CTBP Journal Club Presentations Archive:

The purpose of the Journal Club is to help junior scientists develop critical thinking skills, to broaden their exposure to modern research examining a number of differnt biological phenomena, and to provide a forum to gain research public speaking experience. Operationally, our intent is to have at least one person from each CTBP associated research laboratory give a Journal Club presentation at least once in every academic year.

The CTBP Journal Club meets on MONDAY at 1:00 pm in Urey Hall room 7130.  To subscribe to the CTBP announcement mail list, go to https://ctbp.ucsd.edu/mailman/listinfo/ctbp-announce.  Announcements and reminders for CTBP events including seminars, journal club meetings, and colloquia are sent on a weekly basis during the academic year. If you would like to volunteer to lead a discussion, please contact Nicki Pyles at npyles@ucsd.edu.

Main Journal Club Page

2003-2004 Academic Year

06/07/04 - Joanna Trylska (McCammon lab)

Paper:  "On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute-Solvent Interaction Energy", R. M. Levy, L.Y. Zhang, E. Gallicchio, and A.K. Felts, JACS, vol. 125, p. 9523-9530 (2003).

05/24/04 - Paul Whitford (CTBP)

Paper:  "Folding Core predictions from network models of proteins",   A.J. Rader and I. Bahar, Polymer, v45, 659-668 (2004).

05/17/04 - Kai Wang (Levine lab)

Paper: "Altered function and regulation of cardiac ryanodine receptors in cardiac disease", X. H. T. Wehrens and A. R. Marks, Trends in Biochemical Sciences, v 28, No. 12, 671-678 (2003).

05/10/04 - Tae Kim (CTBP)

Paper:  "The genetics of geometry", E. Coen, A. Rolland-Lagan, M. Matthews, J.A. Bangham, and P. Prusinkiewicz, PNAS, v101, 4728-4735 (2004).

05/03/04 - Jennifer Bui (McCammon lab)

Paper:  "Enhanced Configurational Sampling in Binding Free-Energy Calculations", C.J. Woods, J. W. Esssex, M A. King, J.
Phys. Chem. B, 107, 13711-13718 (2003).

04/26/04 - Aleksandra Walczak (Wolynes lab)

Paper:  "Epigenetics as a First Exit Problem", E. Aurell and K. Sneppen, PRL, 88 (4), 048101 (2002).

04/19/04 - Leslie Chavez (Onuchic lab)

Paper:  "Two-State Allosteric Behavior in a Single-Domain Signaling Protein", B.F. Volkman, D. Lipson, D.E. Weemer, and D. Kern, Science 291, 2429-2433 (2001).

04/12/04 - Garegin Papoian (Wolynes lab)

Paper:  "Biomolecular cryocrystallography: Structural changes during flash-cooling", Bertil Halle, Proc. Natl. Acad. Sci. USA, v 101, pp 4793-4798, (2004).

04/05/04 - Sachin Talathi (Abarbanel lab)

Paper:  "Bistatbility in Ca2+/Calmodlin Dependent Protein, Kinase-Phosphatase System", A. Zhabatinski, Biophys Journal, Vol 79, 2211-2221 (2000).

03/15/04 - Weiqun Peng (Hwa lab)

Paper:  "The Origins of Genome Complexity", M. Lynch and J. S. Conery, Science, Vol 302, 1401-1404, (2003).

03/08/04 - Yuhui Cheng (McCammon lab)

Paper:  "ATP synthase: two motors, two fuels", G. Oster and H. Wang, Structure, Vol 7, R67-R72, (1999).

03/01/04 - Daniel Schultz (Wolynes Lab)

Paper: "Drosophila Rhomboid-1 Defines a Family of Putative Intramembrane Serine Proteases", S. Urban,
J. R. Lee, and M. Freeman, Cell, Vol. 107, 173-182 (2001).

02/23/04 - Shachi Gosavi (Onuchic Lab)

Paper:  "Myoglobin forms amyloid fibrils by association of unforlded polypeptide segments", M. Fandrich, V. Forge, K. Buder, M. Kittler, C. Dobson, and S. Diekmann, PNAS, Vol 100, Num 26, 15463-15468, (2003).

02/09/04 - Joel Gilmore, Department of Physics, University of Queensland
Paper:  "Spin-boson models for quantum decoherence of electronic excitations of biomolecules and quantum dots in a solvent"
This paper can be found in Arxiv (cond-mat/0401444).

02/02/04 - Chenghang Zong (Wolynes lab) 

Paper:  "A motor that makes its own track: helicase unwinding of DNA", M.D. Betterton and Frank Julicher, Phys.Rev.Let., Vol 91, Num 25, 258103, (2003).

01/26/04 - Daniel Schultz (Wolynes lab)

Paper:  "Intrinsic and extrinsic contributions to stochasticity in gene expression",  Peter S. Swain, Michael B. Elowitz and Eric D. Siggia, PNAS, vol 99, no. 20, 12795-12800 (2002).

