ArticleBiochemistry2026
Mechanistic Insights into Dioxygen Transport Routes in the PHD2 Oxygenase from Long-Time Scale Simulations.
Article in Biochemistry, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Understanding how dioxygen accesses buried catalytic centers in metalloenzymes is critical for elucidating enzymatic kinetics and guiding strategies to modulate catalytic activity. Here, we report over 20 μs of classical molecular dynamics simulations of the PHD2 oxygenase, a metalloenzyme regulating hypoxia signaling via HIF-1α hydroxylation. Our extended simulations reveal multiple dynamic dioxygen transport routes from solvent-exposed regions through the cupin fold to the metal active site, capturing transient interconverting channels and kinetic heterogeneity inaccessible to prior short-time scale studies. Dioxygen transport occurs on widely differing time scales, from rapid exchange (∼250 ps) to long residence times within internal hydrophobic cavities lasting hundreds of nanoseconds. These internal cavities act as dynamic reservoirs, modulating dioxygen availability and potentially contributing to the high K
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