Purification and characterization of eukaryotic ATP-dependent transporters homologously expressed in Pichia pastoris for structural studies by cryo-electron microscopy.

Membrane proteins play an essential role in all living organisms. Although there have been numerous efforts in the past to elucidate the structure and function of eukaryotic primary active transporters, knowledge about the majority of these membrane proteins is still minimal. This is often due to their low availability and complex handling. In this study, we homologously expressed three ATP-dependent transport proteins, STE6-2p, NEO1-p, and YPK9-p, in Pichia pastoris and subsequently optimized the solubilization and purification processes. Sequential use of different mild detergents and utilization of hydrophilic matrices in the purification procedure allowed us to obtain all three transporters monodisperse and in high purity, enabling initial structural analysis by cryo-electron microscopy. Using the respective substrates, we determined the specific activity of all target proteins using an ATPase assay. This study opens the door to further functional and structural studies of this pharmacologically important class of membrane proteins. • P. pastoris , a promising expression system for ATP-dependent transport proteins. • Sequential use of different mild detergents resulted in high yields of target proteins. • Hydrophilic IMAC matrices essential for monodisperse, active transport proteins. • Low-resolution cryo-EM density maps of NEO1-p and YPK9-p were generated. • P-, N- and A-domains of NEO1-p and YPK9-p identified by comparing with homologs. [ABSTRACT FROM AUTHOR]