When a folded protein is placed in D₂O, backbone amide hydrogens (N–H) exchange for deuterium. Each residue's observed exchange rate depends on how much the local structure protects that amide from solvent (EX2 kinetics):
k_obs = k_int / P
D(t) = 1 − e^(−k_obs · t)
P = protection factor (10^(burial · P_max))
Amides buried in a hydrogen-bonded helix or a packed core have a high protection factor P (exchange slowed by up to 10⁵–10⁶×); amides on flexible surface loops have P ≈ 1 and exchange almost as fast as a free peptide. In this model each residue's burial is its normalized distance from the molecule's centroid, viewed here top-down — buried "core" turns near the middle light up blue (protected) at short times, while surface "loop" turns further out light up red (exchanged) almost immediately.
- Labeling time — the deuterium exposure duration (log scale, 1 s–~2.8 h), exactly as an HDX-MS time-course experiment quenches and digests samples at several time points.
- Play exposure sweep — animates labeling time automatically, like stepping through an experiment's time series.
- Native / Destabilized — toggles the core's maximum protection factor (P_max), modeling a comparability study where a formulation change, mutation, or stress condition partially unfolds the core and speeds up exchange there — while surface loops, already unprotected, barely change.
- Segments flagged — at the current labeling time, counts how many of the 8 peptide-level segments differ by more than 15 percentage points in %D uptake between the native and destabilized state — the same "differential HDX" logic regulators use (per ICH Q6B) to detect a higher-order-structure (HOS) change between a reference and test biologic.
- Drag / scroll — drag the map to pan, scroll (or pinch) to zoom in on individual residues.
Real HDX-MS pepsin-digests the deuterated protein into ~5–15 residue peptides and measures each one's mass shift by LC-MS; this simulator shows the same peptide-segment resolution directly on a 2D top-down map of the folded backbone instead of a mass spectrum.