DOI: 10.1073/pnas.1802177115
论文题名: Structure of the emre multidrug transporter and its use for inhibitor peptide design
作者: Ovchinnikov V. ; Stone T.A. ; Deber C.M. ; Karplus M.
刊名: Proceedings of the National Academy of Sciences of the United States of America
ISSN: 0027-8424
出版年: 2018
卷: 115, 期: 34 起始页码: E7932
结束页码: E7941
语种: 英语
英文关键词: Drug resistance
; Membrane proteins
; Molecular dynamics
; Stapled peptides
; Structure refinement
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
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. Citation statistics:
资源类型: 期刊论文
标识符: http://119.78.100.158/handle/2HF3EXSE/163675
Appears in Collections: 气候变化与战略
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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
Recommended Citation:
Ovchinnikov V.,Stone T.A.,Deber C.M.,et al. Structure of the emre multidrug transporter and its use for inhibitor peptide design[J]. Proceedings of the National Academy of Sciences of the United States of America,2018-01-01,115(34)