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DOI	10.1073/pnas.1802177115
	Structure of the emre multidrug transporter and its use for inhibitor peptide design
	Ovchinnikov V.; Stone T.A.; Deber C.M.; Karplus M.
发表日期	2018
ISSN	0027-8424
起始页码	E7932
结束页码	E7941
卷号	115 期号:34
英文摘要	Small multidrug resistance (SMR) pumps represent a minimal paradigm of proton-coupled membrane transport in bacteria, yet no high-resolution structure of an SMR protein is available. Here, atomic-resolution structures of the Escherichia coli efflux-multidrug resistance E (EmrE) multidrug transporter in ligand-bound form are refined using microsecond molecular dynamics simulations biased using low-resolution data from X-ray crystallography. The structures are compatible with existing mutagenesis data as well as NMR and biochemical experiments, including pKas of the catalytic glutamate residues and the dissociation constant (KD) of the tetraphenylphosphonium+ cation. The refined structures show the arrangement of residue side chains in the EmrE active site occupied by two different ligands and in the absence of a ligand, illustrating how EmrE can adopt structurally diverse active site configurations. The structures also show a stable, well-packed binding interface between the helices H4 of the two monomers, which is believed to be crucial for EmrE dimerization. Guided by the atomic details of this interface, we design proteolysis-resistant stapled peptides that bind to helix H4 of an EmrE monomer. The peptides are expected to interfere with the dimerization and thereby inhibit drug transport. Optimal positions of the peptide staple were determined using free-energy simulations of peptide binding to monomeric EmrE. Three of the four top-scoring peptides selected for experimental testing resulted in significant inhibition of proton-driven ethidium efflux in live cells without nonspecific toxicity. The approach described here is expected to be of general use for the design of peptide therapeutics. © 2018 National Academy of Sciences. All Rights Reserved.
英文关键词	Drug resistance; Membrane proteins; Molecular dynamics; Stapled peptides; Structure refinement
语种	英语
scopus关键词	ABC transporter subfamily B; efflux multidrug resistance E; ethidium; glutamic acid derivative; ligand; monomer; peptide; protein inhibitor; tetraphenylphosphonium; unclassified drug; antiporter; EmrE protein, E coli; Escherichia coli protein; peptide; alpha helix; Article; bacterial cell; controlled study; cytotoxicity; dimerization; dissociation constant; drug design; drug resistance; drug transport; lipid membrane; molecular dynamics; multidrug resistance; nonhuman; pKa; priority journal; protein degradation; protein structure; structure analysis; X ray crystallography; antagonists and inhibitors; chemistry; enzyme active site; Escherichia coli; molecular dynamics; multidrug resistance; protein multimerization; protein quaternary structure; Antiporters; Catalytic Domain; Drug Resistance, Multiple, Bacterial; Escherichia coli; Escherichia coli Proteins; Molecular Dynamics Simulation; Peptides; Protein Multimerization; Protein Structure, Quaternary
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/160479
作者单位	Ovchinnikov, V., Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States; Stone, T.A., Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Deber, C.M., Division of Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada, Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Karplus, M., Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States, Laboratoire de Chimie Biophysique, Institut de Science et d’Ingenierie Supramoleculaires, Université de Strasbourg, Strasbourg, 67000, France
推荐引用方式 GB/T 7714	Ovchinnikov V.,Stone T.A.,Deber C.M.,et al. Structure of the emre multidrug transporter and its use for inhibitor peptide design[J],2018,115(34).
APA	Ovchinnikov V.,Stone T.A.,Deber C.M.,&Karplus M..(2018).Structure of the emre multidrug transporter and its use for inhibitor peptide design.Proceedings of the National Academy of Sciences of the United States of America,115(34).
MLA	Ovchinnikov V.,et al."Structure of the emre multidrug transporter and its use for inhibitor peptide design".Proceedings of the National Academy of Sciences of the United States of America 115.34(2018).