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Membrane Chemistry Tunes the Structure of a Peptide Transporter.

ABSTRACT: Membrane proteins require lipid bilayers for function. While lipid compositions reach enormous complexities, high-resolution structures are usually obtained in artificial detergents. To understand whether and how lipids guide membrane protein function, we use single-molecule FRET to probe the dynamics of DtpA, a member of the proton-coupled oligopeptide transporter (POT) family, in various lipid environments. We show that detergents trap DtpA in a dynamic ensemble with cytoplasmic opening. Only reconstitutions in more native environments restore cooperativity, allowing an opening to the extracellular side and a sampling of all relevant states. Bilayer compositions tune the abundance of these states. A novel state with an extreme cytoplasmic opening is accessible in bilayers with anionic head groups. Hence, chemical diversity of membranes translates into structural diversity, with the current POT structures only sampling a portion of the full structural space.

SUBMITTER: Lasitza-Male T

PROVIDER: S-EPMC7590137 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Membrane Chemistry Tunes the Structure of a Peptide Transporter.

Lasitza-Male Tanya T Bartels Kim K Jungwirth Jakub J Wiggers Felix F Rosenblum Gabriel G Hofmann Hagen H Löw Christian C

Angewandte Chemie (International ed. in English) 20200911 43

Membrane proteins require lipid bilayers for function. While lipid compositions reach enormous complexities, high-resolution structures are usually obtained in artificial detergents. To understand whether and how lipids guide membrane protein function, we use single-molecule FRET to probe the dynamics of DtpA, a member of the proton-coupled oligopeptide transporter (POT) family, in various lipid environments. We show that detergents trap DtpA in a dynamic ensemble with cytoplasmic opening. Only ...[more]

PMID: 32744783

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Project description:YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of Escherichia coli to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10-19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8-26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this 'auto-binding' is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.

Dataset Information

Membrane Chemistry Tunes the Structure of a Peptide Transporter.

Publications

Membrane Chemistry Tunes the Structure of a Peptide Transporter.

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