Bringing proteomics into the lab: Proteomics Lab 101

Abstract

With the increasing importance and visibility of proteomics there is a notable lack of teaching tools that can be used for "hands on" proteomic experience. Here we describe a simple lab for teaching proteomics that is based on the two-hybrid system. Using only simple modifications of a commercial system, an experiment set is described that takes the student from the identification of potential protein:protein interactors from a large set of proteins through the classification of the disruption of these interactions in response to the presence of a neurotoxin, in this case lead. The lab uses a prokaryotic two-hybrid system and two human neuronal cDNA libraries as the pool from which the initial interactors are drawn. The prokaryotic system provides increased transformation efficiencies, which translate into better cDNA library representation. The lab concludes with the identification of protein:protein interactions that are affected by increasing amounts of neurotoxin and the sequencing of the cDNA-encoded genes. Students not only gain hands on proteomic experience but also then relate their sequence to an entry in one of the burgeoning sequence databases to glean information about the identified molecular target. The experiment set is flexible and could be adapted for use with any compound that affects protein complex formation. © 2003 by The International Union of Biochemistry and Molecular Biology.