Thermodynamic Preference of Fe2+ for a C-Terminal Coordination Site in Human Frataxin Revealed by Multiscale Simulations
Journal of Chemical Information and Modeling, vol.66, no.11, pp.6676-6694, 2026 (SCI-Expanded, Scopus)
- Publication Type: Article / Article
- Volume: 66 Issue: 11
- Publication Date: 2026
- Doi Number: 10.1021/acs.jcim.6c00960
- Journal Name: Journal of Chemical Information and Modeling
- Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Aerospace Database, Compendex, EMBASE, MEDLINE, Materials Science & Engineering Collection (ProQuest), Technology Collection (ProQuest)
- Page Numbers: pp.6676-6694
- Bilecik Şeyh Edebali University Affiliated: Yes
Abstract
Frataxin (FXN) is a mitochondrial metallochaperone whose deficiency causes Friedreich’s ataxia (FRDA), the most prevalent inherited ataxia, yet the thermodynamically preferred Fe2+ coordination site has not been determined at atomic resolution under dynamic conditions. Here, we present a multiscale computational investigation of Fe2+ coordination to human frataxin (PDB: 1EKG), integrating 3.4 μs of aggregate simulation time across unbiased molecular dynamics, well-tempered metadynamics, alchemical free energy perturbation (FEP), DFT cluster calculations (B3LYP-D3BJ/def2-TZVP), and force field sensitivity analysis. Our simulations identify a previously uncharacterized C-terminal coordination site (Pocket 2, lined by HIS183, GLU184, ASP199, and LYS208, with GLU184 and the LYS208 C-terminal carboxylate serving as first-shell ligands) computationally predicted to be thermodynamically preferred over the canonical acidic ridge by ΔΔG = −16.85 ± 9.5 kJ/mol; while the magnitude of this preference should be interpreted with caution given the known limitations of nonpolarizable FEP for divalent cations, the consistent direction across multiple independent methods supports Pocket 2 as a higher-affinity site. Both sites retain Fe2+ for 500 ns with a metadynamics-derived dissociation barrier of ∼115 kJ/mol, and the coordination geometry (first-shell RDF peak at 1.92 Å, exclusively O/N ligands; Mayer BVA = 0.099) is consistent with experimental XAS/EXAFS data. Fe2+ binding is associated with global conformational rigidification, narrowing of the conformational ensemble, and emergence of correlated motion between the C-terminal coordination region and the acidic ridge, supporting a working dual-site binding hypothesis that may provide a new structural framework for understanding frataxin’s metallochaperone function in Friedreich’s ataxia.