Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B

Abstract

Nitrogenase is the only enzyme that can convert N2 to NH3. Crystallographic structures have indicated that one of the sulfide ligands of the active‐site FeMo cluster, S2B, can be replaced by an inhibitor, like CO and OH−, and it has been suggested that it may be displaced also during the normal reaction. We have investigated possible proton transfer pathways within the FeMo cluster during the conversion of N2H2 to two molecules of NH3, assuming that the protons enter the cluster at the S3B, S4B or S5A sulfide ions and are then transferred to the substrate. We use combined quantum mechanical and molecular mechanical (QM/MM) calculations with the TPSS and B3LYP functionals. The calculations indicate that the barriers for these reactions are reasonable if the S2B ligand remains bound to the cluster, but they become prohibitively high if S2B has dissociated. This suggests that it is unlikely that S2B reversibly dissociates during the normal reaction cycle.

How Protons Move in Enzymes─The Case of Nitrogenase

“…The transition state for the straightforward proton transfer is shown in Figure . A rather large barrier of 15.6 kcal/mol was obtained in line with results obtained in the previous studies. − …”

The binding of reducible N2 in the reaction domain of nitrogenase

“…[77][78][79] S3B is the proposed delivery destination for protons transferred along the proton wire to FeMo-co, [80][81][82] and so S3B-H is included here as nascent H to be introduced into the reaction domain. QM/MM calculations by Ryde and coworkers indicate that S4B and S5A could be involved in proton transfer from the proton wire to FeMo-co. 83 There are variable conformations for H on S3B 52 but only the '3b2' conformation, in which the S3B-H bond is directed towards Fe6, is considered here. This same conformation of S3B-H occurs as an S3B-H-Fe6 bridge when H-Fe6 is in bonding range.…”

[4Fe–4S]-Mediated Proton-Coupled Electron Transfer Enables the Efficient Degradation of Chloroalkenes by Reductive Dehalogenases

“…However, only the ground states of the [4Fe–4S] 1+ and [4Fe–4S] 2+ species are involved in the present study, and the singlet ground state wavefunction of the [4Fe–4S] cluster from the broken-symmetry DFT (BS-DFT) has the same spin coupling pattern as that from DMRG-CASSCF . In addition, BS-DFT has been proven to be practical for studying catalytic reactions of metalloenzymes. ,− For example, recent work has shown that BS-DFT methods are reliable for the electronic structure of FeMoco in nitrogenase, as well as for redox potential calculations in iron–sulfur clusters . Unlike small model [4Fe–4S] clusters, ,− the current system with a large QM region (148 atoms) is challenging to study with MC-SCF methods.…”