Ruprecht Karls Universität Heidelberg
Hauptseminar Sommersemester 2009: Theory of molecular and cellular biophysics

Hauptseminar Sommersemester 2009:
Theory of molecular and cellular biophysics

Ulrich Schwarz and Wolfgang Wenzel

This seminar takes place in the summer term 2009 every Thursday from 2.00 - 3.30 pm in seminar room 10/1 in the physics building. Each talk should last approximately for 45 min and is followed by a discussion. Each speaker can choose to present in German or English. The seminar started with an introduction on April 23 2009.

  1. Go-models for protein folding (Alexander Biewer, 7.5., supervision Wenzel, pdf)

    • Shakhnovich, E., Farztdinov, G., Gutin, A.M., and Karplus, M. (1991). Protein Folding Bottlenecks: A Lattice Monte Carlo Simulation. Phys. Rev. Lett. 67, 1665-1668.
    • Dill, K.A., and Chan, H.S. (1997). From Levinthal to Pathways to Funnels: The "New View" of Protein Folding Kinetics. Nature structural biology 4, 10-19.
    • Schug, A., Whitford, P.C., Levy, Y., and Onuchic, J.N. (2007). Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proceedings of the National Academy of Sciences 104, 17674-17679.

  2. Stochastic transport and reactions (Fridtjof Kowald, 14.5., supervision Schwarz, pdf)

    • J.S. van Zon and P.R. ten Wolde. Greens-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space. The Journal of Chemical Physics, 123:234910, 2005.
    • J. Elf and M. Ehrenberg. Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. Systems Biology, IEE, 1(2):230-236, 2004.
    • D. Fange and J. Elf. Noise-induced min phenotypes in E. coli. PLoS Comput Biol, 2(6):e80, 2006.

  3. NMR for protein structure / global downhill folding (Valentin Bolsinger, 28.5., supervision Wenzel, pdf)

    • Kubelka J, Hofrichter J, Eaton WA. (2004). The protein folding 'speed limit'. Curr Opin Struct Biol 14:76-88.
    • Sadqi, M., Fushman, D., and Munoz, V. (2006). Atom-by-atom analysis of global downhill protein folding. Nature 442, 317-321.
    • Ferguson, N., Sharpe, T.D., Johnson, C.M., Schartau, P.J., and Fersht, A.R. (2007). Structural Biology: Analysis of 'downhill' protein folding. Nature 445, E14-E15.
    • Religa, T. L., Markson, J. S., Mayor, U., Freund, S. M. V. and Fersht, A. R. Nature 437, 10532261056 (2005).

  4. Physics of receptor-ligand binding (David Gruia, 4.6., supervision Schwarz, pdf)

    • H. C. Berg and E. M. Purcell. Physics of chemoreception. Biophys. J., 20:193-219, 1977.
    • E. M. Purcell. Life at low Reynolds number. Am. J. Phys., 45:3-11, 1977.
    • D. Shoup and A. Szabo. Role of diffusion in ligand binding to macromolecules and cell-bound receptors. Biophys. J., 40:33-39, 1982.

  5. Virus assembly (Alex Kunz, 18.6., supervision Schwarz, pdf)

    • B. Berger, PW Shor, L. Tucker-Kellogg, and J. King. Local Rule-Based Theory of Virus Shell Assembly. 91(16):7732-7736, 1994.
    • DC Rapaport. Self-assembly of polyhedral shells: A molecular dynamics study. 70(5):51905, 2004.
    • M.F. Hagan and D. Chandler. Dynamic Pathways for Viral Capsid Assembly. 91(1):42, 2006.

  6. Force spectroscopy on single molecules (Frank Bandenburg, 25.6., supervision Schwarz, pdf)

    • E. Evans and K. Ritchie. Dynamic strength of molecular adhesion bonds. Biophys. J., 72:1541-1555, 1997.
    • R. Merkel, P. Nassoy, A. Leung, K. Ritchie, and E. Evans. Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy. Nature, 397:50-53, 1999.
    • M. Raible, M. Evstigneev, F.W. Bartels, R. Eckel, M. Nguyen-Duong, R. Merkel, R. Ros, D. Anselmetti, and R. Reimann. Theoretical analysis of single-molecule force spectroscopy experiments: heterogeneity of chemical bonds. Biophys. J., 90:3851-3864, 2006.

  7. Beta-Amyloid Fibrils (Maffre Pauline, 2.7., supervision Wenzel, pdf)

    • Urbanc, B., Cruz, L., Yun, S., Buldyrev, S.V., Bitan, G., Teplow, D.B., and Stanley, H.E. (2004). In silico study of amyloid beta-protein folding and oligomerization. Proceedings of the National Academy of Sciences of the United States of America 101, 17345-17350.
    • Vendruscolo, M., and Dobson, C.M. (2007). Chemical biology: More charges against aggregation. Nature 449, 555.

  8. Cellular force generation by motor ensembles (Jerome Soine, 9.7., supervision Schwarz, pdf)

    • T. A. J. Duke. Molecular model of muscle contraction. PNAS, 96:2770-2775, 1999.
    • F. Jülicher and J. Prost. Spontaneous oscillations of collective molecular motors. Phys. Rev. Lett., 78:4510-4513, 1997.
    • S. Klumpp and R. Lipowsky. Cooperative cargo transport by several molecular motors. Proc Natl Acad Sci U S A. 2005 Nov 29;102(48):17284-9.

  9. Protein Structure Prediction (Jens Mohrmann, 16.7., supervision Wenzel)

    • Baker, D., and Sali, A. (2001). Protein Structure Prediction and Structural Genomics. Science 294, 93-96.
    • Kryshtafovych, A., Venclovas, C., Fidelis, K., and Moult, J. (2005). Progress over the first decade of CASP experiments. Proteins: Structure, Function and Bioinformatics,.
    • Bradley, P., Misura, K.M.S., and Baker, D. (2005). Toward High-Resolution de-novo Structure Prediction for small proteins. Science 309, 1868-1871.

  10. Biophysics of hearing (Orkide Ordu, 23.7., supervision Schwarz)

    • VM Eguíluz, M. Ospeck, Y. Choe, AJ Hudspeth, and MO Magnasco. Essential Nonlinearities in Hearing. Physical Review Letters, 84(22):5232-5235, 2000.
    • S. Camalet, T. Duke, F. Julicher, and J. Prost. Auditory sensitivity provided by self-tuned critical oscillations of hair cells. Proceedings of the National Academy of Sciences, 97(7):3183, 2000.

    • P Martin, AJ Hudspeth, and F Julicher. Comparison of a hair bundle's spontaneous oscillations with its response to mechanical stimulation reveals the underlying active process. PNAS, 98(25):14380-14385, DEC 4 2001.

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