Importance of Weak Protein-Protein Interactions

Weak protein-protein interactions are always assumed to be less important or more prone to artifact than strong interactions.  However, interactions are driven by both affinity and concentration.  Since the cellular concentration of proteins is much higher than what is typically studied in vitro, many interactions that could be very important pharmacologically and biologically are little studied.  The development of single molecule studies by TIRF (total internal reflectance fluorescent) microscopy allows interactions as weak as millimolar to be studied. Using these methods we plan to scan for meaningful interactions at the whole proteome level and assay pharmacological agents that would disrupt them. We have recently begun work on whole genome binding interactions using TIRF. Recent mass spec experiments of ours on the partitioning of nuclear and cytoplasmic proteins suggests that most small peptides in the cell are combined into larger complexes.   Many of these may be held weakly.

Q1. How pervasive are weak protein-protein interactions and do these serve to define new regulatory pathways?

Q2.  Can one develop high throughput small molecule screens against potentially important weak protein-protein interactions? 

Q3. Natural selection is readily seen to be a powerful means for selecting improvements but it more obscure for understanding novelty.  The earliest events in protein evolution are likely to be obscured in the production of weak binding interactions.  Can we find an experimental approach for studying binding novelty with tools for weak interaction?