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Title: Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics

Abstract

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 of 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 ismore » 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

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1001565
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Inorganic Biochemistry, 101(3):375-384; Journal Volume: 101; Journal Issue: 3
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ATOMS; DECAY; ELECTRON TRANSFER; EXCITATION; EXCITED STATES; FOURIER TRANSFORMATION; GROUND STATES; LASERS; NORMAL-MODE ANALYSIS; OSCILLATIONS; PROBES; PROTEINS; RELAXATION; RESONANCE; RUBREDOXIN; SPECTRA; SPECTROSCOPY; TIME DELAY; Environmental Molecular Sciences Laboratory

Citation Formats

Tan, Ming-Liang, Bizzarri, Anna R., Xiao, Yuming, Cannistraro, Salvatore, Ichiye, Toshiko, Manzoni, Cristian, Cerullo, Giulio, Adams, Michael W., Jenney, Francis E., and Cramer, Stephen P.. Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics. United States: N. p., 2007. Web. doi:10.1016/j.jinorgbio.2006.09.031.
Tan, Ming-Liang, Bizzarri, Anna R., Xiao, Yuming, Cannistraro, Salvatore, Ichiye, Toshiko, Manzoni, Cristian, Cerullo, Giulio, Adams, Michael W., Jenney, Francis E., & Cramer, Stephen P.. Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics. United States. doi:10.1016/j.jinorgbio.2006.09.031.
Tan, Ming-Liang, Bizzarri, Anna R., Xiao, Yuming, Cannistraro, Salvatore, Ichiye, Toshiko, Manzoni, Cristian, Cerullo, Giulio, Adams, Michael W., Jenney, Francis E., and Cramer, Stephen P.. Thu . "Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics". United States. doi:10.1016/j.jinorgbio.2006.09.031.
@article{osti_1001565,
title = {Observation of Terahertz Vibrations in Pyrococcus Furiosus Rubredoxin Via Impulsive Coherent Vibrational Spectroscopy and Nuclear Resonance Vibrational Spectroscopy – Interpretation by Molecular Mechanics},
author = {Tan, Ming-Liang and Bizzarri, Anna R. and Xiao, Yuming and Cannistraro, Salvatore and Ichiye, Toshiko and Manzoni, Cristian and Cerullo, Giulio and Adams, Michael W. and Jenney, Francis E. and Cramer, Stephen P.},
abstractNote = {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 of 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.},
doi = {10.1016/j.jinorgbio.2006.09.031},
journal = {Journal of Inorganic Biochemistry, 101(3):375-384},
number = 3,
volume = 101,
place = {United States},
year = {Thu Mar 01 00:00:00 EST 2007},
month = {Thu Mar 01 00:00:00 EST 2007}
}