Compact peptide cages for lanthanides and zinc
Two short peptide scaffolds sized for solid-phase synthesis: DB-LANM1 is a 36-residue stapled macrocycle that wraps an eight-oxygen coordination cage around a single trivalent lanthanide ion, and DB-ZNCAGE1 is a 25-residue peptide discovered by six-frame translation of a metagenomic contig that assembles into a D2 homotetramer clamping two Zn2+ ions across subunit interfaces.
Where they stand: both constructs held their fold and metal coordination in explicit-water molecular dynamics up to 62–77 °C and have been synthesized by a commercial peptide vendor (identity and purity confirmed by HPLC and mass spectrometry). Wet-lab metal-binding, quaternary assembly, and luminescence assays have not yet been run.
DB-LANM1: octadentate lanthanide cage
Designed from a bacterial lanmodulin EF-hand loop and locked into a 36-residue macrocycle. In the two-chain model shown here, each chain wraps eight oxygen donors around a single Tb3+ ion at 1.89–2.65 Å.
1. Five carboxylates plus a backbone carbonyl
Each Tb3+ ion is coordinated by Asp7 (OD1 at 2.16–2.17 Å), bidentate Asp9 (OD1/OD2 at 2.36–2.64 Å), Asp11 (OD1 at 1.89–1.91 Å), the residue-13 backbone carbonyl oxygen (2.65 Å), Asp15 (OD1 at 2.26–2.28 Å), and bidentate Glu18 (OE1/OE2 at 2.24–2.37 Å).
2. Synthesized S13Y antenna variant
The synthesized peptide replaces Ser13 with Tyr13 to place an aromatic chromophore on the rim of the binding loop while retaining the residue-13 backbone carbonyl donor. Sensitized terbium luminescence is a design hypothesis to be tested in wet-lab titration.
3. Switch to DB-ZNCAGE1 in the viewer
Use the toggle in the toolbar to inspect DB-ZNCAGE1, where four 25-residue helices assemble into a D2 bundle and coordinate two Zn2+ ions across chain interfaces via His2 and His5.
Lead 01 · Lanthanide-binding stapled macrocycle (DB-LANM1)
Full-length lanmodulin carries four EF-hand domains across ~110 residues and requires recombinant expression. DB-LANM1 compresses the coordination sphere into a single 36-residue macrocycle that can be manufactured by standard solid-phase peptide synthesis (SPPS) for heavy rare-earth (Dy3+/Tb3+) separation or radiometal chelation testing.
| Parameter | Measured on model | Notes |
|---|---|---|
| Chain length & assembly | 36 AA per chain (2 chains + 2 Tb3+ modeled) | Each 36-residue monomer forms a complete octadentate cage around one trivalent lanthanide ion. |
| Oxygen coordination sphere | 8 oxygen donors at 1.89–2.65 Å | Asp7 OD1 (2.16–2.17 Å), Asp9 OD1/OD2 (2.36–2.64 Å), Asp11 OD1 (1.89–1.91 Å), residue-13 backbone O (2.65 Å), Asp15 OD1 (2.26–2.28 Å), and Glu18 OE1/OE2 (2.24–2.37 Å). |
| Model confidence | Mean all-atom pLDDT 87.0 (Cα mean 86.8; Tb3+ ion pLDDT 91.0–92.1) | Backbone and coordinating carboxylates are well ordered in the co-folded complex. |
| Explicit-water MD | Holds fold & cage to 62 °C | Ser13 parent sequence retains octadentate coordination with zero inner-sphere water displacement in explicit-water molecular dynamics from 25 to 62 °C. |
| Synthesized variant | S13Y substitution (N-acetylated, C-amidated) | Places a tyrosine chromophore near the lanthanide pocket as a candidate luminescence antenna (zero methionine); delivered in linear reduced dithiol form (4,052.4 Da observed by ESI-MS) for Cys1–Cys36 disulfide cyclization. |
| Stage & synthesis status | Synthesized | Synthesized by a commercial peptide vendor (HPLC and mass spectrometry verified). U.S. provisional patent applications on file; wet-lab metal-binding and luminescence assays have not yet been run. |
Lead 02 · Binuclear zinc metallocage (DB-ZNCAGE1)
Discovered by six-frame translation of a metagenomic contig while screening short open reading frames for symmetric homo-oligomers whose metal-binding sites form only upon quaternary assembly. Four identical 25-residue helices pack into an antiparallel D2 bundle and clamp two Zn2+ ions at opposite ends of the core.
| Parameter | Measured on model | Notes |
|---|---|---|
| Chain length & symmetry | 25 AA per chain (D2 homotetramer, 100 AA total) | Short single-helix monomer suitable for solid-phase peptide synthesis. |
| Interfacial Zn2+ sites | 2 Zn2+ ions; 4 His Nδ1 per ion at 2.12–2.26 Å | Site E is held by chains B & C (His2 at 2.12–2.13 Å, His5 at 2.22–2.25 Å); Site F is held by chains A & D (His2 at 2.14–2.16 Å, His5 at 2.24–2.26 Å). Each Zn2+ sits in a coordinatively saturated interfacial His4 shell across the four-helix bundle; neither site exists in the isolated monomer. |
| Model confidence | Mean all-atom pLDDT 83.5 (Cα mean 84.2) | Co-folded as a four-chain, two-ion assembly. |
| Explicit-water MD | Holds tetramer & Zn2+ sites to 77 °C | Met1 parent sequence retains the antiparallel D2 bundle and both interfacial Zn2+ coordination spheres in explicit-water molecular dynamics from 27 to 77 °C. |
| Synthesized variant | M1L substitution (N-acetylated, C-amidated) | Replaces the N-terminal methionine with leucine to avoid oxidation during synthesis and storage; zero cysteine, zero methionine. |
| Stage & synthesis status | Synthesized | Synthesized by a commercial peptide vendor (HPLC and mass spectrometry verified). U.S. provisional patent application on file; wet-lab Zn2+ binding and quaternary assembly assays have not yet been run. |