1. An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium.
- Author
-
Lin QT, Colussi DM, Lake T, and Stathopulos PB
- Subjects
- Humans, Nuclear Magnetic Resonance, Biomolecular, Membrane Proteins chemistry, Membrane Proteins metabolism, Membrane Proteins genetics, Protein Binding, Binding Sites, Hydrophobic and Hydrophilic Interactions, Hydrogen-Ion Concentration, Amino Acid Sequence, Calcium-Binding Proteins, Calcium metabolism, Mitochondria metabolism, Models, Molecular, EF Hand Motifs
- Abstract
AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca
2+ ) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions 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 with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+ , respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)- Published
- 2024
- Full Text
- View/download PDF