Hello,
In the literature, I have generally noticed that protein protein interactions can be classified as either obligate, or transient. Obligate meaning two proteins, or most likely chains, join together quickly after translation and stay that way until degradation, or transient, where two distinct proteins interact for a brief period of time. Is the time scale of interactions continuous, with interactions on a range from obligate to transient, or is it a bimodal distribution?
I ask this because I am trying to get good numbers on the enrichment of certain amino acid types in PPI sites in transient sites only, and have noticed different values for obligate vs. transient.
Adam.
The majority of what is commonly called 'protein-protein interaction' is somewhere in between what you define as 'obligate' or transient'. The protein partners are in an equilibrium which is characterized by an 'on-rate' and an 'off-rate', which can be measured separately, e.g. by SPR experiments. The time a given protein spends in an interaction is governed by the two rates and can be nearly 'permanent' (if the off-rate is very low) or very transient (if the off-rate is much higher than the on-rate. There is clearly a continuum between the possibilities.
What is usually stored in protein-interaction databases (and is detected e.g. by two-hybrid screens or co-IP experiments) are protein pairs that remain bound for an extended time period, otherwise they would not be detected. If you are looking for very transient interactions, they are typically found between enzymes and their substrates (kinases, proteases, etc). They are not seen in the usual interaction screens but can be detected through their permanent effect (protein B being permanently cleaved or phosphorylated by protein A, although the interaction between the two was very transient).
Occasionally, enzyme-substrate pairs can be found in interaction databases, e.g. if the enzyme has an additional substrate-binding domain that works independently of the catalytic action.
Very nice answer by Lyco (+1). I would add that because of the mention of kinases and proteases in that response, enzyme inhibitors often bind with very different time parameters than do substrates. An inhibitor is likely to remain bound for a (much) longer time period than a substrate. Also, the time duration for which the protein-protein interaction occurs can change according to other parameters - some as mundane as salt concentration or more relevant such as a cofactor (eg, heme group or ATP).
yes it does, thank you for your thorough response.