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TitleBottom-up design of Ca channels from defined selectivity filter geometry.
Journal, issue, pagesNature, Vol. 648, Issue 8093, Page 468-476, Year 2025
Publish dateOct 22, 2025
AuthorsYulai Liu / Connor Weidle / Ljubica Mihaljević / Joseph L Watson / Zhe Li / Le Tracy Yu / Sagardip Majumder / Andrew J Borst / Kenneth D Carr / Ryan D Kibler / Tamer M Gamal El-Din / William A Catterall / David Baker /
PubMed AbstractNative ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices. Protein design has been harnessed to generate pore- ...Native ion channels play key roles in biological systems, and engineered versions are widely used as chemogenetic tools and in sensing devices. Protein design has been harnessed to generate pore-containing transmembrane proteins, but the design of selectivity filters with precise arrangements of amino acid side chains specific for a target ion, a crucial feature of native ion channels, has been constrained by the lack of methods for placing the metal-coordinating residues with atomic-level precision. Here we describe a bottom-up RFdiffusion-based approach to construct Ca channels from defined selectivity filter residue geometries, and use this approach to design symmetric oligomeric channels with Ca selectivity filters having different coordination numbers and different geometries at the entrance of a wider pore buttressed by multiple transmembrane helices. The designed channel proteins assemble into homogeneous pore-containing particles and, for both tetrameric and hexameric ion-coordinating configurations, patch-clamp experiments show that the designed channels have higher conductances for Ca than for Na and other divalent ions (Sr and Mg) that are eliminated after mutation of selectivity filter residues. Cryogenic electron microscopy indicates that the design method has high accuracy: the structure of the hexameric Ca channel is nearly identical to that of the design model. Our bottom-up design approach now enables the testing of hypotheses relating filter geometry to ion selectivity by direct construction, and provides a roadmap for creating selective ion channels for a wide range of applications.
External linksNature / PubMed:41125887
MethodsEM (single particle)
Resolution3.75 - 4.62 Å
Structure data

47340

9dzw

EMDB-47340, PDB-9dzw:
De novo calcium channel hexamer, CalC6_3 with DHR extensions
Method: EM (single particle) / Resolution: 3.75 Å

47356

9e0h

EMDB-47356, PDB-9e0h:
De novo calcium channel heptamer, CalC6_3 with DHR extensions. Off target multimerization state
Method: EM (single particle) / Resolution: 4.62 Å

Source
  • synthetic construct (others)
KeywordsDE NOVO PROTEIN / Calcium Channel / CalC6_3 / De novo / Membrane protein / CalC6_3 with DHR extensions / hexamer / pore / Ca / heptamer

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