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Studying Bioinformatics in Saarbrücken
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Seminar:
Theoretical Analysis of
Protein-Protein Interactions

Summer Semester 2004


Lecturer: Prof. Dr. Volkhard Helms

Tutors: Dr. Alexander Spaar, Saurabh Kumar Shakya

Requirements: Knowledge according to lectures "Bioinformatics II" and "Computational Chemistry".

Time: The seminar starts on Thursday, June 3, 4.00pm in building 45, room 0.14. The last meeting is on Thursday, July 8. Each meeting will have two presentations.

Preliminary discussion and placement of the topics: Wednesday, April 21, 4.00 pm, building 45, room 016.

Condition for certification: Successful presentation, regular participation.

Leistungspunkte: 8

The course language is English.

Contents:

Overview: http://www.imb-jena.de/jcb/ppi/
                 http://itgmv1.fzk.de/www/itg/uetz/publications/Uetz2003-PPI.pdf

Possible topics are:

  1.      Statistics and Overview: Types of Interactions, Properties and Proteins/Contact Surfaces
            Vortrag Melanie Zimmer
  1. Glaser, F., Steinberg, D.M., Vakser, A., and Ben-Tal, N., (2001) Proteins, 43, 89-102. Residue Frequencies and Pairing Preferences at Protein-Protein Interfaces.
  2. Jones, S. and Thornton, J.M., (1996) PNAS, 93, 13-20. Principles of Protein-Protein Interactions.
  3. Jones, S., Marin, A., and Thornton, J.M., (2000) Protein Engineering,13, 77-82. Protein Domain Interfaces: Characterization and Comparison with Oligomeric Protein Interfaces,
  4. Ofran,Y. and Rost, B., (2003) J. Mol. Biol., 325, 377-387. Analysing Six Types of Protein-Protein Interfaces.
  1. Experimental Methods for Protein-Protein Interactions
    Vortrag Stefan Nickels
  1. Phizicky, E.M. and Fields, S., (1995) Microbiol. Rev., 59, 94-123. Protein-Protein Interactions: Methods for Detection and Analysis.
  2. Kenworthy, A.K., (2001) Methods, 24, 289-296. Imaging Protein-Protein Interactions Using Fluorescence Resonance Energy Transfer Microscopy.
  3. Rajagopal, P., Waygood, E.B., Reizer, J., Saier-Jr., M.H., and Klevit, R.E., (1997) Protein Science, 6, 2624-2627. Demonstration of Protein-Protein Interaction Specificity by NMR Chemical Shift Mapping.
  4. Kohlbacher, O., Burchardt, A., Moll, A., Hildebrandt, A., Bayer, P., and Lenhof, H.-P., (2001) J. Biol. NMR, 20, 15-21. Structure Prediction of Protein Complexes by a NMR-based Protein Docking Algorithm.
  1. Scoring Functions
    Vortrag Silke Ruzek
  1. Moont, G., Gabb, H.A., and Sternberg, M.J.E., (1999) Proteins, 35, 364-373. Use of Pair Potentials Across Protein Interfaces in Sreening Predicted Docked Complexes.
  2. Zhang, C., Vasmatzis, G., Cornette, J.L., and DeLisi, C., (1997) J. Mol. Biol., 267, 707-726. Determination of Atomic Desolvation Energies from the Structures of Crystallized Proteins.
  3. Murphy, J., Gatchell, D.W., Prasad, J.C., and Vajda, S., (2003) Proteins, 53, 840-854. Combination of Scoring Functions Improves Discrimination in Protein-Protein Docking.
  1. Docking Methods
    Vortrag Andreas Schlicker
  1. Althaus, E., Kohlbacher, O., Lenhof, H.-P., and Muller, P., (2002) J. Comput. Biol., 9, 597-612. A Combinatorial Approach to Protein Docking with Flexible Side-Chains.
  2. Katchalski-Katzir, E., Shariv, I., et al., (1992) PNAS, 89, 2195-2199. Molecular Surface Recognition: Determination of Geometric Fit between Proteins and their Ligands by Correlation Techniques.
  3. Desmet, J., De Maeyer, M., Hazes, B., and Lasters, I., (1992) Nature, 356, 539-542. DEE Theorem and its Use in Protein Side Chain Positioning.
  1. Virtual Screening: Predicting Pairs from Sequence
    Vortrag Anna Hobler
  1. Ofran, Y. and Rost, B., (2003) FEBS Let, 544, 236-239. Predicted Protein-Protein Interaction Sites from Local Sequence Information.
  2. Yan, C., Honavar, V., and Dobbs, D., (2002) . Predicting Protein-Protein Interaction Sites from Amino Acid Sequence.
