Biophysical
Journal Club Web Page - Fall 2006 - Spring 2007
Meetings: Room 4.238 Welch,
Wednesdays, at noon.
Course number: CH 190, "Structural biology
seminar", unique number: 55810
Contact: David Hoffman,
email: dhoffman@mail.utexas.edu
Link to last
year's J. Club web page
****************** Schedule for
Fall 2006 - Spring 2007 **********************
Sept 13,
2006 - Marv Hackert. "Hemoglobin - New
chapters in an old classic". References:
"Lumbricus erythrocrurin at 3.5 A resolution: Architecture of a
megadalton respiratory complex". W.E. Royer, H. Sharma, K. Strand, J.E.
Knapp & B. Bhyravbhatla. Structure,
14, 1167-1177 (2006). Link
to abstract. Link
to full text. Also, Hackert & Riggs, "When size matters". Structure, 14, 1094-1096. Link.
Sept
20, 2006 - Shuangluo
Xia. "Molecular basis for the inhibition of human NMPRTase, a
novel target for
anticancer agents". Nature
Structural & Molecular Biology, 13, 582 - 588
(2006) Link
to full text
Sept
27, 2006 - Mitra Rana. "Analytical ultracentrifugation and
characterization of macromolecules"
This talk will be designed to be of use to those who wish to use the
method in the future (or maybe have not considered it because of
inadequate information). Centrifugation techniques have been
undergoing a bloom in recent years, with new instrumentation and
software becoming available. The capability of the analytical ultra-centrifugation (if done right) has vastly increased.
The talk will briefly cover instrumentation/optical systems,
experimental design, data analysis using various methods, and software
available freely on the internet. Both equilibrium and velocity
techniques will be discussed.
Oct
4, 2006 - Whitney Yin. "Ammonia Channel Couples
Glutaminase with Transamidase Reactions in GatCAB", Science 30 June
2006, vol. 312, pp. 1954-1958. Link
to paper.
Oct
11, 2006 - Travis Johnson. "Structure of the exon
junction core complex with a trapped DEAD-box ATPase bound to RNA." by
Andersen et al. (2006) Science, 313, 1968-72. Epub 2006 Aug
24. Link
to article.
Oct
18, 2006 - open
date
Oct 25, 2006 - Seema Namboori. "The structure of
H5N1 avian influenza neuraminidase suggests new opportunities
for drug design." Nature. 2006 Sep 7;443(7107):45-9. Link
to full text
Nov
1, 2006 - open
date
Nov
8, 2006 - Bryan Kaehr. "Molecular Sorting by
Electrical Steering of Microtubules in Kinesin-Coated Channels". Link to
article.
Nov
15, 2006 - Rick Russell.
"Psi analysis: A new method for probing the structures of folding
transition states and identifying multiple pathways?"
Results and analysis will be presented from the two papers below.
Sosnick TR, Dothager RS, Krantz BA.
Differences in the folding transition state of ubiquitin indicated by
phi and psi analyses.
Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17377-82. Link
to Pubmed
Krantz BA, Dothager RS, Sosnick TR.
Discerning the structure and energy of multiple transition states in
protein folding using psi-analysis.
J Mol Biol. 2004 Mar 19;337(2):463-75. Link
to Pubmed
Nov
22, 2006 - Brian Cannon. "Sequence-Resolved Detection of
Pausing by Single RNA Polymerase Molecules.
Cell, Volume 125, Issue 6, Pages 1083-1094. K. Herbert, A. La
Porta, B. Wong, R. Mooney, K. Neuman, R. Landick, S. Block. Link
to article.
Nov
29, 2006 - visit from Qiagen representative Ruth Crowe.
Refreshments provided.
The two part seminar will focus on two main components:
-Pros and cons of in vivo and in vitro expression. Novel
technologies that are easier to use and provide higher yield.
-Innovations in crystallography that allow you to do crystallography in
4 steps! Also new screens and kits that simplify your screening
strategies.
Dec 6, 2006 - Hae Ryung Chang. "The antibiotic kasugamycin mimics mRNA
nucleotides to destabilize tRNA binding and inhibit canonical
translation initiation." Nat
Struct Mol Biol. 2006 Oct;13(10):871-8. Epub 2006 Sep 24.
