| Protein-Nucleic Acids Journal Club | Thursdays, 2:30p-3:30p, LGRT 703 |
| Chem 797B (Spire 24157) | This WEB page last updated: 5/3/07, 1:55 PM |
Organizers: Craig Martin, Karsten Theis, Chris Woodcock, Bob Zimmermann
| Date | Presenters | Topic |
|---|---|---|
| Feb 8 | Ruthanne & Rochelle |
(1) Privalov, P. L., Dragan, A. I., Crane-Robinson, C., Breslauer, K. J., Remeta, D. P., and Minetti, C. A. (2007) What drives proteins into the major or minor grooves of DNA? J Mol Biol 365, 1-9.
(2) Tolstorukov, M. Y., Jernigan, R. L., and Zhurkin, V. B. (2004) Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol 337, 65-76. |
| Feb 15 | Hoa & Elam | Simon, M. D., Feldman, M. E., Rauh, D., Maris, A. E., Wemmer, D. E., and Shokat, K. M. (2007) Structure and properties of a re-engineered homeodomain protein-DNA interface. ACS Chem Biol 1, 755-60. |
| Feb 22 | Ankit & Raja |
Bondarenko, V. A., Steele, L. M., Ujvari, A., Gaykalova, D. A., Kulaeva, O. I., Polikanov, Y. S., Luse, D. S., and Studitsky, V. M. (2006) Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II. Mol Cell 24, 469-79.
(Background) Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-60. |
| March 1 | Oscar & Shannon | Ivanov, I., et al., Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res, 2006. 34(20): p. 6023-33. |
| Mar 8 | Virginie & Adriana | Rogacheva, M., Ishchenko, A., Saparbaev, M., Kuznetsova, S., and Ogryzko, V. (2006) High resolution characterization of formamidopyrimidine-DNA glycosylase interaction with its substrate by chemical cross-linking and mass spectrometry using substrate analogs. J Biol Chem 281, 32353-65. |
| Mar 15 | Khadine & Mark | Charvin, G., Strick, T. R., Bensimon, D., and Croquette, V. (2005) Topoisomerase IV bends and overtwists DNA upon binding. Biophys J 89, 384-92. |
| Mar 22 | Spring Break | |
| Mar 29 | Xiaoqing & Aruni | Kim, Y.G., et al., A peptide with alternating lysines can act as a highly specific Z-DNA binding domain. Nucleic Acids Res, 2006. 34, 4937-42. |
| Apr 5 | Sarit & Shiv | Wang, D., Bushnell, D. A., Westover, K. D., Kaplan, C. D., and Kornberg, R. D. (2006) Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127, 941-54. |
| Apr 12 | Partha & Jeff Martin | Stone, M. D., Mihalusova, M., O'Connor C, M., Prathapam, R., Collins, K., and Zhuang, X. (2007) Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein. Nature 446, 458-61. |
| Apr 19 | Mrinmoy & Raghunath | Gustafsdottir, S. M., Schlingemann, J., Rada-Iglesias, A., Schallmeiner, E., Kamali-Moghaddam, M., Wadelius, C., and Landegren, U. (2007) In vitro analysis of DNA-protein interactions by proximity ligation. Proc Natl Acad Sci U S A 104, 3067-72. |
| Apr 26 | Jeff C & Malar | Malta, E., Moolenaar, G. F., and Goosen, N. (2006) Base flipping in nucleotide excision repair. J Biol Chem 281, 2184-94. |
| May 3 | Bob H & Archana | Stickle, D. F. and Fried, M. G. (2007) Cation binding linked to a sequence-specific CAP-DNA interaction. J Biophys Chem 126, 106-16.
Johnston, D., Tavano, C., Wickner, S., and Trun, N. (2006) Specificity of DNA binding and dimerization by CspE from Escherichia coli. J Biol Chem 281, 40208-15. |
| May 10 | Jonathan & Suriyakala | Krasnoslobodtsev, A. V., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (2007) Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy. J Mol Biol 365, 1407-16. |
| May 17 | Volunteers needed... |
|
Sarit Agasti
Rochelle Arvizo Malar Azagarsamy Jeff Chiecko Shannon Coates Mrinmoy De Wayne Decatur Selase Enuameh |
Agya Frimpong
Han Gang Partha Ghosh Rajarshi Ghosh Peng Gong Ruthanne Hassey Bob Herbst Khadine Higgins Suriyakala Ramalingan |
Aruni Karunanayake
Archana Krovi Arthur LaPlante Jonathan Leung Xiaoqing Liu Jeffrey Martin Oscar Miranda Mark Olbris Shiv Redhu |
Raghunath Roy
Elam Savariar Virginie Sjoelund Karsten Theis Hoa Tran Ankit Vahia Chris Woodcock Adriana Zeledon Bob Zimmermann |