  3. Zhou, H.X. and Shan, Y.B., (2001) Proteins, 44, 336-343. Prediction of Protein Interaction Sites from Sequence Profile and Residue Neighbor List.
  1. Homology Modelling of Protein Complexes
    Vortrag Daniela Reimer
  1. Aloy, P. and Russell R.B., (2002) PNAS, 99, 5896-5901. Interrogating Protein Interaction Networks through Structural Biology.
  2. Weng, Z., Vajda, S., and Delisi, C., (1996) Protein Science, 5, 614-626. Prediction of Protein Complexes Using Empirical Free Energy Functions.
  3. Jackson, R.M., (1999) Protein Science, 8, 603-613. Comparison of Protein-Protein Interactions in Serine Protease-Inhibitor and Antibody-Antigen Complexes: Implications for the Protein Docking Problem.
  1. Genetic Algorithm and Ligand Design
    Vortrag Andrea Volkamer
  1. Budin, N., Majeux, N., Tenette-Souhaille, C., and Caflish, A.,, (2001) J. Comp. Chem., 22, 1956-1970. Structure-Based Ligand Design by a Build-Up Approach and Genetic Algorithm Search in Conformational Space.
  2. Park, H.S., Lin, Q., and Hamilton, A.D., (1999) PNAS, 99, 5105-5109. Modulation of Protein-Protein Interactions by Synthetic Receptors: Design of Molecules that Disrupt Serine Protease-Proteinaceous Inhibitor Interaction.
  3. Prebys, E.K., (1999) MIT Undergraduate Journal of Mathematics, 165-170. The Genetic Algorithm in Computer Science.
  1. Theory of Association & Brownian Dynamics - Algorithms
    Vortrag Christian Dammer
  1. Huber, G.A. and Kim, S., (1996) Biophys. J., 70, 97-110. Weighted-Ensemble Brownian Dynamics Simulations for Protein Association Reactions.
  2. Ermak, D.L. and McCammon, J.A., (1978), J. Chem. Phys., 69, 1352-1360. Brownian Dynamics with Hydrodynamic Interactions.
  3. Gabdoulline, R.R. and Wade, R.C., (1998), Methods, 14, 329-341. Brownian Dynamics Simulation of Protein-Protein Diffusional Encounter.
  4. Gabdoulline, R.R. and Wade, R.C., (1999), J. Mol. Recogn., 12, 226-234. On the Protein-Protein Diffusional Encounter Complex.
  1. Steered Molecular Dynamics, Jarzynski Equation
  1. Jarzynski, C., (1997) Phys. Rev. E, 56, 5018-5035. Equilibrium Free-Energy Differences from Nonequilibrium Measurements: A Master-Equation Approach.
  2. Park, S. and Schulten, K., (2004), J. Chem. Phys., 120, 5946-5961. Calculating Potentials of Mean Force from Steered Molecular Dynamics Simulations.
  3. Izrailev, S., Stepaniants, S., Isralewitz, B., Kosztin, D., Lu, H., Molnar, F., Wriggers, W., and Schulten, K., (1998) Computational Molecular Dynamics: Challenges, Methods, Ideas, Vol. 4 of Lecture Notes in Computational Science and Engineering, p. 39-65, Springer Verlag; Berlin: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A., Skeel, D., and Reich, S., editors. Steered Molecular Dynamics.
  1. Association in Crowded Environment Excluded Volume Effects, Polymer Physis
    Vortrag Ina Meiser
  1. Rivas, G., Ferrone, F., and Herzfeld, J., (2004) EMBO Reports, 5, 23-27. Life in an Crowded World: Workshop on the Biological Implications of Macromolecular Crowding.
  2. Hall, D. and Minton, A.P., (2003), Biochim. Biophys. Acta, 1649, 127-139. Macromolecular Crowding: Qualitative and Semi-Quantitative Successes, Quantitative Challenges.
  3. Elcock, A.H., (2003) Pro. Natl. Acad. Sci. USA, 100, 2340-2344. Atomic-Level Observation of Macromolecular Crowding Effects: Escape of a Protein from the GroEL Cage.
  1. Lipid-Mediated Interactions between Membrane Proteins
    Vortrag Julia Weiß
  1. Bohinc, K., Kralj-Iglic, V., and May, S., (2003) J. Chem. Phys., 119, 7435-7444. Interaction between two Cylindrical Inclusions in a Symmetric Lipid Bilayer.
  2. May, S. and Ben-Shaul, A., (2000), PCCP, 2, 4494-4502. A Molecular Model for Lipid-Mediated Interaction between Proteins in Membranes.
  3. Lagüe, P., Zuckermann, M.J., and Roux, B., (2000) Biophys. J., 79, 2867-2879. Lipid-Mediated Interactions between Intrinsic Membrane Proteins: A Theoretical Study Based on Integral Equations.
  4. Sintes, T. and Baumgärtner, A., (1997) Biophys. J., 73, 2251-2259. Protein Attraction in Membranes Induced by Lipid Fluctuations.
