Inactivation of [FeFe]‐hydrogenase by O₂. Thermodynamics and frontier molecular orbitals analyses

Abstract

The oxidation of H-cluster in gas phase, and in aqueous enzyme phase, has been investigated by means of quantum mechanics (QM) and combined quantum mechanics-molecular mechanics (QM/MM). Several potential reaction pathways (in the above mentioned chemical environments) have been studied, wherein only the aqueous enzyme phase has been found to lead to an inhibited hydroxylated cluster. Specifically, the inhibitory process occurs at the distal iron (Fed) of the catalytic H-cluster (which is also the atom involved in H2 synthesis). The processes involved in the H-cluster oxidative pathways are O2 binding, e- transfer, protonation, and H2O removal. We found that oxygen binding is non-spontaneous in gas phase, and spontaneous for aqueous enzyme phase where both Fe atoms have oxidation state II; however, it is spontaneous for the partially oxidized and reduced clusters in both phases. Hence, in the protein environment the hydroxylated H-cluster is obtained by means of completely exergonic reaction pathway starting with proton transfer. A unifying endeavor has been carried out for the purpose of understanding the thermodynamic results vis-à-vis several other performed electronic structural methods, such as frontier molecular orbitals (FMO), natural bond orbital partial charges (NBO), and H-cluster geometrical analysis. An interesting result of the FMO examination (for gas phase) is that an e- is transferred to LUMOα rather than to SOMOβ, which is unexpected because SOMOβ usually resides in a lower energy rather than LUMOα for open-shell clusters.

MetREx: A protein design approach for the exploration of sequence‐reactivity relationships in metalloenzymes

“…). It has been shown by theoretical prediction and experiment that Fe d is most likely the place of catalysis and plays a crucial role in O 2 ‐induced inhibition . In fact, coordination of O 2 to Fe d (see Fig.…”

O2 sensitivity and H2 production activity of hydrogenases—A review

“…The inactivation kinetics was first studied using PFV under numerous conditions with varying [O 2 ], [H 2 ], and/or redox potential (Goldet et al, ; Stripp et al, ; Vincent et al, ). The earlier work (Baffert et al, ; Dogaru, Motiu, & Gogonea, ; Goldet et al, ; Goris et al, ; Lambertz et al, ; Lautier et al, ; Stripp et al, ; Vincent et al, ) showed that [NiFe] and [FeFe] hydrogenases undergo inactivation at significantly different rates (Table ), which also go through unequal intermediate states (Figure a). The half‐life of the former in the air‐saturated buffer is in the order of tens of minutes while it is in the order of tens of seconds for the latter.…”

“…Infrared (IR) spectroscopy confirmed the formation of the O 2 ‐bound state within few hundreds of milliseconds (Bingham, ) while the degradation proceeded in the order of minutes (Bingham et al, ; Goldet et al, ; Koo & Swartz, ; Koo et al, ; Lambertz et al, ; Lautier et al, ; Orain et al, ; Swanson et al, ). A series of reactions are suspected to be involved in the degradation (Dogaru et al, ; Finkelmann, Stiebritz, & Reiher, ; Hong & Pachter, ; Kubas et al, ; Lambertz et al, ; Stiebritz & Reiher, ), with the end product being the hydrogenase lacking the 2Fe subcluster in the active site. Notably, the end product of the O 2 ‐driven [FeFe] hydrogenase inactivation is able to restore the enzymatic activity when incubated in vitro with maturation machinery, namely HydE, F, and G (Swanson et al, ).…”

Residue mutations in [FeFe]‐hydrogenase impedes O2 binding: A QM/MM investigation

“…Previous density functional theory (DFT) as well as hybrid quantum mechanics/molecular mechanics (QM/MM) calculations 1, 17–23 have been successful in clarifying some aspects of the catalytic properties of the H‐cluster. As in previous computational studies 1, 18, CH 3 S is substituted for cysteine, and a H + replaces the proximal cubane.…”