Nanosecond ligand migration and functional protein relaxation in ba₃ oxidoreductase: Structures of the B₀, B₁ and B₂ intermediate states

Nanosecond time-resolved step-scan FTIR spectroscopy (nTRS ² -FTIR) has been applied to literally probe the active site of the carbon monoxide (CO)-bound thermophilic ba₃ heme-copper oxidoreductase as it executes its function. The nTRS ² - snapshots of the photolysed heme a₃ Fe-CO/Cu_B species captured a "transition state" whose side chains prevent the photolysed CO to enter the docking cavity. There are three sets of ba₃ photoproduct bands of docked CO with different orientation exhibiting different kinetics. The trajectories of the "docked" CO at 2122, 2129 and 2137 cm^{- 1} is referred to in the literature as B₂, B₁ and B₀ intermediate states, respectively. The present data provided direct evidence for the role of water in controlling ligand orientation in an intracavity protein environment.