ABSTRACT
Living organisms generate their complex repertoire of proteins by the stepwise assembly of small chemical entities (amino acids). After a folding process and/or further enzymatic transformations these complicated molecules attain their final three-dimensional structures, which determine their biological activities through the specific interactions with their ligands. An infinite variety of different molecular structures can be realized by varying the length of the chains and the sequence of the building units. Specific protein-protein interactions are used by all living organisms for a large variety of functions, including regulation, building of super molecular structures, the immune response, cell recognition and more. Those who study protein-protein interactions hope to resolve the high resolution structure of the complex, and indeed, more and more of these are being solved. However, whether or not this goal is reached, biophysical data must be collected in order to gain insight into the affinity, kinetics and thermodynamics of the interaction. Methods for measuring rate constants and affinities of interaction can be grouped according to those which measure the interaction of proteins in solution in homogeneous phase and those where the interaction of a protein in solution is monitored through binding to a second, surface-bound protein (heterogeneous phase measurements). Probing the interaction in solution involves techniques such as optical spectroscopy, measurements of activity (or inhibition), analytical ultracentrifugation, isothermal titration calorimetry and equilibrium dialysis. Heterogeneous phase measurements are done using ELISA assays or a variety of transducer based techniques, which are the focus of this book. Homogeneous and heterogeneous phase measurements mimic protein interactions found in nature. For example the interaction between proteases and their protein inhibitors occur between two proteins in homogeneous phase, while the interaction between a ligand and its receptor is in the heterogeneous phase.
