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Title: Normal mode analysis of pyrococcus furiosus rubredoxin via nuclearresonance vibrational spectroscopy (nrvs) and resonance ramanspectroscopy

Abstract

No abstract prepared.

Authors:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
COLLABORATION - Univeristy of California,Davis
OSTI Identifier:
893615
Report Number(s):
LBNL-61546
Journal ID: ISSN 0002-7863; JACSAT; R&D Project: 4499-10; TRN: US200625%%433
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Chemical Society; Journal Volume: 127; Journal Issue: 42; Related Information: Journal Publication Date: 2005
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; 60 APPLIED LIFE SCIENCES; NORMAL-MODE ANALYSIS; RAMAN SPECTROSCOPY; RESONANCE; RUBREDOXIN; SPECTROSCOPY

Citation Formats

Xiao, Yuming M., Wang, Hongxin, George, Simon J., Smith, Matt C., Adams, Michael W.W., Jenney, Frank E., Sturhahn, Wolfgang, Alp, Ercan E., Zhao, J.O., Yoda, Yoshitaka, Dey, A., Solomon, Edward I., and Cramer, StephenP. Normal mode analysis of pyrococcus furiosus rubredoxin via nuclearresonance vibrational spectroscopy (nrvs) and resonance ramanspectroscopy. United States: N. p., 2006. Web.
Xiao, Yuming M., Wang, Hongxin, George, Simon J., Smith, Matt C., Adams, Michael W.W., Jenney, Frank E., Sturhahn, Wolfgang, Alp, Ercan E., Zhao, J.O., Yoda, Yoshitaka, Dey, A., Solomon, Edward I., & Cramer, StephenP. Normal mode analysis of pyrococcus furiosus rubredoxin via nuclearresonance vibrational spectroscopy (nrvs) and resonance ramanspectroscopy. United States.
Xiao, Yuming M., Wang, Hongxin, George, Simon J., Smith, Matt C., Adams, Michael W.W., Jenney, Frank E., Sturhahn, Wolfgang, Alp, Ercan E., Zhao, J.O., Yoda, Yoshitaka, Dey, A., Solomon, Edward I., and Cramer, StephenP. Sun . "Normal mode analysis of pyrococcus furiosus rubredoxin via nuclearresonance vibrational spectroscopy (nrvs) and resonance ramanspectroscopy". United States. doi:.
@article{osti_893615,
title = {Normal mode analysis of pyrococcus furiosus rubredoxin via nuclearresonance vibrational spectroscopy (nrvs) and resonance ramanspectroscopy},
author = {Xiao, Yuming M. and Wang, Hongxin and George, Simon J. and Smith, Matt C. and Adams, Michael W.W. and Jenney, Frank E. and Sturhahn, Wolfgang and Alp, Ercan E. and Zhao, J.O. and Yoda, Yoshitaka and Dey, A. and Solomon, Edward I. and Cramer, StephenP.},
abstractNote = {No abstract prepared.},
doi = {},
journal = {Journal of the American Chemical Society},
number = 42,
volume = 127,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}
  • We have used {sup 57}Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S{sub cys})4 site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm{sup -1}; upon reduction these modes shift to 300-320 cm{sup -1}. This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at {approx}150 cm{sup -1} for the oxidized protein and only slightly lower in the reducedmore » case. A third band occurs near 70 cm{sup -1} for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The {sup 57}Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D{sub 2d} Fe(SC){sub 4} model. A C{sub 1} Fe(SCC){sub 4} model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant KFe-S for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/Angstrom. KFe-S is clearly diminished in reduced Rd; values from {approx}0.89 to 1.00 mdyn/Angstrom were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, HS-Fe-S, were 0.18 mdyn/Angstrom for oxidized Rd and 0.15 mdyn/Angstrom for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.« less
  • The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We have used impulsive coherent vibrational spectroscopy (ICVS) to study the Fe(S-Cys)4 site in oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). In this experiment, a 15 fs visible laser pulse is used to coherently pump the sample to an excited electronic state, and a second <10 fs pulse is used to probe the change in transmission as a function ofmore » the time delay. PfRd was observed to relax to the ground state by a single exponential decay with time constants of ~255–275 fs. Superimposed on this relaxation are oscillations caused by coherent excitation of vibrational modes in both excited and ground electronic states. Fourier transformation reveals the frequencies of these modes. The strongest ICV mode with 570 nm excitation is the symmetric Fe–S stretching mode near 310 cm⁻1, compared to 313 cm⁻1 in the low temperature resonance Raman. If the rubredoxin is pumped at 520 nm, a set of strong bands occurs between 20 and 110 cm⁻1. Finally, there is a mode at ~500 cm⁻1 which is similar to features near 508 cm⁻1 in blue Cu proteins that have been attributed to excited state vibrations. Normal mode analysis using 488 protein atoms and 558 waters gave calculated spectra that are in good agreement with previous nuclear resonance vibrational spectra (NRVS) results. The lowest frequency normal modes are identified as collective motions of the entire protein or large segments of polypeptide. Motion in these modes may affect the polar environment of the redox site and thus tune the electron transfer functions in rubredoxins.« less
  • We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and {sup 57}Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu){sub 4}N]{sub 2}[Fe{sub 4}S{sub 4}(SPh){sub 4}]. This [Fe{sub 4}S{sub 4}(SR){sub 4}]{sup 2-} complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with {sup 36}S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra weremore » interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after {sup 36}S substitution were used as an additional constraint. A D{sub 2d} symmetry Fe{sub 4}S{sub 4}S{sub 4} model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D{sub 2d} Fe{sub 4}S{sub 4}(SPh){sub 4} model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between 50 and 100 cm{sup -1} were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe{sub 4}S{sub 4} cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to rotational lattice modes. We also reassign the 430 cm{sup -1} band as primarily an elongation of the thiophenolate ring, with 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT theory is shown to provide remarkable agreement with the experimental NRVS data. These results provide a reference point for the analysis of more complex Fe-S clusters in proteins.« less
  • In this communication the authors present new experiments and theoretical simulations, using iron L-edge X-ray absorption spectroscopy, to study the metalloprotein Pyrococcus furiosus rubredoxin. the 3d transition metal L-edges are found between 400 and 1100 eV, in the soft X-ray region. Synchrotron radiation beam lines producing the high photon flux and high-energy resolution necessary to observe and resolve 3d transition metal L-edge spectra have only become available in the last few years. L-edge spectra are interesting not only because of the 3-4-fold-higher energy resolution (vs K-edges) but also for the sensitivity to spin state, oxidation state, and ligand field offeredmore » by p{r_arrow}d transitions. In addition, the X-ray magnetic circular dichroism (XMCD) of transition metal L-edges is predicted to be strong, and experiments have confirmed these predictions. 21 refs., 1 fig.« less