Interfacial water in the PRDX1-sulfiredoxin repair intermediate: an all-atom molecular dynamics study

Abstract

Peroxiredoxins protect cells from oxidative damage, and sulfiredoxin (Srx) restores their activity by repairing the overoxidized catalytic cysteine; how the two proteins recognize one another is central to redox signaling and to oxidative-stress-associated disease. We characterize the human peroxiredoxin-1 (PRDX1)-Srx repair intermediate (PDB 2RII) and four related catalytic-cysteine states by all-atom molecular dynamics (three replicas of 200 ns per system; 3.0 microsecond total), using geometric and kinetic observables only, with across-replica statistics. The disulfide-linked complex is stable (backbone RMSD 2.5- 3.2 Angstrom) and the peroxidatic Cys52 is buried in the interface (buried surface area 71-76 Angstrom^2). The interface is extensive, with 202 consensus residue-residue contacts, and predominantly water-mediated: 20 reproducible, hydrogen-bond-validated water bridges centered on the PRDX1 165-170 region, against three persistent salt bridges. Removing the engineered tether and modeling Cys52 as the sulfinate on which Srx acts leaves the interface intact (189 consensus contacts) and the water network larger (36 bridges), new bridges linking the sulfinate to the Srx catalytic pocket. At the free Cys52, first-shell water responds to charge state as electrostatics predicts, and at matched water counts the thiolate shows no additional clustering, separating generic hydration from the specific interfacial organization. An equalized, permutation-controlled comparison of the Srx-bound and free intra-PRDX1 contact networks leaves them statistically indistinguishable: of 14,127 residue pairs only one exceeds both floors, and it does not reproduce across independent trajectory sets. A covalent celastrol-Cys173 adduct retains its thioether bond while the tethered ligand reorients widely, so covalent attachment fixes the anchor rather than the pose.