The Arg108Cys Variant of Methylmalonyl-CoA Mutase: Clinical Implications for the Mexican Population Based on Molecular Dynamics and Docking

Abstract

Methylmalonic acidemia (MMA) is a genetic condition associated with intellectual disability and a high mortality rate. It is caused by pathogenic variants in the MMUT gene, which codes methylmalonyl-CoA mutase enzyme (MUT). In the Mexican population, the variant NM_000255.4:c.322C>T or p.(Arg108Cys) is the most frequently found, but its structural pathogenic effect is scarcely studied. To describe the clinical picture of p.(Arg108Cys) homozygous patients and to predict its structural pathogenic effect, we performed an analysis of the medical files from six MMA Mexican p.(Arg108Cys) homozygous patients. The structural changes in MUT caused by this variant were analyzed through molecular dynamics simulations (MDS) and docking and compared with the wild-type (Wt) enzyme. The main clinical symptoms presented by the patients were feeding difficulties, lethargy, and neurodevelopmental delay, with a predominance of early-onset phenotype and a mortality rate of 83%. We found significant structural changes in MUT structure, particularly in the catalytic domain, with increased volume cavity, shortening of the binding substrate tunnel, and aberrant accommodation. Also, the dimerization interface area increased from 1343 Ų in the Wt to 3386 Ų, and the dimer formation involved a different set of amino acids. The NM_000255.4:c.322C>T or p.(Arg108Cys) MMUT variant is associated with a severe outcome in MMA Mexican patients, and the enzyme was associated with ostentatious topological changes in the secondary and tertiary structure, which impacted the catalytic domain, the accommodation of the substrate, and the dimerization interface. Further ex vivo functional studies are needed to confirm these predictions, such as enzymatic activity measurements in fibroblasts of patients.

Keywords: genetic diseases; inborn errors of metabolism; methylmalonic acidemia; propionate defects; rare diseases.

Figure 1

Clinical (A) and biochemical characteristics (B) of the MUTd patients homozygous for the NM_000255.4:c.322C>T or p.(Arg108Cys) variant and geographical distribution of the families in Mexico. (C) The numbers in a circle indicate the cases in each location.

Figure 2

Structures from MDS of human methylmalonyl-CoA mutase after 110 ns simulation. Wt MUT after MDS (A) is compared by amino acids RMSD with the NM_000255.4:c.322C>T or p.(Arg108Cys) variant after MD, (B) and 3D structural alignment of both structures after MDS are shown. (C) RMSD corresponds to the structures extracted from the MD simulations (frames from 105–110 ns). Structures are visualized in ribbons.

Figure 3

Root mean square deviation (RMSD), (A) root mean square fluctuation (RMSF) (B), and radius of gyrus (Rgyr) (C) plots of the Wt MUT and p.(Arg108Cys) variant of methylmalonyl-CoA mutase. The figures represent the average values of three MDS replicates. For the Wt MUT, the mean RMSD was 2.44 ± 0.32 Å, the mean RMSF was 1.08 ± 0.63 Å, and the mean Rgyr was 22.98 Å ± 0.10. For the p.(Arg108Cys) variant, the mean RMSD was 2.28 ± 0.26 Å, the mean RMSF was 1.10 ± 0.60 Å, and the mean Rgyr was 22.79 Å ± 0.07.

Figure 4

Solvent-accessible surface area (SASA) during the MD simulation of the Wt MUT and p.(Arg108Cys) variant. The graph represents the mean ± standard deviation of SASA for Wt MUT (296.20 ± 3.60 nm²) and for the p.(Arg108Cys) variant (294.25 ± 4.54 nm²) from three MDS replicates.

Figure 5

Interface amino acid interactions of the Wt MUT homodimer vs. NM_000255.4:c.322C>T or p.(Arg108Cys) homodimer. (A) Amino acids that constitute the interface between two Wt MUT monomers. (B) Amino acids that constitute the interface between two NM_000255.4:c.322C>T or p.(Arg108Cys) variant monomers.

Figure 6

Local changes exerted by the arginine 108 residue: (A) change in the Wt MUT monomer by cysteine; (B) hydrogen bonds are shown with dotted yellow lines. Structures are visualized in ribbons and sticks.

Figure 7

Differences in the cavity volume between Wt MUT and NM_000255.4:c.322C>T or p.(Arg108Cys) variant. The volume of the cavity of Wt MUT (A) is the smallest and shows the deepest tunnel (green-colored, right side), where the substrate is adequately bound. (B) The cavity of the p.(Arg108Cys) variant shows the largest volume (C) with a shortened tunnel (green-colored, right side), causing an aberrant accommodation of the substrate (D). The close-ups highlight the depth of the pockets and the disposition of the residue 108. MDS frames from the last 105–110 ns were used for the cavity analysis.