Characterization of the [3Fe–4S]^0/1+cluster from the D14C variant of Pyrococcus furiosus ferredoxin via combined NRVS and DFT analyses

Abstract

The D14C variant of Pyrococcus furiosus ferredoxin provides an extraordinary framework to investigate a [3Fe-4S] cluster at two oxidation levels and compare the results to its physiologic [4Fe-4S] counterpart in the very same protein. Our spectroscopic and computational study reveals vibrational property changes related to electronic and structural aspects of both Fe-S clusters.

On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase

“…For comparison with the NIS experiment, the Fe DOS values were simulated with the Q‐Spector program, which we obtained courtesy of Dr. Vladimir Pelmentschikov . Uniform Gaussian line broadening with full width at half maximum (FWHM)=14 cm −1 , which corresponds to the experimental energy resolution of 2 meV, was used to model DOS.…”

“…To this end, an initial model for a given stationary point was first optimised with the atomic charges for the QM region as for the preceding structure. [63,64] Uniform Gaussian line broadening with full width at half maximum (FWHM) = 14 cm À1 , which corresponds to the experimental energy resolution of 2meV,was used to model DOS. Finally,t he geometry was reoptimised with the new set of QM charges.…”

Insights from 125Te and 57Fe nuclear resonance vibrational spectroscopy: a [4Fe–4Te] cluster from two points of view

“…S6a vs. b†). Both Te/S chalcogenide alternatives display only minor (Te-variant) to moderate (S-variant) redox-dependent alterations in their spectra, where the S-variant behaves similar to the [4Fe–4S] +/2+ cofactor from ferredoxin characterized by 57 Fe-NRVS earlier 19,20. The major bands display blue shifts within 10 cm –1 upon oxidation, explained by +0.8/+1.5% larger volume of respectively the [4Fe–4Te/S] 1+ vs. [4Fe–4Te/S] 2+ cores (Table S3†).…”

“…For example, in the case of 57 Fe-enriched proteins, this allows one to select exclusively the normal modes involving the 57 Fe nuclei in a background of thousands of other vibrations involving the protein matrix. 57 Fe-NRVS has already been used to investigate a wide variety of Fe-containing proteins, including rubredoxins, ferredoxins,19,20 heme proteins,21 hydrogenases,22,23 dioxygenases,24 NO sensors, and nitrogenase 25…”

NRVS for Fe in Biology: Experiment and Basic Interpretation

“…Besides non-Rieske [2Fe2S] 22 and [3Fe4S] 23 proteins and [4Fe4S] 24 proteins, It is important to note that 57 Fe NRVS has been expanded to study electron transfer in larger enzymes and their catalytic metallocofactors such as (but not comprehensively) the NiFe site in [NiFe] hydrogenase, 3, 25–26 the diiron site in [FeFe] hydrogenase, 27–28 the P [8Fe7S]- and M [7Fe9SMo]- clusters of Mo-Nitrogenase, 29–32 heme systems, 33–34 non-heme systems, 35–36 and nitric-oxide sensing [4Fe4S] clusters. 37 Further as the systems of interest have become more complicated, with multiple FeS clusters of differing composition, innovative strategies of site-specific 57 Fe labeling have been implemented that target maturation 28 or a modified cofactor insertion.…”