Ubiquitinylation of proteins is quite diverse, and can be based on the addition of only one moiety or a a chain of ubiquitin peptides. E3 ligases do both things, anyway their function is conferring the specificity of the reaction by selecting the substrate (that is why they are so many!). In most cases the addition of a polyubiquitin moiety via the E3 ligase will target the protein to the proteasome for rapid degradation. It seems like this is your case. The interaction between the ligase and its substrate is probably transient and quick, so a way to increase its life-time can be to block the following process, degradation. This is what you do by inhibiting the proteasome with the MG132.

In other cases where monoubiquitylation is used for different reasons (nuclear export, membrane trafficking, etc) there will be no need to use the drug. Still, the interaction might be too quick to be caught by co-IP. If you have a way to increase the ubiquitynilation of your substrate, so to have many molecules undergoing the process at a same time, a CLIP (cross-linking IP) might help.

MG132 targets proteasom but not E3 ligase，why can it stabilize iteraction between E3 uand substrate?

Pietro is exactly right.  The MG132 will inhibit the proteasome.  Because your ligase's substrate is no longer being degraded, you will be able to see a stable interaction between your ligase and its substrate.  

Agree with the above answers. Depending on the stability of the protein interaction and the relative abundance of the proteins, co-immunoprecipitated proteins can be hard to detect, so MG132 is sometimes used to increase the abundance of the protein of interest.

Good luck