Molecular dynamics analysis of superoxide dismutase 1 mutations suggests decoupling between mechanisms underlying ALS onset and progression

Abstract

Mutations in the superoxide dismutase 1 (SOD1) gene are the second most common known cause of ALS. SOD1 variants express high phenotypic variability and over 200 have been reported in people with ALS. It was previously proposed that variants can be broadly classified in two groups, 'wild-type like' (WTL) and 'metal binding region' (MBR) variants, based on their structural location and biophysical properties. MBR variants, but not WTL variants, were associated with a reduction of SOD1 enzymatic activity. In this study we used molecular dynamics and large clinical datasets to characterise the differences in the structural and dynamic behaviour of WTL and MBR variants with respect to the wild-type SOD1, and how such differences influence the ALS clinical phenotype. Our study identified marked structural differences, some of which are observed in both variant groups, while others are group specific. Moreover, collecting clinical data of approximately 500 SOD1 ALS patients carrying variants, we showed that the survival time of patients carrying an MBR variant is generally longer (∼6 years median difference, p < 0.001) with respect to patients with a WTL variant. In conclusion, our study highlighted key differences in the dynamic behaviour between WTL and MBR SOD1 variants, and between variants and wild-type SOD1 at an atomic and molecular level, that could be further investigated to explain the associated phenotypic variability. Our results support the hypothesis of a decoupling between mechanisms of onset and progression of SOD1 ALS, and an involvement of loss-of-function of SOD1 with the disease progression.

Keywords: Amyotrophic lateral sclerosis; Diseaseassociated SOD1 mutations; Molecular dynamics (MD) simulations; Performed principal component analysis; Superoxide Dismutase type 1 (SOD1); Survival analysis.

Graphical abstract

Fig. 1

SOD1 monomer structure coloured in grey, the residues which form WTL variants are coloured in blue and the residues which form the MBR variants are coloured in green.

Fig. 2

Boxplots depicting the RMSF distribution of the WTL (green), MBR (blue) variants and wt-SOD1 (coral) in the a) Metal binding loop b) Electrostatic loop. RMSF is calculated for the Cα atoms. The whisker bars represent the range of minimum and maximum RMSF, the median is represented by a line subdividing the box. Wilcoxon rank-sum test, p-value annotation legend: ns: p < = 1.00e+ 00, * : 1.00e-02 < p < = 5.00e-02, * *: 1.00e-03 < p < = 1.00e-02, * ** : 1.00e-04 < p < = 1.00e-03, * ** *: p < = 1.00e-04.

Fig. 3

a) Box plots depicting RMSD analysis of the MD simulations performed on the wt-SOD1 (coral), WTL (green) and MBR (blue) variants. The RMSD is calculated for the Cα atoms of the wt-SOD1 and the variants. The whisker bars represent the range of minimum and maximum RMSD, the median is represented by a line subdividing the box. b) Box plots depicting radius of gyration (Rg) comparison of the wt-SOD1 (coral), WTL (green) and MBR (blue) variants simulations. The whisker bars represent the range of minimum and maximum Rg, the median is represented by a line subdividing the box.

Fig. 4

PCA analysis of the concatenated trajectories. Porcupine plots corresponding to the a) PC1 b) PC2. The wt-SOD1 and variant protein backbone is coloured in grey, the metal binding loop in blue and electrostatic loop in red. The vectors coloured in green represent the direction and magnitude of the domain motion. WTL variants are highlighted in green and MBR variants are highlighted in blue.

Fig. 5

Mean number of hydrogen bonds formed in the wt-SOD1 (coral), WTL (green) and MBR (blue) variants during the entire length of the simulation.

Fig. 6

a) Box plots depicting Closeness centrality comparison of the wt-SOD1 and the variants. For each variant the boxplot on the left (respectively on the right) is obtained considering only the residues belonging to the metal binding loop (respectively to the electrostatic loop). The dotted line represents the mean Closeness centrality of the wt-SOD1 residues. b) Hierarchical clustering of the wt-SOD1 and its variants obtained considering the Closeness centrality indexes of the residues belonging to the MBL. c) Same as in c) but for the ESL residues. d) Mean difference (in percentage) between the closeness centrality indexes of the residues of the variants with respect to the wild-type ones for the metal binding loop. e) Same as in d) but for the electrostatic loop.

Fig. 7

a) Mean correlation between the covariance matrices of the atomic coordinates of the wt-SOD1 and the variants. Bars represent the Standard Error of the Mean. Hierarchical clustering of the wt-SOD1 and variants obtained considering the covariances of the atomic coordinates of all the residues belonging to the b) MBL. c) ESL. d) covariances between the residues of the MBL and ESL.

Fig. 8

Age at onset (a) and survival (b) curves from the cox proportional hazard analysis (all WTL variants VS all MBR variants).