ic7b02158_si_001.pdf (4.42 MB)
QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site
journal contribution
posted on 2017-10-20, 19:19 authored by Bardi Benediktsson, Ragnar BjornssonNitrogenase is one
of the most fascinating enzymes in nature, being responsible for all
biological nitrogen reduction. Despite decades of research, it is
among the enzymes in bioinorganic chemistry whose mechanism is the
most poorly understood. The MoFe protein of nitrogenase contains an
iron–molybdenum–sulfur cluster, FeMoco, where N2 reduction takes place. The resting state of FeMoco has been
characterized by crystallography, multiple spectroscopic techniques,
and theory (broken-symmetry density functional theory), and all heavy
atoms are now characterized. The cofactor charge, however, has been
controversial, the electronic structure has proved enigmatic, and
little is known about the mechanism. While many computational studies
have been performed on FeMoco, few have taken the protein environment
properly into account. In this study, we put forward QM/MM models
of the MoFe protein from Azotobacter vinelandii, centered on FeMoco. By a detailed analysis of the FeMoco geometry
and comparison to the atomic resolution crystal structure, we conclude
that only the [MoFe7S9C]1– charge is a possible resting state charge. Further, we find that
of the three lowest energy broken-symmetry solutions of FeMoco, the
BS7-235 spin isomer (where 235 refers to Fe atoms that are “spin-down”)
is the only one that can be reconciled with experiment. This is revealed
by a comparison of the metal–metal distances in the experimental
crystal structure, a rare case of spin-coupling phenomena being visible
through the molecular structure. This could be interpreted as the
enzyme deliberately stabilizing a specific electronic state of the
cofactor, possibly for tuning specific reactivity on specific metal
atoms. Finally, we show that the alkoxide group on the Mo-bound homocitrate
must be protonated under resting state conditions, the presence of
which has implications regarding the nature of FeMoco redox states
as well as for potential substrate reduction mechanisms.