title: 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.
abstract: We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. 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 ∼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 (57)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 [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
authors.affiliation: Department of Applied Science, University of California , Davis, CA 95616, USA.
authors.forename: Devrani
authors.initials: D
authors.lastname: Mitra
authors.forename: Vladimir
authors.initials: V
authors.lastname: Pelmenschikov
authors.forename: Yisong
authors.initials: Y
authors.lastname: Guo
authors.forename: David A
authors.initials: DA
authors.lastname: Case
authors.forename: Hongxin
authors.initials: H
authors.lastname: Wang
authors.forename: Weibing
authors.initials: W
authors.lastname: Dong
authors.forename: Ming-Liang
authors.initials: ML
authors.lastname: Tan
authors.forename: Toshiko
authors.initials: T
authors.lastname: Ichiye
authors.forename: Francis E
authors.initials: FE
authors.lastname: Jenney
authors.forename: Michael W W
authors.initials: MW
authors.lastname: Adams
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Yoda
authors.forename: Jiyong
authors.initials: J
authors.lastname: Zhao
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Cramer
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D005288:Ferredoxins / Q000737:chemistry* / Q000378:metabolism; D007501:Iron / Q000737:chemistry* / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010084:Oxidation-Reduction; D020027:Pyrococcus furiosus / Q000378:metabolism*; D013059:Spectrum Analysis, Raman; D013455:Sulfur / Q000737:chemistry* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005288:Ferredoxins; D013455:Sulfur; D007501:Iron