Mechanical probes of SOD1 predict systematic trends in metal and dimer affinity of ALS-associated mutants
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Updated: May 15, 2026
Assay Development for High Content Quantification of Sod1 Mutant Protein Aggregate Formation in Living Cells
Published on: October 4, 2017
1Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada V6T 1Z1.
Abstract:
Mutations and oxidative modification in the protein Cu,Zn superoxide dismutase (SOD1) have been implicated in the death of motor neurons in amyotrophic lateral sclerosis (ALS), a presently incurable, invariably fatal neurodegenerative disease. Here we employ steered, all-atom molecular dynamics simulations in implicit solvent to investigate the significance of either mutations or post-translational modifications (PTMs) to SOD1 on metal affinity, dimer stability, and mechanical malleability. The work required to induce moderate structural deformations as a function of sequence index constitutes a "mechanical fingerprint" measuring structural rigidity in the native basin, from which we are able to unambiguously distinguish wild-type SOD1 from PTM variants and measure the severity of a given PTM on structural integrity. The cumulative distribution of work values provided a way to cleanly discriminate between SOD1 variants. Disulfide reduction destabilizes dimer stability more than the removal of either metal, but not moreso than the removal of both metals. Intriguingly, we found that disulfide reduction mechanically stabilizes apo-SOD1 monomer, underscoring the differences between native basin mechanical properties and equilibrium thermodynamic stabilities and elucidating the presence of internal stress in the apo state. All PTMs and ALS-associated mutants studied showed an increased tendency to lose either Cu or Zn and to monomerize-processes known to be critical in the progression of ALS. The valence of Cu strongly modulates its binding free energy. As well, several mutants were more susceptible to loss of metals and monomerization than the disulfide-reduced or apo forms of SOD1. Distance constraints are required to calculate free energies for metal binding and dimer separation, which are validated using thermodynamic cycles. When distance constraints are removed, the results agree with those obtained from direct application of the Jarzynski equality.
Insights
Mutations and oxidative modifications in copper, zinc superoxide dismutase (SOD1) impact its metal binding and stability, contributing to motor neuron death in amyotrophic lateral sclerosis (ALS). Understanding these changes is key to ALS research.
Area of Science:
- Biochemistry
- Neuroscience
- Computational Biology
Background:
- Mutations and oxidative damage to Cu,Zn superoxide dismutase (SOD1) are linked to motor neuron degeneration in amyotrophic lateral sclerosis (ALS).
- SOD1 dysfunction plays a critical role in the pathogenesis of this incurable neurodegenerative disease.
Purpose of the Study:
- To investigate how mutations and post-translational modifications (PTMs) affect SOD1's metal affinity, dimer stability, and mechanical properties.
- To establish a 'mechanical fingerprint' for distinguishing SOD1 variants and assessing PTM severity.
Main Methods:
- Utilized steered, all-atom molecular dynamics simulations in implicit solvent.
- Analyzed the work required for structural deformations to create mechanical fingerprints.
- Calculated free energies for metal binding and dimer separation using distance constraints and thermodynamic cycles.
Main Results:
- Distinct mechanical fingerprints differentiate wild-type SOD1 from PTM variants and mutants.
- Disulfide reduction destabilizes dimer stability more than single metal removal but less than dual metal removal.
- PTMs and ALS mutants show increased propensity for metal loss and monomerization, critical processes in ALS progression.
- Disulfide reduction mechanically stabilizes apo-SOD1 monomer, revealing internal stress in the apo state.
Conclusions:
- SOD1 variants associated with ALS exhibit altered metal affinity, dimer stability, and mechanical malleability.
- These alterations, particularly metal loss and monomerization, are crucial in ALS pathogenesis.
- Molecular dynamics simulations provide a powerful tool to characterize SOD1 variants and their role in neurodegeneration.
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