Replacing the eleven native tryptophans by directed evolution produces an active P-glycoprotein with site-specific, non-conservative substitutions

Douglas J. Swartz,Joshua N. Thomas,Joachim Weber,Narong Sok,Anukriti Singh,Ina L. Urbatsch

doi:10.1038/s41598-020-59802-w

Abstract

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 hydrolysis-driven 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.

Highlights

P-glycoprotein (Pgp) pumps an array of hydrophobic compounds out of cells, and has major roles in drug pharmacokinetics and cancer multidrug resistance
Pgp is a plasma membrane protein with the ability to pump a wide range of hydrophobic substances out of cells using the energy of ATP hydrolysis[1,2,3]
W158 and W799 are located within the intracellular loops (ICLs) that extend from the transmembrane domains (TMDs) and make contact with the nucleotide binding domains (NBDs), and W1104 is in the C-terminal NBD (NBD2)

Summary

Introduction

P-glycoprotein (Pgp) pumps an array of hydrophobic compounds out of cells, and has major roles in drug pharmacokinetics and cancer multidrug resistance. 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. Pgp ( known as multidrug resistance protein, MDR1 or ABCB1) is a plasma membrane protein with the ability to pump a wide range of hydrophobic substances out of cells using the energy of ATP hydrolysis[1,2,3] It is important in determining the pharmacokinetics of drugs by extruding them from cells and by participating in transepithelial transport of drugs and metabolites[4,5]. Complex competitive and mixed-type inhibition were observed in drug-stimulated ATPase assays suggesting positional overlap of classical transport substrates with ligands localized in the structures[39]. A number of proteins[56,57,58,59,60,61,62,63,64,65,66], including some membrane proteins[67,68,69,70,71,72], have been rendered

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