Biophysical Journal Club Web Page - Fall 2005 & Spring 2006

Meetings:  Room 4.238 Welch, noon, Wednesdays.

Contact:  David Hoffman, email:  dhoffman@mail.utexas.edu   

 Link to the new Biophysical J. Club web page (Fall 2006 - Spring 2007)

******************   Schedule for Fall 2005 to Spring 2006   ***********************

Sept 7, 2005 - Gisela Kramer.  "Structural basis for the function of the ribosomal L7/L12 stalk in factor binding and GTPase activation" by M. Diaconu et al., Cell 121, 991-1004, 2005.   Abstract at PubMed    Article at Cell

Sept 14, 2005 - Claire Yan Bai "Binding of the anti-tubercular drug isoniazid to the arylamine N-acetyltransferase protein from Mycobacterium smegmatis".   Abstract at PubMed   Full text at Protein Science  

Sept 21, 2005 - Hae Ryung Chang "Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS"  Abstract at PubMed, with link to full article  

Sept 28, 2005 - Matthew Lluis.  "The crystal structure of gankyrin, an oncoprotein found in complexes with
cyclin-dependent kinase 4, a 19 S proteasomal ATPase regulator, and the tumor suppressors Rb and p53."
Abstract at PubMed, with link to full article 

Oct 5, 2005 - Young-Sam Lee.  "Cytomegalovirus DNA Polymerase Subunit UL44 Forms a C Clamp-Shaped Dimer" published by Molecular Cell in 2004.  Abstract with link to article   
   
Oct 12, 2005 - Amanda Chadee. "Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism." Nat. Struct. Mol. Biol. 2005 Sep;12(9):756-62.  Link to abstract and article  

Oct 19, 2005 - Hari Bhaskaran.  "Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain"by Katherine M. Brendza, Wei Cheng, Christopher J. Fischer , Marla A. Chesnik, Anita Niedziela-Majka and Timothy M. Lohman, published in PNAS.    Link to ariticle 

Oct 26, 2005 - Youzhong Guo "Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II", Cell, 121, 1043-1057.   Link to article at Cell

Nov 2, 2005 - Shuangluo Xia. "Structural Basis for the Activation of Cholera Toxin by Human ARF6-GTP".  Claire J. O'Neal, Michael G. Jobling, Randall K. Holmes, Wim G. J. Hol, Science, 309, 1093-1096. 12 August 2005.
Link to abstract and article

Nov 9, 2005 - Yaqi Wan. "RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex.  J Mol Biol. 2005 Aug 12;351(2):371-82.   Link to article

Nov 16, 2005 - Jon Robertus.  "Evolutionary information for specifying a protein fold by Michael Socolich, Steve W. Lockless, William P. Russ, Heather Lee, Kevin H. Gardner & Rama Ranganathan".  Link to article at Nature

Nov 23, 2005 - Dexter Kennedy.  "Structures of complement component C3 provide insights into the function and
evolution of immunity", Nature, 437, 505-511 (2005).  Link to abstact and article

Jan 18, 2006 - Brian Cannon.  "Compact and ordered collapse of randomly generated RNA sequences".  Schultes, E.A., Spasic, A., Mohanty, U. & Bartel, D.P. (2005) Nature Struct. Biol., 12, 1130-1136.  Link to article

Jan 25, 2006 - Travis Johnson. "Structural basis for double stranded RNA processing by dicer".  Science, 311, 195-198 (2006). Link to article           

Feb 1, 2006 - Eric Montemayor.  "Crystal structures of Fms1 and its complex with spermine reveal substrate specificity". (2005) Q. Huang, Q. Liu & Q. Hao.  J. Mol. Biol., 348, 951-959.    Link to abstract and article

Feb 8, 2006 - open date

Feb 15, 2006 - David Hoffman. "The SAXS solution structure of RF1 differs from its crystal structure
and is similar to its ribosome bound cryo-EM structure".  (2005) Mol. Cell, 20, 929-938.  Link to abstract & article

Feb 22, 2006 - Mitra Rana.  "Human full-length Securin is a natively unfolded protein".  Nuria Sánchez-Puig, Dmitry B. Veprintsev and Alan R. Fersht, Protein Sci., 2005 Jun;14(6):1410-8.  Link to article

March 29, 2006 - Art Monzingo. "Exotoxin A−eEF2 complex structure indicates ADP ribosylation by ribosome mimicry". René Jørgensen, A. Rod Merrill, Susan P. Yates, Victor E. Marquez, Adrian L. Schwan, Thomas Boesen and Gregers R. Andersen. Nature 436, 979-984 (18 August 2005).  Link to abstract and article    

April 5, 2006 - Rick Russell.   "Three metal ions at the active site of the Tetrahymena group I ribozyme". 
Proc Natl Acad Sci USA. 1999 Oct 26;96(22):12299-304.  Link to article

and  "Structural evidence for a two-metal-ion mechanism of group I intron splicing". 
Science. 2005 Sep 2;309(5740):1587-90.  Link to article

April 12, 2006 -  Dave Graham.  "X-ray Structure of a Self-Compartmentalizing Sulfur Cycle Metalloenzyme", by Tim Urich, Cláudio M. Gomes, Arnulf Kletzin, and Carlos Frazão.  Science 17 February 2006: Vol. 311 no. 5763, pp. 996-1000.
     Link to article   

April 19, 2006 - Greg Sawyer.  "Structural Basis for Vertebrate Filamin Dimerization"by Regina Pudas, Tiila-Riikka Kiema, P. Jonathan G. Butler, Murray Stewart and Jari Ylaenne. Structure, Vol. 13, 111-119, January 2005.  Link

and,  "The Molecular Basis of Filamin Binding to Integrins and Competition with Talin" by Tiila Kiema, Yatish Lad, Pengju Jiang, Camilla L. Oxley, Massimiliano Baldassarre, Kate L. Wegener, Iain D. Campbell, Jari Ylaenne and David A. Calderwood.  Molecular Cell 21, 337-347, February 3, 2006.  Link

April 26, 2006 - Christian Antonio.  "In-cell NMR spectroscopy".  ChemBioChem (2005) 6, 1601-1606.
                             Link to article     

May 3, 2006 - Seema Namboori. "A model of anthrax toxin lethal factor bound to protective antigen". Proc Natl
Acad Sci U S A. 2005 Nov 8;102(45):16409-14.  Link to article 

May 10, 2006 - Angeline Lyon.  "Using NMR to investigate the binding of small ligands by proteins."

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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.