Venom-derived peptide toxins can modify the gating characteristics of excitatory channels in neurons. How they bind and interfere with the fl ow of ions without directly blocking the ion permeation pathway remains elusive. Here we report the crystal structure of the trimeric chicken Acid-sensing ion channel 1 in complex with the highly selective gating modifi er Psalmotoxin 1 at 3.0 Å resolution. The structure reveals the molecular interactions of three toxin molecules binding at the proton-sensitive acidic pockets of Acid-sensing ion channel 1 and electron density consistent with a cation trapped in the central vestibule above the ion pathway. A hydrophobic patch and a basic cluster are the key structural elements of Psalmotoxin 1 binding, locking two separate regulatory regions in their relative, desensitized-like arrangement. Our results provide a general concept for gating modifi er toxin binding suggesting that both surface motifs are required to modify the gating characteristics of an ion channel.
Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies. To target the limited hydrophilic surfaces of membrane proteins, we designed three sybody libraries that exhibit different shapes and moderate hydrophobicity of the randomized surface. A robust binder selection cascade combining ribosome and phage display enabled the generation of conformation-selective, high affinity sybodies against an ABC transporter and two previously intractable human SLC transporters, GlyT1 and ENT1. The platform does not require access to animal facilities and builds exclusively on commercially available reagents, thus enabling every lab to rapidly generate binders against challenging membrane proteins.
(150 words)Single domain antibodies called nanobodies are excellent affinity reagents for membrane proteins.However, their generation relies on immunizations, which is only amenable to robust proteins and impedes selections in the presence of non-covalent or toxic ligands. To overcome these key limitations, we developed a novel in vitro selection platform, which builds on synthetic nanobodies called sybodies. Inspired by the shape diversity of natural nanobodies, three sybody libraries exhibiting different randomized surface shapes were engineered for high thermal stability. Using ribosome display, exceptionally large libraries were pre-enriched against membrane protein targets and subsequently funneled into a robust phage display process, thereby reducing selection bias. We successfully generated conformation-selective, high affinity sybodies against the human glycine transporter GlyT1, the human equilibrative nucleotide transporter ENT1 and a bacterial ABC transporter. Our platform builds exclusively on commercially available reagents and enables nonspecialized labs to generate conformation-specific binders against previously intractable protein targets.
Fermentation experiments with Streptomyces toxytricini were performed using (5Z,8Z)-[10,11,12,12-(2)H]tetradeca-5,8-dienoic acid or a mixture of [2,2-(2)H(2)]- and [8,8,8-(2)H(3)]octanoic acid as supplements. (2)H NMR and mass spectroscopy confirmed the incorporation of (5Z,8Z)-[10,11,12,12-(2)H]tetradeca-5,8-dienoic acid into the C(13) side chain as well as into the C(6) side chain of lipstatin. Moreover, deuterium was incorporated into the C(6) side chain of lipstatin from the 8-position but not from the 2-position of octanoate. The data establish that the beta-lactone moiety of lipstatin is formed by condensation of a C(8) and a C(14) fatty acid with a concomitant exchange of the H-2 atoms of the C(8) fatty acid.
Three putative intermediates in the biosynthesis of the lipase inhibitor lipstatin were synthesized in stable isotope-labeled form and were added to fermentation cultures of Streptomyces toxytricini. Biosynthetic lipstatin was isolated and analyzed by NMR spectroscopy. [3,10,11,12-(2)H]-(3S,5Z,8Z)-3-hydroxytetradeca-5,8-dienoic acid (9) was shown to serve as a direct biosynthetic precursor of lipstatin. [7,8-(2)H(2)]Hexylmalonate (11) was also incorporated into lipstatin, albeit at a relatively low rate. The leucine moiety of [(13)C-formyl,(15)N]-N-formylleucine (10) was diverted to lipstatin under loss of the (13)C-labeled formyl residue.
The lipophilic beta-lactone, lipstatin, inhibits pancreatic lipase and has been shown earlier to be biosynthesized by Claisen condensation of two fatty acid moieties. We present data from incorporation experiments with [U-13C6]leucine showing that a branched chain analogue of lipstatin is biosynthesized from leucine.
The human glycine transporter 1 (GlyT1) regulates glycine mediated neuronal excitation and inhibition through sodium- and chloride-dependent reuptake of the neurotransmitter1-3. Inhibition of glycine reuptake via GlyT1 prolongs neurotransmitter signaling and has long served as a key therapeutic development strategy for treatment of a broad range of central nervous system disorders including schizophrenia and cognitive impairments4. Using an inhibition state-selective sybody and serial synchrotron crystallography, we determined the structure of GlyT1 in complex with a benzoylpiperazine chemotype inhibitor at 3.4 Å resolution. The inhibitor locks GlyT1 in an inward-open conformation and binds at the intracellular gate of the release pathway, overlapping with the glycine release site. The inhibitor likely reaches GlyT1 from the cytoplasmic leaflet of the plasma membrane. The study defines the mechanism of non-competitive inhibition and enables the rational design of new, clinically efficacious GlyT1 inhibitors.
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