Functional Analysis of a Novel Pathogenic Glycine Amidinotransferase Mutant in Hereditary Fanconi Syndrome

Abstract

The mutant glycine amidinotransferase (GATM) protein polymerizes into a characteristic crystal, resulting in mitochondrial dysfunction in proximal tubules and Fanconi syndrome with progressive kidney failure. We identified a novel hereditary Fanconi syndrome characterized by mutant GATM proteins in a Japanese family, the first in Asia. Kidney biopsies exhibited typical histological features, confirmed by immunofluorescent staining with anti-GATM and anti-ATP synthase β subunit (ATPB) antibodies and electron microscopy. Quantitative immunofluorescence analysis showed a significant correlation between ATPB and GATM–ATPB colocalization, suggesting mitochondrial pathogenicity of the mutant. Previously reported GATM mutations, clustered in the fourth of 5 β-sheets of the GATM protein, are assumed to have increased adhesive properties, changing the β-sheet from its original dimeric form to a unique polymerization. Targeted panel sequencing showed a novel mutation (Q268E) in the GATM gene (NM_001482.3: c.802C>G), distinct from this sheet. Because conventional methods failed to detect the significance, we employed an advanced molecular dynamics approach—hypersound-perturbed molecular dynamics simulations. This analysis effectively demonstrated that the Q268E mutation enhanced conformational flexibility of region-spanning residues that are spatially positioned between the mutated site and the sheet, leading to the pathological polymerization of the mutant protein. This simulation offers valuable insights into the pathological mechanisms of abnormal protein conformation.