An AI-informed NMR structure reveals a LETM1 F-EF-hand for two-way mitochondrial calcium regulation.

Abstract

AlphaFold2 can accurately predict high-resolution protein structure from sequence but does not account for solvent conditions, ligands, post-translational modifications, lowly populated states or rare folds. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but whether and how calcium (Ca2+) binding affects structure and function remains enigmatic. Here, we developed an approach that used highly confident AlphaFold2 C positions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand domain with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing by His662, linking the canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding led to increased and decreased matrix Ca2+ levels, respectively, establishing F-EF as a two-way mitochondrial Ca2+ potentiator. Collectively, we show how AlphaFold2 can be synergized with NMR data to produce solution-specific structures, revealing here an extraordinary LETM1 F-EF-hand sensor.