Immunoprecipitation for the Analysis of Macromolecular Complexes in Trypanosoma cruzi

Immunoprecipitation is a helpful tool to assess interactions between proteins and proteins or nucleic acids (DNA or RNA). Its principle consists in capturing and enriching one or multiple target proteins from a complex sample with a specific antibody conjugated to a solid matrix and isolating the RNA and/or protein molecules associated to those target(s) group of proteins that can be further identified by advanced techniques such as RNA-seq and/or mass spectrometry. Since this technique allows for identifying, mapping, and checking new protein-protein and protein-RNA interactions, its use is very convenient in situations where many proteins remain with their functions uncharacterized, as is the case of the protozoan Trypanosoma cruzi. Here we describe a protocol that is based on the cryogrinding method for cell lysis and the use of antibodies conjugated to magnetic beads to capture and purify protein complexes in a robust and efficient way.