Structural Biology Journal Club

Meetings: Wednesdays at noon in NHB 4.202

Generally, there is a 30-45 minute presentation on a recent journal paper (or papers) or on the presenter’s own research. The emphasis is on structural work but non-structural topics in biochemistry and molecular biology are also welcome. Meetings are open to all who are interested.

  • April 5 – Jennifer Stamos – The vestigial tail of the spliceosome: the strange connection between Next-Gen RNA-seq and the evolution of eukaryotes
  • CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. T.H. Nguyen, W.P. Galej, S.M. Fica, P.C. Lin, A.J. Newman, K. Nagai. Curr. Opin. Struct. Biol. 36, 48-57 (2016).
  • April 12 – Pat Byrne – Structure of the full-length VEGFR-1 extracellular domain in complex with VEGF-A. S. Markovic-Mueller, E. Stuttfeld, M. Asthana, T. Weinert, S. Bliven, K.N. Goldie, K. Kisko, G. Capitani, K. Ballmer-Hofer. Structure 25, 341-352 (2017).
  • April 19 – Jessica Meinke – The structure of the pleiotropic transcription regulator CodY provides insight into its GTP-sensing mechanism. A.R. Han, H.R. Kang, J. Son, D.H. Kwon, S. Kim, W.C. Lee, H.K. Song, M.J. Song, K.Y. Hwang. Nucleic Acids Res. 44, 9483-9493 (2016).
  • April 26 – Tara Shea – Mechanistic basis for the recognition of a misfolded protein by the molecular chaperone Hsp90. J. Oroz, J.H. Kim, B.J. Chang, M. Zweckstetter. Nat. Struct. Mol. Biol. 24, 407–413 (2017).
  • May 3 – John Cheong – Capture of a third Mg²⁺ is essential for catalyzing DNA synthesis. Y. Gao, W. Yang. Science 352, 1334-1337 (2016).
  • May 10 – Professor Pinglong Xu – Hippo-sized nucleic acid sensing and antiviral defenses
  • Hippo signalling governs cytosolic nucleic acid sensing through YAP/TAZ-mediated TBK1 blockade. Q. Zhang, F. Meng, S. Chen, S.W.Plouffe, S. Wu, S. Liu, X. Li, R. Zhou, J. Wang, B. Zhao, J. Liu, J. Qin, J. Zou, X.H. Feng, K.L. Guan, P. Xu. Nat. Cell Biol. 19, 362-374 (2017).
  • September 30 – Marvin Hackert – X-ray Crystallography – basics to benefits
  • October 7 – Connie Bailey – A trans-acyltransferase ketoreductase reveals structural features and sequence signatures of split bimodules
  • October 14 – Sarah Wong – Structure and functional studies of the PRC1.1 complex
  • Structure of the Polycomb Group protein PCGF1 (NSPC1) in complex with BCOR reveals basis for binding selectivity of PCGF homologs. S.E. Junco, R. Wang, J.C. Gaipa, A.B. Taylor, V. Schirf, M.D. Gearhart, V..J. Bardwell, B. Demeler, P.J. Hart, C.A. Kim. Structure 21, 665-671 (2013).
  • October 21 – Jake LeVieux – Structure and function of hydratase-aldolase enzymes in bacterial polycyclic aromatic hydrocarbon degradation
  • October 28 – Amanda Hughes – Structure and function of the Escherichia coli Tol-Pal stator protein TolR. J.A. Wojdyla, E. Cutts, R. Kaminska, G. Papadakos, J.T.S. Hopper, P.J. Stansfeld, D. Staunton, C.V. Robinson. C. Kleanthous. J. Biol. Chem. epub (2015).
  • November 4 – Jia Zeng – Architecture of vertical interactions in trans-AT polyketide synthases
  • November 11 – Myong Koag – The replication of DNA lesions by human DNA polymerase β
  • November 18 – Seema Irani – Solving the crystal structure of a novel C-S lyase
  • December 2 – Drew Wagner – Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å. Y. Umena, K. Kawakami, J.-R. Shen, N. Kamiya. Nature 473, 55–60 (2011).
  • October 2 – Kevin Entzminger – Computational design of ligand-binding proteins with high affinity and selectivity. C.E. Tinberg, S.D. Khare, J. Dou, L. Doyle, J.W. Nelson, A Schena, W. Jankowski, C.G. Kalodimos, K. Johnsson, B.L. Stoddard, D. Baker. Nature 501, 212-216 (2013).
  • October 9 – Brent Halling – Calcium dependent stoichiometries of the SK intracellular domain/complex in solution.
  • October 16 – Drew Wagner – Crystallographic interrogation of bacillaene ketosynthase 6.
  • October 23 – Myong Koag – Structural basis for slow preferential misincorporation of dTTP opposite O6-methylguanine by human DNA polymerase ß.
  • October 30 – Marvin Hackert – IYCr2014 – Celebrating 100 years of X-ray crystallography.
  • November 6 – Wupeng Yan – Structure determination of the non-heme binding alpha-ketoglutarate-dependent dioxygenase FtmOX1 and cystathionine gamma-lyase.
  • November 13 – Chris Fage – BktB: The tale of a twinned thiolase.
  • November 20 – Lilian Lamech – Mitochondrial TyrRS: Evolving a function beyond translation.
  • December 4 – Yi Kou – Initial study of N7mG lesion with DNA polymerase beta.

  1. Create an introduction that provides a broad perspective for the specific work being presented. For example, if you are presenting a paper on a new reverse transcriptase (RT) structure, you should provide some background on RTs in general. Don’t assume that everyone in your audience knows the background. Provide historical perspective, such as when was the first RT discovered? When was the first structure of a member of the RT family solved? Why do we care about RT? This will provide a context for introducing what is special about the paper you are presenting. Also, explain enough about the work that came immediately before your paper (often from the same research group) so that your audience understands the starting point for the paper you are presenting.
  2. Explain why you chose the paper you did. What do you find most interesting about it? Why is it important? Also, why is the topic interesting and important?
  3. Instead of simply describing the methods used, look at the methods critically, with an eye for anything interesting or unusual. Point out anything that might be generally useful. For example, did the authors use any unusual purification or expression tricks? The people in your audience, many of whom are struggling with purification and expression, may find this helpful.
  4. What is the most significant contribution of the specific work to the field in general?
  5. As much as possible, make your own cartoons and schematic diagrams – don’t copy these from the paper. When you make your own figure, you can be sure that it makes exactly the points you want, no more and no less.
  6. Do the results suggest any additional experiments to answer any new questions raised by the work? Hint for 2nd year grad students: These presentations can be a good source of ideas for qualifying exam topics.
  7. Clearly explain the significance of the results. Results by themselves are dull, unless they have significance. The significance may not be obvious to the audience, so point it out specifically. Also, try to think critically about the author’s work. For example, are there any possible alternative interpretations of the results?
  8. Try to appear truly interested (even excited!) about the work you are presenting. Enthusiasm is contagious, and keeps your audience interested. Can you think of anything to make your presentation unique? An unusual prop or visual aid? Make your presentation “professional”. That means, stand up in front, look directly at your audience, and don’t “read” your slides.
  9. Arrive at the conference room early. Make sure you can get into the room. Make sure you can make the projector work, and make sure you have everything you need for your presentation, such as a pointer.
  10. Practice your talk!