Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations

作者：Mitra Devrani; Pelmenschikov Vladimir; Guo Yisong; Case David A; Wang Hongxin; Dong Weibing; Tan Ming Liang; Ichiye Toshiko; Jenney Francis E Jr; Adams Michael W W; Yoda Yoshitaka; Zhao Jiyong; Cramer Stephen P^*

来源：Biochemistry, 2011, 50(23): 5220-5235.

DOI：10.1021/bi200046p

We have used Fe-57 nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (PfD14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with S-36 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(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and similar to 400 cm(-1). 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-57 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 PfFd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe4S4](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

• 出版日期2011-6-14
• 单位rutgers