  1. Proteins in Membranes: Demixing Phenomena
    Vortrag Daniel Andres
  1. May, S., Harries, D., and Ben-Shaul, A., (2000) Biophys. J., 79, 1747-1760. Lipid Demixing and Protein-Protein Interactions in the Adsorption of Charged Proteins on Mixed Membranes.
  2. Borodich, A., Rojdestvenski, I., and Cottam, M., (2003), Biophys. J., 85, 774-789. Lateral Heterogeneity of Photosystems in Thylakoid Membranes Studied by Brownian Dynamics Simulations.
  1. Hydrophobic Mismatch between Proteins and Lipids in Membranes
    Vortrag Susanne Pfeifer
  1. Killian, J.A., (1998) Biochimica et Biophysica Acta (BBA) - Reviews on Biomembranes, 1376, 401-415. Hydrophobic Mismatch between Proteins and Lipids in Membranes.
  2. Fattal, D.R, and Ben-Shaul, A., (1993), Biophys. J., 65, 1795-1809. A Molecular Model for Lipid-Protein Interaction in Membranes: The Role of Hydrophobic Mismatch.
  3. Nielsen, C., Goulian, M., and Andersen, O.S., (1998), Biophys. J., 74, 1966-1983. Energetics of Inclusion-Induced Bilayer Deformations.
  1. Electron Transfer in Proteins
    Vortrag Markus Krier
  1. Moser, C., Keske, J.M., Warncke, K., Farid, R.S., and Dutton, P.L., (1992) Nature, 355, 796-802. Nature of Biological Electron Transfer.
  2. Farid, R.S., Moser, C.C., and Dutton, P.L., (1993),Curr. Opin. Struct. Biol., 3, 225-233. Electron Transfer in Proteins.
  3. Balabin, I.A. and Onuchic, J.N., (2000), Science, 290, 114-117. Dynamically Controlled Protein Tunneling Paths in Photosynthetic Reaction Centers.
  4. Kobayashi, C., Baldridge, K., and Onuchic, J.N., (2003), J. Chem. Phys., 119, 3550-3558. Multiple versus Single Pathways in Electron Transfer in Proteins: Influence of Protein Dynamics and Hydrogen Bonds.
  1. Signal Transduction Cascades
  1. Heinrich, R., Neel, B.G., and Rapoport, T.A., (2002) Mol. Cell, 9, 957-970. Mathematical Models of Protein Kinase Signal Transduction.
  2. Huang, C.-Y.F. and Ferrell, J.E.Jr., (1996), PNAS, 93, 10078-10083. Ultrasensitivity in the Mitogen-Activated Protein Kinase Cascade.
  1. Protein-Protein Binding Interfaces
    Vortrag Lennart Heinzerling
  1. Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R., (2003) PNAS, 100, 5772-5777. Protein-Protein Interactions: Structurally Conserved Residues Distinguish between Binding Sites and Exposed Protein Surfaces.
  2. Pazos, F., Helmer-Citterich, M., Ausiello, G., and Valencia, A., (1997), J. Mol. Biol., 271, 511-523. Correlated Mutations Contain Information about Protein-Protein Interaction.
  3. Glaser, F., Steinberg, D.M., Vakser, I.A., and Ben-Tal, N., (2001), Proteins, 43, 89-102. Residue Frequencies and Pairing References at Protein-Protein Interfaces.
  4. Pazos, F. and Valencia, A., (2002), Proteins, 47, 219-227. In Silico Two-Hybrid System for the Selection of Physically Interacting Protein Pairs.
  1. Protein-Protein Interaction Networks
    Vortrag Gautam Chaurasia
  1. Pereira-Leal, J.B., Enright, A.J., and Ouzounis, C.A., (2004) Proteins, 54, 49-57. Detection of Functional Modules from Protein Interaction Networks.
  2. Thomas, A., Cannings, R., Monk, N.A.M., and Cannings, C., (2003) Biochem. Soc. Trans., 271, 511-523. On the Structure of Protein-Protein Interaction Networks.
  3. Wagner, A., (2001), Mol. Biol. Evol., 18, 1283-1292. The Yeast Protein Interaction Network Evolves Rapidly and Contains Few Redundant Duplicate Genes.
  1. The Second Virial Coefficient: A Measure for Protein-Protein Interactions
  1. Elcock, A.H. and McCammon, J.A., (2001) Biophys. J., 80, 613-625 . Calculation of Weak Protein-Protein Interactions: The pH Dependence of the Second Virial Coefficient.
  2. Bloustine, J., Berejnov, V., and Fraden, S., (2003) Biophys. J., 85, 2619-2623. Measurements of Protein-Protein Interactions by Size Exclusion Chromatography.
  3. Neal, B.L., Asthagiri, D., and Lenhoff, A.M., (1998), Biophys. J., 75, 2469-2477. Molecular Origins of Osmotic Second Virial Coefficients of Proteins.