Thermodynamically constrained exclusive occupancy of p65 Cysteine 38 resolves the persulfidation–overoxidation competition in neuronal oxygen–glucose deprivation

Abstract Ischemic injury is described through a therapeutic window whose molecular content has never been specified, and the candidate switch, the redox state of a reactive cysteine, is measured only as a population average over whole proteins. Modifications of one cysteine are alternative fates of a single sulfur atom, yet no kinetic representation treats them as competing occupants of one site. Cysteine 38 of the NF-κB p65 subunit is represented here as a point on a probability simplex whose six vertices are its chemically distinct states, evolving under a generator whose rate constants are produced from state free energies, edge barriers and cosubstrate free-energy changes, so that every cycle affinity depends on chemical potentials alone. The residue layer is coupled to the bioenergetic collapse of oxygen–glucose deprivation and to a bistable survival decision. Cycle affinities proved invariant to the state free energies to $$\:4\times\:{10}^{-15}RT$$ , and detailed balance was recovered exactly, with net cycle flux below $$\:{10}^{-18}{min}^{-1}$$ . Persulfide occupancy rose to 0.44 while oxygen was absent and collapsed on restoration, when sulfinate occupancy reached 0.33, identifying restoration rather than deprivation as the vulnerable interval. Only representations enforcing exclusive occupancy reproduced the reported reversal of the sulfide effect with concentration, raising survival from 0.53 to 0.57 before falling. The thermodynamic constraint removed exactly the six parameter directions the observations cannot constrain, improving identifiability from 9 of 22 directions to 11 of 16 without altering any trajectory. Results are computational; no experimental measurement is reported.