Dynamics of Rhodobacter capsulatus [2FE-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy.
We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(2)S(2)(Cys)(4) sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm(-1), and additional features observed as high as the B(2u) mode at approximately 421 cm(-1). Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B(3u) mode at approximately 288 cm(-1), attributed to an asymmetric combination of the two FeS(4) breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS(4) breathing. NRVS and RR analysis of isotope shifts with (36)S-substituted into bridging S(2-) ions in Rc FdVI allowed quantitation of S(2-) motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at approximately 190 cm(-1) in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields. Progressively more complex D(2h) Fe(2)S(2)S'(4), C(2h) Fe(2)S(2)(SCC)(4), and C(1) Fe(2)S(2)(Cys)(4) models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated for analysis of data on the reduced FdVI. Finally, the degree of collectivity was used to quantitate the delocalization of the dynamic properties of the redox-active Fe site. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.
Department of Applied Science, University of California, Davis, California 95616, USA.
Yuming
Y
Xiao
Ming-Liang
ML
Tan
Toshiko
T
Ichiye
Hongxin
H
Wang
Yisong
Y
Guo
Matt C
MC
Smith
Jacques
J
Meyer
Wolfgang
W
Sturhahn
Ercan E
EE
Alp
Jiyong
J
Zhao
Yoshitaka
Y
Yoda
Stephen P
SP
Cramer
D000465:Algorithms; D001419:Bacteria / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry*; D005288:Ferredoxins / Q000737:chemistry*; D007501:Iron / Q000737:chemistry; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011487:Protein Conformation; D016354:Rhodobacter capsulatus / Q000378:metabolism; D013057:Spectrum Analysis / Q000379:methods*; D013059:Spectrum Analysis, Raman / Q000379:methods*; D013455:Sulfur / Q000737:chemistry; D014732:Vibration
C081714:2Fe-2S ferredoxin; D001426:Bacterial Proteins; D005288:Ferredoxins; D013455:Sulfur; D007501:Iron