Question

Under what conditions you use ITC or fluorescence anisotropy (aka polarization) to study protein/protein interactions and how you develop a strategy to investigate the structure, dynamics, and function of protein with mixed regions of order and disorder.

Answer 1

Answer:

ITC or Isothermal titration calorimetry is used to directly measure the thermodynamic parameters during a binding event as a result of interaction of a ligand-protein or protein-protein. It is used for biophysical characterisation of protein-protein interaction when prior information of such existence of interaction is already detected by other experimental methods. The complete thermodynamic profile of the interaction (binding affinity, stoichiometry, enthalpy, entropy, free energy) can be known directly through a single ITC experiment. It is also possible to elucidate the binding mechanism of the interaction in most of such cases.

On the other hand, the measurement of binding constants and kinetics of protein-protein interactions can be estimated through fluorescence anisotropy. However, the measured binding affinity is indirect and not as accurate as from ITC. However, the dynamics of the interaction under different conditions can be fairly estimated from this technique. Either intrinsic or extrinsic fluorescence is used to determine the tumbling rate or molecular orientation of the protein molecules in space. The result of binding event will decrease the motion or tumbling rate and leads to more retention of polarisation. Thereby, it results in an increase in measurement of fluorescence anisotropy.

The structure of the protein at high resolution can be accurately determined by X-ray Crystallography. However, this method cannot be used to know dynamics and other methods like NMR, SAXS (Small angle X-ray scattering) etc can be used to investigate the dynamics of the protein. However, the structure-function relationship is accurately known through mutational analysis and the elucidation of structure and function with the above mentioned methods. It is also important to complement the information from low resolution biophysical techniques to study equilibrium-denaturation and renaturation studies to understand the dynamics of the protein.

Thank you.