Abstract
Metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis (ALS). All of the amino acids found in the bimetallic center have been associated with ALS except for two positions. H63 which forms the bridging imidazolate ion in the bimetallic center and K136 which is not directly involved in coordination but located in the bimetallic center were not reported to be mutated in any of the identified ALS cases. In this study, we investigated the structure and flexibility of five SOD1 variants by using classical molecular dynamics simulations. These variants include three substitutions on the non-ALS-linked positions; H63A, H63R, K136A and ALS-linked positions; G37R, H46R/H48D. We have generated four systems for each variant differing in metallation and presence of the intramolecular disulfide bond. Overall, a total of 24 different dimers including the wild-type were generated and simulated at two temperatures, 298 and 400 K. We have monitored backbone mobility, fluctuations and compactness of the dimer structures to assess whether the hypothetical mutations would behave similar to the ALS-linked variants. Results showed that particularly two mutants, H63R and K136A, drastically affected the dimer dynamics by increasing the fluctuations of the metal binding loops compared with the control mutations. Further, these variants resulted in demetallation of the dimers, highlighting probable ALS toxicity that could be elicited by the SOD1 variants of H63R and K136A. Overall, this study bridges two putative SOD1 positions in the metallic center and ALS, underlining the potential use of atomistic simulations for studying disease variants.
Highlights
Amyotrophic lateral sclerosis (ALS) which is characterized by degeneration of upper and lower motor neurons (Rowland and Shneider, 2001) is the most common late-onset motor neuron disease (Renton et al, 2014)
Many studies on superoxide dismutase 1 (SOD1) variants have converged that demetallation of SOD1 structure can significantly alter stability of the enzyme inducing formation of misfolded neurotoxic aggregates (Tiwari et al, 2009; Banci et al, 2007; Ding and Dokholyan, 2008; Wright et al, 2019; Wang et al, 2002, 2003, 2007)
While all amino acids that were directly involved in metal coordination of the Cu/Zn SOD1 have been reported to be somehow associated with ALS, two amino acids, H63 and K136, that are located in the fist shell of the bimetallic center have not been linked to this disease
Summary
Amyotrophic lateral sclerosis (ALS) which is characterized by degeneration of upper and lower motor neurons (Rowland and Shneider, 2001) is the most common late-onset motor neuron disease (Renton et al, 2014). Human Cu/Zn SOD1 gene encodes a highly conserved (Fridovich, 1995) 153-aa long protein which folds into a wellstudied 8-stranded β-barrel structure (Figure 1B) from the immunoglobulin fold family (Richardson et al, 1976) This barrel structure is flanked by two large loops connecting the strands of β4-β5 and β7-β8 that hold the Cu/Zn bimetallic center. While multiple structural features such as dimerization and the conserved intramolecular disulfide bond between C57 and C146 (Figure 1B) were shown to contribute to the extreme stability of SOD1 (Furukawa and O’Halloran, 2005; Goodsell and Olson, 2000), the imidazolate-bridged metallic center was associated with the structural stability of the enzyme (Arnesano et al, 2004). Our results pointed out that essentially H63 and K136 variants behaved similar to the ALS-linked variants reflecting the potential toxicity associated with these novel positions
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