Characterization of [4Fe-4S] Cluster Vibrations and Structure in Nitrogenase Fe Protein at Three Oxidation Levels via Combined NRVS, EXAFS, and DFT Analyses

• Published in: Journal of the American Chemical Society 2013-02, Vol.135 (7), p.2530-2543
• Main Authors: Mitra, Devrani, George, Simon J, Guo, Yisong, Kamali, Saeed, Keable, Stephen, Peters, John W, Pelmenschikov, Vladimir, Case, David A, Cramer, Stephen P
• Format: Article
• Language: English
• Subjects: Azotobacter vinelandii; Fourier Analysis; iron; Models, Molecular; nitrogenase; oxidation; Oxidation-Reduction; Oxidoreductases - chemistry; Quantum Theory; Raman spectroscopy; Vibration
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/ja307027n

Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10–30 cm–1 decrease in Fe–S stretching frequencies with each added electron. The “oxidized” [4Fe-4S]2+ state spectrum is consistent with and extends previous resonance Raman spectra. For the “reduced” [4Fe-4S]1+ state in Fe protein, and for any “all-ferrous” [4Fe-4S]0 cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe–S and Fe–Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe–Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å–1 indicates a 1:1 ratio of Fe–Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe–S and Fe–Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.