Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics

Tan, Ming-Liang; Bizzarri, Anna Rita; Xiao, Yuming; Cannistraro, Salvatore; Ichiye, Toshiko; Manzoni, Cristian; Cerullo, Giulio; Adams, Michael W. W.; Jenney, Francis E.; Cramer, Stephen P.

doi:10.1016/j.jinorgbio.2006.09.031

Cited by 16 publications

(21 citation statements)

References 52 publications

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“…By fitting the DT/T data with an exponential decay plus an offset, we found that the population of the electronic excited state decays with a time constant of roughly 200 fs. This time constant is similar to the 230-300 fs values recently observed in rubredoxin [27] and in a [2Fe-2S] ferredoxin, [31] suggesting that rapid nonradiative coupling between excited and ground states is a general characteristic of Fe-S chromophores.…”

supporting

confidence: 86%

“…To date, ICVS has been applied to the study of several biochemical systems, including heme proteins, [17][18][19] green fluorescent protein, [20] blue copper proteins such as azurin, [21] plastocyanin, [22][23][24][25] and umecyanin, [26] and the Fe(Cys) 4 site in the electrontransfer protein rubredoxin. [27] In our ICVS experiments, a benzenethiolate-treated FeMoco solution was pumped by 15 fs pulses centered at 450 nm, and probed by sub-10 fs pulses with a broadband spectrum spanning the 500-700 nm range. [28,29] Figure 1 a shows the steady-state absorption spectrum for this FeMoco solution, together with the spectra of the pump and probe pulses.…”

mentioning

confidence: 99%

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Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump–Probe Spectroscopy

et al. 2010

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Hochgepumpt: Die Dynamik des durch Resonanz‐Raman‐Spektroskopie nicht charakterisierbaren FeMo‐Cofaktors (siehe Bild) wurde nun mit kohärenter Puls‐Schwingungsspektroskopie als Sonde untersucht: Ein Laserpuls mit sichtbarem Licht (15 fs) pumpte die Probe in einen angeregten elektronischen Zustand, und ein zweiter Puls (<10 fs) untersuchte die Änderung in der Transmission als Funktion des Zeitabstands.

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confidence: 86%

mentioning

confidence: 99%

Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump–Probe Spectroscopy

et al. 2010

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“…By analogy with rubredoxin, below 100 cm −1 there will also be features involving motion of the Fe site with larger regions of protein [45].…”

Section: Hmd Nrvs Spectramentioning

confidence: 99%

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

et al. 2008

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We have used 57 Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur-cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO) 2 -ligated Fe model compound, Fe(S 2 C 2 H 4 )(CO) 2 (PMe 3 ) 2 , as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results.Previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm −1 , interpreted as evidence for cis-Fe(CO) 2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm −1 , consistent with the proposed cis-Fe(CO) 2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at ~311 cm −1 , and another reproducible feature at ~380 cm −1 . The 57 Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a 5-coordinate cis-(CO) 2 -ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a 3-dimensional structure for the active site.

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“…Techniques to access this energy range include neutron scattering, Raman/Brillouin scattering, Mössbauer scattering and far infrared (FIR) or THz spectroscopy. Mössbauer scattering can have limited application, because it requires a Mössbauer active isotope, usually 57 Fe, and reports on those motions that include the motion of this atom (Achterhold et al 2002;Tan et al 2007;Xiao et al 2005). Recently, there have been reports of global correlated motion measurements using inelastic scattering techniques (Biehl et al 2008;Liu et al 2008;Rheinstadter et al 2009).…”

Section: Challenges To Measuring Long-range Vibrationsmentioning

confidence: 99%

Terahertz optical measurements of correlated motions with possible allosteric function

Niessen

Markelz

2015

Biophys Rev

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A suggested mechanism for allosteric response is the distortion of the energy landscape with agonist binding changing the protein structure's access to functional configurations. Intramolecular vibrations are indicative of the energy landscape and may have trajectories that enable functional conformational change. Here, we discuss the development of an optical method to measure the intramolecular vibrations in proteins, namely, crystal anisotropy terahertz microscopy, and the various approaches which can be used to identify the spectral data with specific structural motions.

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Observation of terahertz vibrations in Pyrococcus furiosus rubredoxin via impulsive coherent vibrational spectroscopy and nuclear resonance vibrational spectroscopy – interpretation by molecular mechanics

Cited by 16 publications

References 52 publications

Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump–Probe Spectroscopy

Observation of Terahertz Vibrations in the Nitrogenase FeMo Cofactor by Femtosecond Pump–Probe Spectroscopy

Characterization of the Fe Site in Iron−Sulfur Cluster-Free Hydrogenase (Hmd) and of a Model Compound via Nuclear Resonance Vibrational Spectroscopy (NRVS)

Terahertz optical measurements of correlated motions with possible allosteric function

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