Modulation of Protein-Protein Interactions
|Summer Semester 2005|
Requirements: understanding of protein structure and energetics
Start: Monday, April 18, 9:00 am - 11:00 am, building 45, room 0.16.
Preliminary discussion and placement of the topics: Monday, March 7,
3.00 pm, building 17.1, room 1.08.
Condition for certification: successful presentation, regular (≥ 75 %) participation.
new study regulations: 5 (proseminar) or 8 (seminar)
old study regulations: 9 (proseminar and seminar)
Possible topics are:
Topic 1 Talk by Yannick Djoumbou
Kinetics of protein-protein associations, in vivo - in vitro, mutations, ionic strength
Topic 2 Talk by Alexander Baldauf
Topic 3 Talk by Thomas Binsl
Topic 4 Talk by Mathieu Papdo
- Rivas, G., Ferrone, F., and Herzfeld, J. (2004) EMBO reports, 5, 23-27. Life in a crowded world.
- Kozer, N. and Schreiber, G. (2003) Journal of Molecular Biology, 336, 763-774. Effect of crowding on protein–protein association rates: Fundamental differences between low and high mass crowding agents.
Topic 5 Talk by Sarah Blaß
- Lipschultz, C.A., Yee, A., Mohan, S., Li, Y., and Smith-Gill, S.J. (2002) Journal of Molecular Recognition, 15, 44-52. Temperature differentially affects encounter and docking thermodynamics of antibody-antigen association.
Topic 6 Talk by Enrico Glaab
- Winn, P.J., Religa, T.L., Battey, J.N.D., Banerjee, A., and Wade, R.C. (2004) Structure, 12, 1563-1574. Determinants of functionality in the ubiquitin conjugating enzyme family.
- Aloy, P., Ceulemans, H., Stark, A., and Russell, R.B. (2003) Journal of Molecular Biology, 332, 989-998. The relationship between sequence and interaction divergence in proteins.
Topic 7 Talk by Christine Jäckels
- Ghirlanda, G., Lear, J.D., Lombardi, A., and DeGrado, W.F. (1998) Journal of Molecular Biology., 281, 379-391. From synthetic coiled coils to functional proteins: automated design of a receptor for the calmodulin-binding domain of calcineurin.
- ROC1: Desjarlais, J.R. and Handel, T.M. (1995) Protein Science, 4, 2006-2018. De novo design of the hydrophobic cores of proteins.
Topic 8 Talk by Sandra Fischer
Topic 9 Talk by Susanne Pfeifer
- Shifman, J.M. and Mayo, S.L. (2002) Journal of Molecular Biology, 323, 417-423. Modulating calmodulin binding specificity through computational protein design.
- Dahiyat, B.I., Sarisky, C.A., and Mayo, S.L. (1997) Journal of Molecular Biology, 1997, 789-796. De Novo protein design: towards fully automated sequence selection.
- Dahiyat, B.I., Mayo, S.L. (1997) Science, Vol. 278, 82-87. De novo protein design: fully automated sequence selection.
Topic 10 Talk by Mareike Moritz
- Liang, S., Liu, Z., Li, W., Ni, L., and Lai, L. (2000) Biopolymers, 54, 515-5237. Construction of protein binding sites in scaffold structures .
- Clark, D.E., Willett, P., and Kenny, P.W. (1987) Journal of Molecular Graphics, 5, 49-56. Pharmacophoric pattern matching in files of three-dimensional chemical structures: use of bounded distance matrices for the representation and searching of conformationally flexible molecules.
Topic 11 Talk by Christine Hedderich
- Verkhivker, G.M., Bouzida, D., Gehlhaar, D.K., Rejto, P.A., Freer, S.T., and Rose, P.W. (2003) Proteins, 53, 201-219. Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.
- Verkhivker, G.M., Rejto, P.A., Gehlhaar, D.K., and Freer,S.T. (1996) Proteins, 25, 342-353. Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes.
Topic 12 Talk by Oliver Müller
- Reina, J., Lacroix, E., et al. (2002) Nature of Structural Biology, 9, 621-627. Computer-aided design of a PDZ domain to recognize new target sequences.
- PERLA: López de la Paz, M., Lacroix, E., Ramirez-Alvarado, M., and Serrano, L. (2001) Journal of Molecular Biology, 312, 229-246. Computer-aided design of beta-sheet peptides.
Topic 13 Talk by Bettina Schneider
- Kortemme, T., Joachimiak, L.A., et al. (2004) Nature of Structural and Molecular Biology, 11, 371-379. Computational redesign of protein-protein interaction specificity.
- Kortemme, T., and Baker, D. (2004) Current Opinion in Chemical Biology, 8, 91-97. Computational design of protein–protein interactions.