Bioinorganic Structure/Function of Complex Fe-S clusters
We made considerable progress in the understanding of the electronic structure and
the composition of the catalytically active, iron-sulfur cluster (H-cluster) of FeFe-hydrogenase.
In our 2006 paper in Chemical Communication  we provided experimental evidence
from sulfur K-edge X-ray absorption spectroscopy (XAS) that the nature of the unique
dithiolate ligand is crucial for tuning the electronic structure of the H-cluster
via Fe-S bond covalency and thus modulating its redox potential. From a comparative
spectroscopic analysis and supporting density functional calculations employing a
non-truncated computational model, we showed that the Hcluster is an electronically
inseparable 6Fe cluster and not just a 2Fe cluster as represented in the literature.
Independently from us, recent advanced EPR studies also came to the same conclusion.
Focusing on the chemical composition of the unique dithiolate ligand, as one of the
last unknown yet crucial structural feature of the H-cluster, we reported in our JACS
2008 paper  an unbiased computational analysis of the H-cluster using a close to
atomic resolution structure of the FeFe-hydrogenase metalloenzyme from Clostridium
pasteurianum in collaboration with the Peters Group at the Department. Contrary to
dithiomethylamine which is the currently favored composition in literature, we found
that a dithiomethylether composition is more likely. Importantly, we also found that
regardless of the composition, the bridge-head group cannot act as a catalytic base.
Its protonated state favors an alternative conformation that has not been observed
in any structural studies. This conformation effectively shuts down the proton transfer
to or from the active site, which is prohibitive if the approximately 9000 molecules
of H2 per second per each hydrogenase enzyme turnover rate is considered.
Furthermore, using a computational chemical approach in our FEBS Letter  we proposed a plausible mechanism for the biosynthesis of the H-cluster. We showed that upon a single hydrogen abstraction from a free glycine amino acid by an S-adenosylmethionine (SAM) radical metalloenzyme, which is a known biochemical process, the glycine radical can spontaneously decompose at a reduced Fe(I) site to CO, CN-, and H2O with the release of two electrons and four protons. These are the ligands of the iron Fe(I) sites in a catalytically active subcluster. Using follow up biochemical studies from the Peters and Broderick groups at the Department, we were able to extend these studies into the biosynthesis of the dithiolate ligand as well . In a parallel study we have rigorously evaluate the role of the dithiolate ligand composition in the electron and spin density distribution of the H-cluster from various angles, and found only limited indication for the dithiolate bridgehead group being involved in any covalent interaction within the cluster.
Another important contribution by our group is the completion of - as one of the reviewers put it - an exhaustive and exhausting study on the chemical composition, charge-, protonation-, and spin-state of the catalytic active cluster, FeMo-co of Mo-nitrogenase . In an unbiased approach we have put all the experimental data from the literature onto the table and evaluated using a spectroscopically validated level of theory and a reasonable computational model. The relative spin state energies of resting and oxidized FeMo-co already allowed exclusion of certain iron oxidation state distributions and interstitial ligand compositions. Geometry-optimized FeMo-co structures of several models further eliminated additional states and compositions, while reduction potentials indicated a strong preference for the most likely charge state of FeMo-co. Mosssbauer and ENDOR parameter calculations were found to be remarkably dependent on the employed training set, density functional, and basis set. Overall, we found that a more oxidized [MoIV-2FeII-5FeIII-9S2â€“-C4â€“] composition with a hydroxyl-protonated homocitrate ligand satisfies all of the available experimental criteria and is thus favored over the currently preferred composition of [MoIV-4FeII-3FeIII-9S2â€“-N3â€“] from the literature.
- Schwab D.E., Tard C., Brecht E., Peters J.W., Pickett C.J., Szilagyi R.K.:, "On the electronic structure of the hydrogenase H-cluster." Chemical Communication, 2006, (35), 3696-3698
- Pandey A.S., Harris T.V., Giles L.J., Peters J.W., Szilagyi R.K.: , "Dithiomethylether as a Ligand in the Hydrogenase H-Cluster." Journal of the American Chemical Society, 2008, 130(13), 4533-4540
- Peters J.W., Szilagyi R.K., Naumov A., Douglas T. , "A radical solution for the biosynthesis of the H-cluster of hydrogenase." FEBS Letters, 2006, 580(2), 363-367
- Grigoropoulos A., Szilagyi R.K:, "Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster." Journal of Biological Inorganic Chemistry, 2010, 15(8), 1177-1182
- Giles L.J., Grigoropoulos A., Szilagyi R.K.: , "Electron and Spin Density Topology of the H-Cluster and Its Biomimetic Complexes." European Journal of Inorganic Chemistry, 2011, 2011(17), 2677-2690
- Harris T.V., Szilagyi R.K.:, "Comparative Assessment of the Composition and Charge State of Nitrogenase FeMo-Cofactor." Inorganic Chemistry, 2011, 50(11), 4811-4824
Structure, Spectroscopy, Physical, Mechanism, Inorganic, Computational, Biophysical, Bioinorganic