强，王志强，等。细菌磷酸烯醇丙酮酸：糖磷酸转移酶系统胞质蛋白复合物的结构、动力学和生物物理学。生物化学进展，2013;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.家蝇DNA转座子末端识别的结构基础。Cell. 2014, 7(2):353-67。12. Ha JH, Eo Y, Grishaev A, Guo M, Smith JA, Sintim HO, Kim EH, Cheong HK, Bentley WE, Ryu KS。LsrR蛋白与磷酸ai -2和两种信号中断类似物复合物的晶体结构揭示了不同的配体识别机制。生物化学学报，2013;35(6):526- 535。13. 李建军，李建军，李建军，李建军，李建军。HIV-1病毒外壳蛋白gp41的内部动力学研究。新化学与国际教育，2013,24(4):3911-5。14. Das R，梁永华，Mariano J，李军，黄涛，King A, Tarasov SG, Weissman AM, Ji X, Byrd RA。E2的变构调节：E3的相互作用促进了进程泛素化机制。EMBO J. 2013, Sep 11;32(18):2504-16。15. 刘建军，李建军，李建军。在拥挤溶液中增加核酶活性。生物化学学报，2014,31(5):2972-7。16. 罗勇，陈斌，周军，何新廷，戴耶TK。E88是一种来自破伤风梭菌的新型环状二gmpⅰ类核糖开关适配体，它与典型的ⅰ类核糖开关Vc2具有相似的折叠，但与c-二gmp类似物结合的方式不同。中华生物医学工程学报，2014;10(3):384-90。

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.