S2004 Methods for characterization of biomolecular interactions – classical versus modern

Faculty of Science
Autumn 2011 - acreditation

The information about the term Autumn 2011 - acreditation is not made public

Extent and Intensity
2/0. 2 credit(s) (plus extra credits for completion). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
prof. RNDr. Michaela Wimmerová, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Michaela Wimmerová, Ph.D.
Department of Biochemistry – Chemistry Section – Faculty of Science
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
At the end of the course students should be able to: understand and explain principles of thermodynamics and kinetics of biomolecular interactions;
evaluate thermodynamics of binding
interpret binding curves
make reasoned decisions about selecting a proper method for particular applications
  • 1. Introduction Biomolecular interactions (significance, biological relevance, equilibrium, association and dissociation constants, kinetics). Types of interactions (hydrophobic, coulombic, hydrogen bonds, van der Waals forces). 2. Classical versus modern methodology Classical methods for characterization of interactions (equilibrium dialysis, frontal chromatography). Direct measurement of complex formation (change in absorbance, fluorescence intensity, fluorescence polarization). Surface plasmon resonance (theoretical background, comparison with ELISA methods). 3. Thermodynamics of protein-ligand interactions Thermodynamics of binding (Gibbs free energy, enthalpy, entropy). Macroscopic and microscopic views. The pH and temperature dependence of complex formation. Entropy-enthalpy compensation. Isothermal titration calorimetry (theoretical background, comparison with surface plasmon resonance). 4. Oligomerization and protein-protein interactions Protein stoichiometry, stereochemistry. Protein folding (hydrophobic effect, hydrophilic interactions, hydrogen bonds, electrostatic forces, water molecules). Subunit-subunit interactions (electrostatic and shape complementarity). Protein-protein recognition sites. Determination of oligomerization (cross-linking, analytical ultracentrifugation). 5. Characterization of interactions on cell level Possibility of whole cell assay within SPR and ITC. Modeling of native conditions (sensor chip versus in-solution measurement). Haemagglutination and fluorescence (theory, application). In vivo living-cell imaging. Host-pathogen interactions imaging in tissues. PRACTICAL EXERCISES 1. Surface plasmon resonance (SPR) Preparation of samples. Direct and inhibition assay. Data evaluation. Demonstration of strong points and weaknesses of SPR method. 2. Isothermal titration calorimetry (ITC) Measurement of high-affinity and low-affinity interactions. Displacement measurement. Data evaluation and analysis. Limits of ITC, possible problems. Single-injection measurement. 3. Cross-linking and analytical ultracentrifugation Cross-linking with several different agents and proteins (importance of suitable experimental set-up). Determination of quaternary structure by analytical ultracentrifugation, pH dependence of oligomerization. Data evaluation. 4. Haemagglutination and fluorescence microscopy Haemagglutination with different proteins and blood types. Inhibition of haemagglutination. Fluorescence microscopy (microscopy with labeled proteins and living cells, combination with haemagglutination). Microscopy of biofilms and living nematodes.
    recommended literature
  • Protein-protein interactions : methods and applications. Edited by Haian Fu. Totowa, N.J.: Humana Press, 2004, xvi, 532. ISBN 1588291200. info
  • Protein-ligand interactions : hydrodynamics and calorimetry : a practical approach. Edited by Stephen E. Harding - Babur Z. Chowdhry. 1st pub. Oxford: Oxford University Press, 2001, xxiv, 330. ISBN 0-19-963749-0. info
  • Protein-ligand interactions : structure and spectroscopy : a practical approach. Edited by S. E. Harding - Babur Z. Chowdhry. 1st pub. Oxford: Oxford University Press, 2001, xxvi, 436. ISBN 0199637474. info
Teaching methods
Intensive course covering lectures, class discussion, and practical exercises
Assessment methods
in-term assessment, final written test
Language of instruction
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.