01/05/04 - David Zhang (McCammon lab)

Paper:  "Computational design of receptor and sensor proteins with novel functions", L. L. Looger, M . A. Dwyer, J .J. Smith & M . W. Hellinga, Nature, 423, 185-19 (2003).  Accompanying comment:  William F. DeGrado: Biosensor Design,
Nature, 423, 132-133.

12/01/03 - Tongye Shen (Wolynes lab)
Paper: "Topological methods for searching berriers and reaction paths", S. Tanase-Nicola and J. Kurchan, PRL, 91, 188302-1 (2003).

11/17/03 - Jessica Swanson (McCammon lab)
Paper: "A microscopic view of ion conduction through K+ channel", S. Bernèche and B. Roux, PNAS, vol. 100 no. 15, 8644-8648 (2003).

11/10/03 - Sichun Yang (Onuchic lab)
Paper: "Phase transitions in systems small enough to be clusters", D. Reguera, R.K. Bowles, Y. Djikaev, and H. Reiss, J Chem Phys, 118, 340-353 (2003).

11/03/03 - Sam Cho (Wolynes lab)
Paper: "Cooperative Organization in a Macromolecular Complex", Seelinger MA, et al., Nature Structural Biology, 10:718-724 (2003).

10/27/03 - cancelled due to UCSD closure

10/20/03 - Ruben Abagyan (The Scripps Institute of Research)
Paper:  "Molecular docking problem and computational ligand design"

10/13/03 - Mike Prentiss (Wolynes lab)
Papers: "How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations", F. Takagi, N. Koga, and S. Takada, PNAS, 100, 11367-11372 (2003). and " Effects of confinement on chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape", A. Baumketner, A. Jewett, and J.E. Shea, JMB, 332, 701-713 (2003).

10/06/03 - John Finke (Onuchic lab)
Paper: "The effect of the polyproline II (PPII) conformation on the denatured state entropy", Ferreon JC and Hilser VJ, Protein Science, 12:447-457 (2003).

09/29/03 - Florence Tama (Brooks lab)
Paper: "Elastic network normal mode analysis to explore conformational rearrangements of large macromolecular assemblies", Tama F. et al., PNAS, 100, 9319-9323 (2003).

07/07/03 - Richard Henchman (McCammon lab)
Paper: "The principle of gating charge movement in a voltage-dependent K+ channel", Y. Jiang, V. Ruta, J. Chen, A. Lee, R. MacKinnon, Nature, 423, 42-48 (2003).

06/23/03 - Joachim Lätzer (Wolynes lab)
Paper: "Determination of the structures of distinct transition state ensembles for a beta-sheet peptide with parallel folding pathways", Davis R, Dobson CM, Vendruscolo M, J. Chem. Phys., 117 (20): 9510-9517 (2002).

06/16/03 - Chenghang Zong (Wolynes lab)
Paper: "Folding at the speed limit", W. Y. Yang and M. Gruebele, Nature, Vol.423 193-197 (2003).

06/09/03 - Sam Cho (Wolynes lab).
Paper: "Dissecting the assembly of AB16-22 amyloid peptides into antiparallel beta sheets", D.K. Klimov and D. Thirumalai, Structure 11, 295-307 (2003).

06/02/03 - Mike Prentiss (Wolynes lab)
Paper: "De Nova Design of Foldable Proteins with Smooth Folding Funnel: Automated Negative Design and Experimental Verification", W. Jin, O. Kambara, H. Sasakawa, A. Tamura and S. Takada, Structure, Vol. 11, 581-590 (2003).

05/19/03 - Joe Hegler (Wolynes lab)
Paper: "Evolution of transcription factors and the gene regulatory network in Escherichia Coli", M. M. Babu and S. A. Teichmann, Nucleic Acids Research, 31(4), 1234-1244 (2003).

05/12/03 - John Finke (Onuchic lab)
Paper: "Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: Statistics", A. Kinjo and S. Takada, Phys Rev E, 66, 031911-(1-9) (2002).

05/05/03 - Cameron Mura (MacCammon lab)
Paper: "Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays", T Clark, C. Sugnet and M Ares, Jr, Science, 296, 907- 910 (2002).

04/28/03 - Iddo Friedberg (Godzik lab, The Burnham Institute)
Paper: "Small libraries of protein fragments model native protein structures accurately", R Kolodny, P Koehl, L Guibas and M Levitt, J Mol Biol, 323, 297, (2002).

04/21/03 - Daniel Schultz (Wolynes lab)
Paper: "Combinatorial Synthesis of Genetic Networks", CC Guet, MB Elowitz, W Hsing and S Leibler, Science, 296, 24, 1466 (2002).

04/15/03 - Koby Levy (Onuchic and Wolynes labs)
Paper: "Robustness of the BMP morphogen gradient in Drosophila embryonic patterning", A Eldar et al, Nature, 419, 304-308 (2002).