Link
to article
Jan
24, 2007 - Gisela Kramer. "Real time observation of
trigger factor function on translating ribosomes." C.M. Kaiser, H.C.
Chang, V.R. Agashe, S.K. Lakshmipathy, S.A. Etchells, M.Hayer-Hart,
F.U. Hartl & J.M. Barral. Nature, 444, 455-460 (2006). Link
to article.
Jan
31, 2007 - David Hoffman. "A scientists nightmare: Software
problem leads to five retractions". Science, 314, 22 December
2006. Link
to article. See also:
"Structure of MsbA from E. coli: A Homolog of the Multidrug
Resistance ATP Binding Cassette (ABC) Transporters". Geoffrey Chang,
Christopher B. Roth, Science, 293, 1793. Link
to article.
Feb
7, 2007 - Hari Bhaskaran. "Structure of the 70S ribosome
complexed with mRNA and tRNA". M. Selmer, C.M. Dunham, F.V.
Murphy, A. Weixlbaumer, S. Petry, A.C. Kelley, J.R. Weir, V.
Ramakrishnan, Science, 313, 1935-1942. Link
to article.
And here is a link to a recent
revew of ribosome structure results.
Feb 14, 2007 - Angeline Lyon.
“The chromatin-remodeling enzyme ACF is an ATP-dependent DNA length
sensor that regulates nucleosome spacing." Yang, J.G. et al Nat.
Struct. Mol. Biol. 2006, 13(12) 1078-1047. Link
to abstract. Link
to article.
Feb
21, 2007 - Eric
Montemayor. "Structure of Dual Function Iron Regulatory Protein 1
Complexed with Ferritin IRE-RNA".
W.E. Walden, A.I. Selezneva, J. Dupuy, A. Volbeda, J.C.
Fontecilla-Camps, E.C. Theil, K. Volz.
Science, December 2006, Vol. 314, pp. 1903-1908. Link
to article.
Feb
28, 2007 - Amanda Chadee. "Structure of an RNAi polymerase
links RNA silencing and Transcription".
P.S. Salgado, M.R.L. Koivunen, E.V. Makeyev, D.H. Bamford, D.I.
Stuart1, J.M. Grimes.
PLOS Biology, Dec. 2006, vol. 4, e434. Link
to article.
March 7, 2007 - Matthew Lluis. "RNA ligase
structures reveal the basis for RNA specificity and conformational
changes that drive ligation forward". Cell 127, 71-84,
2006. Link
to article.
March 14, 2007 - spring break
March
28, 2007 -
Xiaoyan Yuan."The structural basis of ribozyme-catalyzed RNA assembly".
Science, 315, 1549-1553. March 2007. By Michael Robertson
and William Scott.
Link
to article. (note: Michael Robertson was a post-doc in
Andy Ellington's lab before going
to Scott's lab).
April
4, 2007 - David Graham. "A Novel Two-domain Architecture Within the
Amino Acid Kinase Enzyme Family
Revealed by the Crystal Structure of Escherichia coli Glutamate
5-kinase."
Marco-Marin C, Gil-Ortiz F, Perez-Arellano I, Cervera J, Fita I, Rubio
V.
J Mol Biol. 2007 367(5):1431-144 Link to article
April
11, 2007 - Art
Monzingo. "Structural definition of a conserved neutralization
epitope on HIV-1 gp120."
Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY,
Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel
GJ, Kwong PD. Nature. 2007 Feb 15;445(7129):732-7.
link
to article
April
18, 2007 - open date
April
25, 2007 - Young-sam Lee. "Crystal structure of the catalytic
alpha subunit of E. coli replicative DNA
polymerase III." Lamers MH, Georgescu RE, Lee SG, O'Donnell M, Kuriyan
J. Cell. 2006 Sep 8;126(5):881-92.
Link
to article.
May 2, 2007 - Yaqi Wan.
Using single molecule approach to dissect the
assembly steps of telomerase. Link
to article.
*****************************************************
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!