Abstract
Proteolytic susceptibility during endolysosomal degradation is decisive for allergic sensitization. In the major birch pollen allergen Bet v 1 most protease cleavage sites are located within its secondary structure elements, which are inherently inaccessible to proteases. The allergen thus must unfold locally, exposing the cleavage sites to become susceptible to proteolysis. Hence, allergen cleavage rates are presumed to be linked to their fold stability, i.e., unfolding probability. Yet, these locally unfolded structures have neither been captured in experiment nor simulation due to limitations in resolution and sampling time, respectively. Here, we perform classic and enhanced molecular dynamics (MD) simulations to quantify fold dynamics on extended timescales of Bet v 1a and two variants with higher and lower cleavage rates. Already at the nanosecond-timescale we observe a significantly higher flexibility for the destabilized variant compared to Bet v 1a and the proteolytically stabilized mutant. Estimating the thermodynamics and kinetics of local unfolding around an initial cleavage site, we find that the Bet v 1 variant with the highest cleavage rate also shows the highest probability for local unfolding. For the stabilized mutant on the other hand we only find minimal unfolding probability. These results strengthen the link between the conformational dynamics of allergen proteins and their stability during endolysosomal degradation. The presented approach further allows atomistic insights in the conformational ensemble of allergen proteins and provides probability estimates below experimental detection limits.
Highlights
With more than 30% of the population affected, immunoglobulin-E-mediated allergy is the most frequent immune disorder worldwide (Valenta, 2002; Valenta et al, 2010; Curin et al, 2018)
We employ classic and enhanced sampling techniques to test whether we are able to characterize the relation between protein dynamics and proteolytic susceptibility
Mimicking the environmental conditions of endolysosomal degradation, we observe a link between the probability of partial unfolding and proteolytic susceptibility for three Bet v 1 variants
Summary
With more than 30% of the population affected, immunoglobulin-E-mediated allergy is the most frequent immune disorder worldwide (Valenta, 2002; Valenta et al, 2010; Curin et al, 2018). The determinants of what makes a protein an allergen are largely unknown (Scheurer et al, 2015; Verhoeckx et al, 2019). It has been demonstrated repeatedly that proteins with substantial similarity in sequence and structure are able to trigger an entirely different immune response (Mitropoulou et al, 2018; Eichhorn et al, 2019; Seutter von Loetzen et al, 2019; Tscheppe et al, 2020). The allergenic potential of a protein often cannot be rationalized, nor predicted, based on sequence or structural similarity to known allergens (Lu et al, 2018). Reliable experimental and computational models of proteolytic susceptibility in the endosome represent promising tools to understand, and possibly even predict, what makes a protein an allergen
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