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

Journal Article · Thu Mar 01 04:00:00 EST 2007 · Journal of Inorganic Biochemistry, 101(3):375-384

DOI:https://doi.org/10.1016/j.jinorgbio.2006.09.031· OSTI ID:1001565

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

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.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1001565
• Journal Information: Journal of Inorganic Biochemistry, 101(3):375-384, Journal Name: Journal of Inorganic Biochemistry, 101(3):375-384 Journal Issue: 3 Vol. 101; ISSN JIBIDJ; ISSN 0162-0134
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
ATOMS
DECAY
ELECTRON TRANSFER
EXCITATION
EXCITED STATES
Environmental Molecular Sciences Laboratory
FOURIER TRANSFORMATION
GROUND STATES
LASERS
NORMAL-MODE ANALYSIS
OSCILLATIONS
PROBES
PROTEINS
RELAXATION
RESONANCE
RUBREDOXIN
SPECTRA
SPECTROSCOPY
TIME DELAY