Recommended Readings: Maria Barna Ph.D. Friday December 9, 2016

Friday Lectures

Friday, December 9, 2016   3:45 p.m.

Caspary Auditorium

Maria Barna, Ph.D.

Assistant Professor,

Departments of Developmental Biology and Genetics at Stanford University

Specialized Ribosomes:

A New Frontier in Gene Regulation, Organismal Biology, & Evolution

Recommended Readings:

Xue, Shifeng; Barna, Maria.   Specialized ribosomes: a new frontier in gene regulation and organismal biology.  NATURE REVIEWS MOLECULAR CELL BIOLOGY    13( 6):355-369     JUN 2012

Amunts, Alexey; Brown, Alan; Bai, Xiao-chen; et al.  Structure of the Yeast Mitochondrial Large Ribosomal Subunit.  SCIENCE   343(6178):1485-1489      MAR 28 2014

Xue, Shifeng; Tian, Siqi; Fujii, Kotaro; et al.  RNA regulons in Hox 5 ‘ UTRs confer ribosome specificity to gene regulation. NATURE   517(7532):33-U55   JAN 1 2015

Wu, XQ; Iyengar, P; RajBhandary, UL.   Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes. EMBO JOURNAL    15(17):4734-4739  SEP 2 1996

Shi, Zhen; Barna, Maria   Trransiating the Genome in Time and Space: Specialized Ribosomes, RNA. Regulons, and RNA-Binding Proteins. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 31   Book Series: Annual Review of Cell and Developmental Biology   V. 31: 31-+    2015

Yadav, Anupama; Radhakrishnan, Aparna; Panda, Anshuman; et al. The Modular Adaptive Ribosome.   PLOS ONE   11(11): Article Number: e0166021    NOV 3 2016


Recommended Readings: Tarun Kapoor, Ph.D., April 18

Monday Lecture Series
Monday, April 18, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Tarun Kapoor, Ph.D.
Pels Family Professor and Head,
Selma and Lawrence Ruben Laboratory of Chemistry and Cell Biology,
The Rockefeller University

New Chemical Probes for Ribosome Biogenesis and Cytoskeleton Organization

Recommended Readings

Kasap, C., Elemento, O., & Kapoor, T. M. (2014). DrugTargetSeqR: a genomics-and CRISPR-Cas9–based method to analyze drug targets. Nature Chemical Biology, 10(8), 626-628. doi: 10.1038/nchembio.1551

See, S. K., Hoogendoorn, S., Chung, A. H., Ye, F., Steinman, J. B., Sakata-Kato, T., … & Chen, J. K. (2015). Cytoplasmic dynein antagonists with improved potency and isoform selectivity. ACS Chemical Biology, 11(1), 53-60. doi:10.1021/acschembio.5b00895

Shimamoto, Y., Forth, S., & Kapoor, T. M. (2015). Measuring pushing and braking forces generated by ensembles of kinesin-5 crosslinking two microtubules. Developmental Cell, 34(6), 669-681. doi:10.1016/j.devcel.2015.08.017

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

Structural Biology Lecture Series: Venki Ramakrishnan Ph.D. Wed Sept 28 2011

Structural Biology Lecture Series

The Structural Basis of Decoding by the Ribosome

Dr. Venki Ramakrishnan

2009 Nobelist

Medical Research Council Laboratory of Molecular Biology

Wednesday September 28, 11 am, Caspary Hall

Recommended Readings:

Voorhees RM; Schmeing TM; Kelley AC; Ramakrishnan V. 2010. The mechanism for activation of GTP hydrolysis on the ribosome. Science 330:835-838.

Schmeing TM; Voorhees RM; Kelley AC; et al.  2009. The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.  Science  326(5953):688-694.

Gao Y-G; Selmer M; Dunham CM; Weixlbaumer A; Kelley AC; Ramakrishnan V. 2009. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326:694-699.

Weixlbaumer A; Hong J; Neubauer C; Voorhees RM; Sabine P; Kelley AC; Ramakrishnan V. 2008. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322:953-956.

Selmer M; Duham CM; Murphy FV; Weixlbaumer A; Sabine P; Kelley AC; Weir JR; Ramakrishnan V. 2006. Science 313:1935-1942.

Petry S; Brodeson DE; Murphy FV; et al.  2005.  Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.  Cell  123(7):1255-1266.

Ogle, JM; Murphy FV; Tarry MJ; et al.  2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form.  Cell  111(5):721-732.

Wimberly BT; Brodeson DE; Clemons WM; et al.  Structure of the ribosomal subunit. 2000. NATURE   407(6802): 327-339.

Carter AP; Clemons WM; Broderson DE; et al.  2000.  Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics.  NATURE  407(6802):340-348.

Observing the Formation of Ribosomes

Identifying and observing the molecules that form ribosomes — the cellular factories that build the proteins essential for life — has been a key goal for biologists that had seemed nearly unattainable. But a new Scripps Research study, appearing in the October 29, 2010 issue of Science, yielded pictures of the chemical intermediate steps in ribosome creation.  The Scripps lead team developed a new technique, dubbed discovery single-particle profiling, which dodges a previously frustrating purification problem by allowing successful imaging of unpurified samples.