Recommended Readings: Rod MacKinnon, M.D., Ph.D., April 11

Monday Lecture Series
Monday, April 11, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Rod MacKinnon, M.D., Ph.D.
John D. Rockefeller Jr. Professor and Head,
Laboratory of Molecular Neurobiology and Biophysics,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Some Experiments That Excite Me Right Now

Recommended Readings

Brohawn, S. G., Campbell, E. B., & MacKinnon, R. (2014). Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel. Nature, 516(7529), 126-130. doi:10.1038/nature14013

Doyle, D. A., Cabral, J. M., Pfuetzner, R. A., Kuo, A., Gulbis, J. M., Cohen, S. L., … & MacKinnon, R. (1998). The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science, 280(5360), 69-77. doi:10.1126/science.280.5360.69

Hite, R. K., Yuan, P., Li, Z., Hsuing, Y., Walz, T., & MacKinnon, R. (2015). Cryo-electron microscopy structure of the Slo2. 2 Na+-activated K+ channel. Nature, 527(7577), 198-203.  doi:10.1038/nature14958

MacKinnon, R. (2004). Potassium channels and the atomic basis of selective ion conduction (Nobel Lecture). Angewandte Chemie, 43(33), 4265-4277.

Recommended Readings: Ying Lu, Ph.D., February 29

Special Lecture Series
Monday, February 29
4:00 p.m., Carson Family Auditorium (CRC)

Ying Lu, Ph.D.,
Postdoctoral Fellow,
Department of Systems Biology,
Harvard Medical School

Specificity, Efficiency and Processivity in the Eukaryotic Protein Degradation System

Recommended Readings

Lu, Y., Lee, B. H., King, R. W., Finley, D., & Kirschner, M. W. (2015). Substrate degradation by the proteasome: A single-molecule kinetic analysis. Science, 348(6231), 1250834. doi: 10.1126/science.1250834.

Lu, Y., Wang, W., & Kirschner, M. W. (2015). Specificity of the anaphase-promoting complex: A single-molecule study. Science, 348(6231), 1248737. doi: 10.1126/science.1248737

Recommended Readings: Gregory Alushin, Ph.D., February 24

Special Lecture Series
Wednesday, February 24, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Gregory Alushin, Ph.D.
Early Independent Scientist,
National Heart Lung and Blood Institute

Cytoskeletal Structural Plasticity in Force Generation and Mechanosensation

Recommended Reading

Alushin, G. M., Lander, G. C., Kellogg, E. H., Zhang, R., Baker, D., & Nogales, E. (2014). High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell, 157(5), 1117-1129. doi: 10.1016/j.cell.2014.03.053.

Kim, L. Y., Thompson, P. M., Lee, H. T., Pershad, M., Campbell, S. L., & Alushin, G. M. (2015). The structural basis of actin organization by vinculin and metavinculin. Journal of Molecular Biology. doi: 10.1016/j.jmb.2015.09.031.

Zhang, R., Alushin, G. M., Brown, A., & Nogales, E. (2015). Mechanistic origin of microtubule dynamic instability and its modulation by EB proteins. Cell, 162(4), 849-859. doi: 10.1016/j.cell.2015.07.012.

Recommended Readings: Eva Nogales, Ph.D., February 20

Friday Lecture Series
Friday, February 20, 2015
3:45 p.m., Caspary Auditorium

Eva Nogales, Ph.D.
Professor of Biochemistry, Biophysics and Structural Biology,
University of California, Berkeley
Senior Faculty Scientist, Life Sciences Division,
Lawrence Berkeley National Laboratory
Investigator, Howard Hughes Medical Institute

Cryo-EM Studies of the Human Transcription Initiation Machinery

Recommended Readings

Cianfrocco, M. a, & Nogales, E. (2013). Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA. Transcription, 4(3), 1–7. doi:10.4161/trns.25291

Cianfrocco, M. A., Kassavetis, G. A., Grob, P., Fang, J., Juven-Gershon, T., Kadonaga, J. T., & Nogales, E. (2013). Human TFIID binds to core promoter DNA in a reorganized structural state. Cell, 152(1-2), 120–131. doi:10.1016/j.cell.2012.12.005

He, Y., Fang, J., Taatjes, D. J., & Nogales, E. (2013). Structural visualization of key steps in human transcription initiation. Nature, 495(7442), 481–486. doi:10.1038/nature11991

Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

Recommended Readings: Roland Beckmann, Ph.D. Monday, Nov 25

Monday, November 25, 2013
4:00 p.m., Carson Family Auditorium

Roland Beckmann, Ph.D.
Chair of Cellular Biochemistry
Gene Center Munich
Ludwig Maximilian University of Munich

Cryo-EM of ribosomal particles:
From ribosome biogenesis to protein translocation and quality control

Recommended Readings:

Empirical Articles

Anger, A. M., Armache, J.-P., Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D. N., & Beckmann, R. (2013). Structures of the human and Drosophila 80S ribosome. Nature, 497(7447), 80–85. doi:10.1038/nature12104

Armache, J.-P., Jarasch, A., Anger, A. M., Villa, E., Becker, T., Bhushan, S., … Beckmann, R. (2010). Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. Proceedings of the National Academy of Sciences of the United States of America, 107(46), 19748–19753. doi:10.1073/pnas.1009999107

Beckmann, R., Spahn, C. M., Eswar, N., Helmers, J., Penczek, P. a, Sali, a, … Blobel, G. (2001). Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell, 107(3), 361–372.

Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., & Yusupov, M. (2011). The structure of the eukaryotic ribosome at 3.0 Å resolution. Science, 334(6062), 1524–1529. doi:10.1126/science.1212642

Leidig, C., Bange, G., Kopp, J., Amlacher, S., Aravind, A., Wickles, S., … Sinning, I. (2013). Structural characterization of a eukaryotic chaperone–the ribosome-associated complex. Nature structural & molecular biology, 20(1), 23–28. doi:10.1038/nsmb.2447

Review Papers

Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., & Ban, N. (2012). Atomic structures of the eukaryotic ribosome. Trends in biochemical sciences, 37(5), 189–198. doi:10.1016/j.tibs.2012.02.007

Granneman, S., & Baserga, S. J. (2004). Ribosome biogenesis: of knobs and RNA processing. Experimental cell research, 296(1), 43–50. doi:10.1016/j.yexcr.2004.03.016

Schmeing, T. M., & Ramakrishnan, V. (2009). What recent ribosome structures have revealed about the mechanism of translation. Nature, 461(7268), 1234–1242. doi:10.1038/nature08403