**4. Examples**

In the previous sections of this chapter, I briefly introduced the forces governing macromolecular associations and characterised methods commonly used to assess these contributions. Here, I will illustrate on several examples of 'real' ligand-protein systems and the way how their binding thermodynamics is studied.

### **4.1 Hydrophobic versus hydrophilic binding pocket: MUP and HBP**

Both histamine-binding protein (HBP) and mouse major urinary protein (MUP) are members of lipocalin family of proteins, so their overall structures are similar (Figure 4). The binding pocket of HBP contains a number of polar and charged residues, hence it is an example of a 'hydrophilic' binder. In contrast to HBP, the binding pocket of MUP is very 'hydrophobic'. Surprisingly, both HBP and MUP are characterised by similar overall entropy of ligand binding.

In our recent study (Syme *et al*., 2010) we compared the driving forces for binding between these two proteins in terms of entropic contributions from ligand, protein, and solvent. We performed an extensive study combining x-ray crystallography, NMR spectroscopy, ITC, MD simulations, and QM calculations.
