Ruprecht Karls Universität Heidelberg

Seminar Single Molecule Biophysics

This seminar addresses master students from physics and biology who are interested in biophysical experiments and theory for single molecules. Bachelor students are also welcome but should already have some experience with biophysics. For physics masters students, this seminar can be taken as MVSem with 6 CPs if one gives a presentation during the seminar and hands in a written text afterwards. The seminar takes place every Monday from 2.15-3.45 pm in seminar room 1.403 at KIP. Typically two students will present on one or two landmark papers from the literature, complemented by additional information from other papers, reviews or books. At the first meeting on April 18 2016, the subjects of the different talks will be explained and distributed. Shaped by the expertise of the two organizers, we will have two main foci in this seminar: single molecule fluorescence (Edward Lemke, EMBL) and mechanics (Ulrich Schwarz, Heidelberg University). Click here for the schedule.

List of subjects and papers

  1. Using microfluidics to monitor protein folding
    • Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Gambin Y, VanDelinder V, Ferreon AC, Lemke EA, Groisman A, Deniz AA. Nat Methods. 2011 Mar;8(3):239-41. doi: 10.1038/nmeth.1568. Epub 2011 Feb 6.
    • Single-molecule measurement of protein folding kinetics. Lipman EA, Schuler B, Bakajin O, Eaton WA. Science. 2003 Aug 29;301(5637):1233-5.
  2. Orientation problem in single molecule FRET
    • Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. Iqbal A, Arslan S, Okumus B, Wilson TJ, Giraud G, Norman DG, Ha T, Lilley DM. Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11176-81. doi: 10.1073/pnas.0801707105. Epub 2008 Aug 1.
  3. Barrier crossing in protein folding
    • Single-molecule fluorescence experiments determine protein folding transition path times. Chung HS, McHale K, Louis JM, Eaton WA. Science. 2012 Feb 24;335(6071):981-4. doi: 10.1126/science.1215768.
    • Single-molecule fluorescence probes dynamics of barrier crossing. Chung HS, Eaton WA. Nature. 2013 Oct 31;502(7473):685-8. doi: 10.1038/nature12649. Epub 2013 Oct 23. PMID: 24153185 [PubMed - indexed for MEDLINE]
  4. Distribution analysis for FRET of disordered systems
    • Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Schuler B, Lipman EA, Eaton WA. Nature. 2002 Oct 17;419(6908):743-7.
    • Single-macromolecule fluorescence resonance energy transfer and free-energy profiles By: Gopich, IV; Szabo, A JOURNAL OF PHYSICAL CHEMISTRY B Volume: 107 Issue: 21 Pages: 5058-5063
  5. Orbital tracking analysis for molecular transport
    • Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9863-8. doi: 10.1073/pnas.1200486109. Epub 2012 Jun 4. Capturing directed molecular motion in the nuclear pore complex of live cells. Cardarelli F, Lanzano L, Gratton E.
    • Biophys J. 2009 Jul 22;97(2):665-73. doi: 10.1016/j.bpj.2009.04.048. Imaging barriers to diffusion by pair correlation functions. Digman MA, Gratton E.
  6. Single molecule force spectroscopy of adhesion bonds
    • Evans, E., & Ritchie, K. (1997). Dynamic strength of molecular adhesion bonds. Biophysical journal, 72(4), 1541-1555.
    • Merkel, R., Nassoy, P., Leung, A., Ritchie, K., & Evans, E. (1999). Energy landscapes of receptor–ligand bonds explored with dynamic force spectroscopy. Nature, 397(6714), 50-53.
  7. Single molecule force spectroscopy of polymeric biomolecules
    • Rief, M., Oesterhelt, F., Heymann, B., & Gaub, H. E. (1997). Single molecule force spectroscopy on polysaccharides by atomic force microscopy. Science, 275(5304), 1295-1297.
    • Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J. M., & Gaub, H. E. (1997). Reversible unfolding of individual titin immunoglobulin domains by AFM. science, 276(5315), 1109-1112.
    • Braun, O., & Seifert, U. (2005). Force spectroscopy of single multidomain biopolymers: A master equation approach. The European Physical Journal E: Soft Matter and Biological Physics, 18(1), 1-13.
  8. Single molecule force spectroscopy and fluctuation theorems
    • Liphardt, J., Dumont, S., Smith, S. B., Tinoco, I., & Bustamante, C. (2002). Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science, 296(5574), 1832-1835.
    • Gore, J., Ritort, F., & Bustamante, C. (2003). Bias and error in estimates of equilibrium free-energy differences from nonequilibrium measurements. Proceedings of the National Academy of Sciences, 100(22), 12564-12569.
  9. DNA-translocation into viruses and the nucleus
