Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

Abstract

We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO) 2 -ligated Fe model compound, Fe(S 2 C 2 H 4 )(CO) 2 (PMe 3 ) 2 , as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results.Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm −1 , interpreted as evidence for cis-Fe(CO) 2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm −1 , consistent with the proposed cis-Fe(CO) 2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm −1 , and another reproducible feature at ~380 cm −1 . The 57 Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO) 2 -ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site.

Hydrogen-activating models of hydrogenases

“…[4,[27][28]71]. Some selected examples are shown in Figure 2, and several of them have very similar structure with the [Fe]-hydrogenase [72][73][74][75][76][77][78][79]. However, until now, none of the [Fe]-hydrogenase models can activate H 2 , even those structurally very similar to the enzyme.…”

Heme-protein vibrational couplings in cytochrome c provide a dynamic link that connects the heme-iron and the protein surface

“…3. The deviation is too large to simply use the DFT result to analyze/assign the experimental spectra by comparison, which has become a common practice in the literature (18,19). However, the deviation between the DFT and experimental NRVS data can be resolved by QCC-NCA simulations, a procedure that allows for the stepwise and systematic optimization of the DFT-calculated force field to reproduce the vibrational energies, isotope shifts, and NRVS intensities of the experimental spectrum (20).…”

Structure and Function of [Fe]‐Hydrogenase and its Iron–Guanylylpyridinol (FeGP) Cofactor

“…The structure of the FeGP cofactor is described in detail below. [6][7][8][9][10] Figure 1. The reaction catalyzed by [Fe]-hydrogenase (H 2 -forming methylenetetrahydromethanopterin dehydrogenase, Hmd).…”