Dynamics of the [ 4 Fe-4 S ] Cluster in Pyrococcus furiosus D 14 C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies , Force Field Simulations , and Density Functional Theory Calculations

Wehave used Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in theD14C variant ferredoxin fromPyrococcus furiosus (PfD14CFd). To assist the normal-mode assignments, we conductedNRVSwith D14C ferredoxin samples with S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph4P)2[Fe4S4Cl4]. Several distinct regions of NRVS intensity are identified, ranging from “protein” and torsional modes below 100 cm , through bending and breathingmodes near 150 cm , to strong bands from Fe S stretchingmodes between 250 and∼400 cm . The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy.We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe4S4] 2þ/þ redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe S proteins. I sulfur clusters are among the most common and ancient prosthetic groups in proteins. The [4Fe-4S] versions, Received: January 11, 2011 Revised: April 15, 2011