Analysis of protein-protein interactions by simulation of small-zone gel filtration chromatography.

Small-zone gel filtration chromatography, combined with analytical-scale columns and fast run times, provides a useful system for the study of protein-protein interactions. A computer simulation (SCIMMS, or Simulated Chromatography of Interactive MacroMolecular Systems) that replicates the small-zone behavior of interacting proteins has been developed. The simulation involves an iterative sequence of transport, equilibration, and diffusion steps. This chapter illustrates the use of the simulation to study the homodimerization of rapidly equilibrating immunoglobulin light chain proteins and for determination of association constants. The simulation can also be used to study heterogeneous interactions, kinetically controlled interactions, and higher-order oligomerization, and it can replicate large-zone and Hummel-Dreyer conditions.