Biophysical Journal Club Web Page - Fall 2007 - Spring 2008

Meetings:  Room 4.238 Welch, Wednesdays, at noon.

Course number: CH 190, "Structural biology seminar", unique number: 56000
Contact:  David Hoffman, email:  dhoffman@mail.utexas.edu 

Link to last year's J. Club web page  

<>****************   Schedule for  Spring 2008   *******************

Jan 30, 2008 - Eric Montemayor. “Photolyases and Cryptochromes: Different jobs for a common light sensor.”

Feb 6, 2008 - Young-Sam Lee. "Structural determination of human mitochondrial DNA polymerase".

Feb 13, 2008 -  Jessica Momb.  "Structure and function of gamma-glutamyl transpeptidase from Helidobacter pylori".
                            The talk will be based in 3 related papers from Joe Barycki's group at the Univ. of Nebraska:

          Boanca, G. Sand, A. Barycki, J. (2006)  J. Biol. Chem. 281 (28) 19029-19036  Link
          Boanca, G. et al. (2007)  J. Biol. Chem. 282 (1) 534-541  Link
          Morrow, A. et al. (2007) Biochemistry 46 (46) 13407-13414.  Link

Feb 20, 2008 -  Yan Bai. ""Discovery of small molecule inhibitors of ubiquitin-like poxvirus
                          proteinase I7l using homology modeling and covalent docking approaches".
                          J Comput Aided Mol Des (2007) 21:549–558.  Link

Mar 5, 2008 -  Matthew Lluis. "Crystal Structure of an Ancient Protein: Evolution by
                         Conformational Epistasis". Eric A. Ortlund et al.  Science 317, 1544 (2007)

Mar 19, 2008 -  Shuangluo Xia.  "Surflex-Dock 2.1: Robust performance from ligand energetic modeling,
                          ring flexibility, and knowledge-based search." Journal of Computer-Aided Molecular Design,
                          Volume 21, Number 5, Page: 281-306, 2007
                          link: http://www.springerlink.com/content/0104l1x8116230x3/

April 2, 2008 -  Yaqi Wan. "tRNA–mRNA mimicry drives translation initiation from a viral IRES"
                          David A Costantino, Jennifer S Pfingsten, Robert P Rambo & Jeffrey S Kieft.
                          Nature Structural & Molecular Biology 15, 57 - 64, Jan 2008.
                          link:   Link to article.

April 16, 2008 -  Art Monzingo. "High-resolution structure prediction and the crystallographic phase problem
                           Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J. McCoy, Randy J.
                           Read & David Baker.  Nature 450, 259-264 (8 November 2007)
                           link:  Link to article 


****************   Schedule for Fall 2007 - Spring 2008   *******************


 Sept 19, 2007 -  David Hoffman.  "Changes in atmospheric CO2, evolution, photosynthesis
                           and the fate of life on earth".  I chose this topic after reading a book by
                           Donald Brownlee and Peter Ward called  The Life and Death of Planet Earth.
                           Although the book is perhaps a bit oversimplified, I found it thought provoking.
                           So I'll summarize my thoughts about it, and try to include some biochemistry.

Sept 26, 2007 -  open date

Oct 3, 2007 -    David Graham. “Evolutionary Links as Revealed by the Structure of Thermotoga
                         maritima S-Adenosylmethionine Decarboxylase” by A.V. Toms et al. (2004)
                         J. Biol. Chem. 279:33837.  doi:10.1074/jbc.M403369200   link to article 
 
Oct 10, 2007 -  Angeline Lyon.  "The structural basis of yeast prion strain variants."
                         Toyama, B.H. et al Nature (2007) 449, 233-238.   link to article 
                         Also, there will be a quick review of what’s currently known about prions.

Oct 17, 2007 -  Mitra Rana.  "A molecular mechanism for osmolyte-induced protein stability"
                         Timothy O. Street, D. Wayne Bolen, and George D. Rose
                         PNAS 2006, September 19;103(38):13997-14002.
                         Link to article

Oct 24, 2007 -  Xiaoyan Yuan. "Tumour invasion and metastasis initiated by microRNA-10b
                          in breast cancer".   Link to article: 
                          http://www.nature.com/nature/journal/v449/n7163/full/nature06174.html

Oct 31, 2007 -   open date

Nov 7, 2007 -  Brian Cannon. "Structure and mechanism of a metal-sensing regulatory RNA."
                         by Charles E. Dann III, Catherine A. Wakeman, Cecelia L. Sieling,
                          Stephanie C. Baker, Irnov Irnov, and Wade C. Winkler.
                          Cell. 2007 Sep 7;130(5):878-92.    Link to article

Nov 14, 2007 -  Rick Russell.  "Direct Measurement of a pK(a) near Neutrality for the Catalytic
                          Cytosine in the Genomic HDV Ribozyme Using Raman Crystallography."
                          J Am Chem Soc. 2007 Oct 31;129(43):13335-13342.  Link to article

Nov 21, 2007 -  Tom Linsky.  Ligand-enzyme computational docking.
                           "A critical assessment of docking programs and scoring functions."
                           Warren GL, Andrews CW, Capelli AM, et al.   J Med Chem. 2006 Oct 5;49(20):5912-31.
                            Link to article

Nov 28, 2007 -  Amanda Chadee.  "Structural determinants of RNA recognition and cleavage by Dicer"
                           by Ian MacRae, Kaihong Zhou Jennifer Doudna,
                           Nature Structural and Molecular Biology, Vol 14, No 10, October 2007 pg 934-940.
                           Link to article
 
Dec 5, 2007 -  Hae Hae Chang.  "The carboxy-terminal coiled-coil of the RNA polymerase beta
                         subunit is the main binding site for Gre factors".
                         Vassylyeva et al.  EMBO Rep. 2007 Nov;8(11):1038-43. Epub 2007 Oct 5.
                         link to article 


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Suggestions for Journal Club presentations:

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 (Natalie Potts on the 5th floor in Robertus' and Hackert's office has a key, as do some of the nearby labs).  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!