P-glycoprotein (Pgp) pumps an array of hydrophobic compounds out of cells, and has major roles in drug pharmacokinetics and cancer multidrug resistance. Yet, polyspecific drug binding and ATP hydrolysisdriven drug export in pgp are poorly understood. fluorescence spectroscopy using tryptophans (trp) inserted at strategic positions is an important tool to study ligand binding. In Pgp, this method will require removal of 11 endogenous Trps, including highly conserved Trps that may be important for function, protein-lipid interactions, and/or protein stability. Here, we developed a directed evolutionary approach to first replace all eight transmembrane Trps and select for transport-active mutants in Saccharomyces cerevisiae. Surprisingly, many Trp positions contained non-conservative substitutions that supported in vivo activity, and were preferred over aromatic amino acids. The most active construct, W(3Cyto), served for directed evolution of the three cytoplasmic Trps, where two positions revealed strong functional bias towards tyrosine. W(3Cyto) and Trp-less Pgp retained wild-type-like protein expression, localization and transport function, and purified proteins retained drug stimulation of ATP hydrolysis and drug binding affinities. The data indicate preferred Trp substitutions specific to the local context, often dictated by protein structural requirements and/or membrane lipid interactions, and these new insights will offer guidance for membrane protein engineering.

Exchangers within the APC superfamily of transporters. Initial homology models were produced from 10 alternative alignments of these distantly related proteins. The alignments were refined by mapping sequence conservation onto these 3D structures. The best model was then fitted to the cryo-EM map by adjusting the position of individual helices and the resulting structure was equilibrated in a lipid bilayer for 200 ns using molecular dynamics. The resulting structure suggests conformational changes relative to UraA in which helices at the dimer interface are tilted relative to the transporter domain, thus providing access to the substrate binding site from the extracellular side of the membrane. Comparison of our Bor1p structure with that from UraA are likely to reflect the structural changes that accompany the alternating access mechanism employed by this family of transporters.