Abstract
Cellular functions are mostly defined by the dynamic interactions of proteins within macromolecular networks. Deciphering the composition of macromolecular complexes and their dynamic rearrangements is the key to getting a comprehensive picture of cellular behavior and to understanding biological systems. In the last decade, affinity purification coupled to mass spectrometry has emerged as a powerful tool to comprehensively study interaction networks and their assemblies. However, the study of these interactomes has been hampered by severe methodological limitations. In particular, the affinity purification of intact complexes from cell lysates suffers from protein and RNA degradation, loss of transient interactors, and poor overall yields. In this chapter, we describe a rapid single-step affinity purification method for the efficient isolation of dynamic macromolecular complexes. The technique employs cell lysis by cryo-milling, which ensures nondegraded starting material in the submicron range, and magnetic beads, which allow for dense antibody-conjugation and thus rapid complex isolation, while avoiding loss of transient interactions. The method is epitope tag-independent, and overcomes many of the previous limitations to produce large interactomes with almost no contamination. The protocol described here has been optimized for the yeast S. cerevisiae.
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Acknowledgments
We thank members of the Oeffinger lab for useful conversations and comments. We also thank Ms. Karen Wei for the development of the liquid N2 decanter depicted in Fig. 1. The Oeffinger laboratory is supported by the Canadian Institutes of Health Research (MOP 106628), the Natural Sciences and Engineering Council of Canada (RGPIN 386315), the Rachel Foundation, the Fonds de recherche Santé Québec, and the Canadian Foundation for Innovation.
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Trahan, C., Aguilar, LC., Oeffinger, M. (2016). Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae . In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 1361. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3079-1_15
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DOI: https://doi.org/10.1007/978-1-4939-3079-1_15
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