    • Smith, D. E., Tans, S. J., Smith, S. B., Grimes, S., Anderson, D. L., & Bustamante, C. (2001). The bacteriophage &phis; 29 portal motor can package DNA against a large internal force. Nature, 413(6857), 748-752.
    • Salman, H., Zbaida, D., Rabin, Y., Chatenay, D., & Elbaum, M. (2001). Kinetics and mechanism of DNA uptake into the cell nucleus. Proceedings of the National Academy of Sciences, 98(13), 7247-7252.
  10. Rotation of F1-ATPase observed step by step
    • Yasuda, R., Noji, H., Kinosita, K., & Yoshida, M. (1998). F 1-ATPase is a highly efficient molecular motor that rotates with discrete 120 steps. Cell, 93(7), 1117-1124.
    • Sowa, Y., Rowe, A. D., Leake, M. C., Yakushi, T., Homma, M., Ishijima, A., & Berry, R. M. (2005). Direct observation of steps in rotation of the bacterial flagellar motor. Nature, 437(7060), 916-919.
  11. Powerstroke of single myosin II motors
    • Finer, J. T., Simmons, R. M., & Spudich, J. A. (1994). Single myosin molecule mechanics: piconewton forces and nanometre steps. Nature, 368(6467), 113-119.
    • Veigel, C., Molloy, J. E., Schmitz, S., & Kendrick-Jones, J. (2003). Load-dependent kinetics of force production by smooth muscle myosin measured with optical tweezers. Nature Cell Biology, 5(11), 980-986.
  12. STED
    • Hell, S. W., & Wichmann, J. (1994). Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy. Optics letters, 19(11), 780-782.
    • Klar, T. A., Jakobs, S., Dyba, M., Egner, A., & Hell, S. W. (2000). Fluorescence microscopy with diffraction resolution barrier broken by stimulated emission. Proceedings of the National Academy of Sciences, 97(15), 8206-8210.
  13. PALM
    • Betzig, E., Patterson, G. H., Sougrat, R., Lindwasser, O. W., Olenych, S., Bonifacino, J. S., ... & Hess, H. F. (2006). Imaging intracellular fluorescent proteins at nanometer resolution. Science, 313(5793), 1642-1645.
    • Hess, S. T., Girirajan, T. P., & Mason, M. D. (2006). Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. Biophysical journal, 91(11), 4258-4272.
  14. STORM
    • Rust, M. J., Bates, M., & Zhuang, X. (2006). Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature methods, 3(10), 793-796.
    • Bates, M., Blosser, T. R., & Zhuang, X. (2005). Short-range spectroscopic ruler based on a single-molecule optical switch. Physical Review Letters, 94(10), 108101.
  15. SIM / Bessel beam / lattice light sheet
    • Planchon, Thomas A., et al. "Rapid three-dimensional isotropic imaging of living cells using Bessel beam plane illumination." Nature methods 8.5 (2011): 417-423.
    • Legant, Wesley R., et al. "High-density three-dimensional localization microscopy across large volumes." Nature methods (2016).
  16. Fluroescent stress sensors
    • Grashoff, Carsten, et al. "Measuring mechanical tension across vinculin reveals regulation of focal adhesion dynamics." Nature 466.7303 (2010): 263-266.
    • Austen, Katharina, et al. "Extracellular rigidity sensing by talin isoform-specific mechanical linkages." Nature cell biology 17.12 (2015): 1597-1606.
    • Stabley, Daniel R., et al. "Visualizing mechanical tension across membrane receptors with a fluorescent sensor." Nature methods 9.1 (2012): 64-67.
    • Zhang, Yun, et al. "DNA-based digital tension probes reveal integrin forces during early cell adhesion." Nature communications 5 (2014).
    • Liu, Yang, et al. "Nanoparticle tension probes patterned at the nanoscale: impact of integrin clustering on force transmission." Nano letters 14.10 (2014): 5539-5546.
  17. Reviews
    • Deniz, A. A., Mukhopadhyay, S., & Lemke, E. A. (2008). Single-molecule biophysics: at the interface of biology, physics and chemistry. Journal of the Royal Society Interface, 5(18), 15-45.
    • Puchner, Elias M., and Hermann E. Gaub. "Single-molecule mechanoenzymatics." Annual review of biophysics 41 (2012): 497-518.
    • Roy, R., Hohng, S., & Ha, T. (2008). A practical guide to single-molecule FRET. Nature methods, 5(6), 507-516.
    • Mehta, A. D., Rief, M., Spudich, J. A., Smith, D. A., & Simmons, R. M. (1999). Single-molecule biomechanics with optical methods. Science, 283(5408), 1689-1695.
    • Ritort, F. (2006). Single-molecule experiments in biological physics: methods and applications. Journal of Physics: Condensed Matter, 18(32), R531.
    • Veigel, C., & Schmidt, C. F. (2011). Moving into the cell: single-molecule studies of molecular motors in complex environments. Nature Reviews Molecular Cell Biology, 12(3), 163-176.
    • Lippincott-Schwartz, Jennifer. "Profile of Eric Betzig, Stefan Hell, and WE Moerner, 2014 Nobel Laureates in Chemistry." Proceedings of the National Academy of Sciences 112.9 (2015): 2630-2632.
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