Protein Destabilization as a Common Factor in Diverse Inherited Disorders

Abstract

Protein destabilization by amino acid substitutions is proposed to play a prominent role in widespread inherited human disorders, not just those known to involve protein misfolding and aggregation. To test this hypothesis, we computationally evaluate the effects on protein stability of all possible amino acid substitutions in 20 disease-associated proteins with multiple identified pathogenic missense mutations. For 18 of the 20 proteins studied, substitutions at known positions of pathogenic mutations are significantly more likely to destabilize the native protein fold (as indicated by more positive values of ∆∆G). Thus, positions identified as sites of disease-associated mutations, as opposed to non-disease-associated sites, are predicted to be more vulnerable to protein destabilization upon amino acid substitution. This finding supports the notion that destabilization of native protein structure underlies the pathogenicity of broad set of missense mutations, even in cases where reduced protein stability and/or aggregation are not characteristic of the disease state.

Keywords: Aggregation; Destabilization; Inherited disorder; Pathogenic mutation; Stability.

Fig. 1

Amino acid substitutions at sites of known disease-linked missense mutations are more destabilizing than those at neutral positions. Histograms show normalized counts of ΔΔG values calculated for all possible substitutions (excluding those involving cysteine) at sites of known disease-linked substitutions (red curves) and all other “neutral” amino acid positions (black curves). Bar graphs show the normalized frequencies of ΔΔG values exceeding n × 10 kcal/mol, where n is the number of subunits in the biological oligomeric assembly of each protein (Color figure online)

Fig. 2

Lower vulnerability to destabilization by amino acid substitution may explain the lack of ALS-linked missense mutations in β3 of SOD1. a Amino acid sequence of SOD1. Sites of ALS-causative missense mutations are shown in red and arrows above the sequence mark β-strand regions. b Secondary structure of SOD1 (PDBID: 1SPD). c Histograms representing calculated DDG values of mutations in neutral and pathogenic sites (as shown in Fig. 1) and in positions comprising each bstrand. d Bar graphs showing the normalized frequencies of DDG values exceeding 20 kcal/mol for neutral, pathogenic, and β-strand amino acid positions (Color figure online)