Determination of the phonon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation

Keppler, C.; Achterhold, Klaus; Ostermann, Andreas; Bürck, U. van; Potzel, W.; Chumakov, A. I.; Baron, Alfred Q. R.; Rüffer, R.; Parak, F.

doi:10.1007/s002490050034

Cited by 50 publications

(33 citation statements)

References 15 publications

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“…vestigate the vibrational dynamics of 57 Fe in protein active sites 9,[14][15][16][17][18][19][20][21][22] and in small molecules. 11,[23][24][25][26][27][28][29][30] Since the use of NRVS to measure low frequency vibrations is restricted only by the experimental resolution (∼10 cm −1 ), it provides an important opportunity to characterize thermally excitable reactive modes.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic identification of reactive porphyrin motions

Barabanschikov

Demidov

Kubo

et al. 2011

The Journal of Chemical Physics

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Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, 57 Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.

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Section: Introductionmentioning

confidence: 99%

Spectroscopic identification of reactive porphyrin motions

Barabanschikov

Demidov

Kubo

et al. 2011

The Journal of Chemical Physics

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“…NRVS achieves the ultimate goal in selectivity, by targeting a single atom in a complex molecule. This method is particularly promising for characterizing the vibrational dynamics of 57 Fe in biological macromolecules [11,15,21,22,[25][26][27], and in small molecules designed to model protein active sites [16,19,20,24,28].…”

Section: Introductionmentioning

confidence: 99%

“…Measurements on oriented samples, such as single crystals, also yield the direction of vibrational motions [10,12,14,18,23,20,26,28]. Other names used for this technique include phonon assisted Mössbauer effect [21,22,25,26], inelastic X-ray scattering of synchrotron radiation [11], nuclear inelastic scattering [18], nuclear inelastic absorption [9], and nuclear resonant inelastic X-ray scattering [29].…”

Section: Introductionmentioning

confidence: 99%

Vibrational dynamics of biological molecules: Multi-quantum contributions

Leu

Zgierski

Wyllie

et al. 2005

Journal of Physics and Chemistry of Solids

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High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of 57 Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.

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“…There have thus been numerous experimental studies of the molecular vibrations in heme and heme-related chromophores. These studies have included resonance Raman (12,13), femtosecond coherence spectroscopy (14), and inelastic x-ray scattering with synchrotron radiation (10,11). The theoretical studies include molecular dynamics (2) as well as density functional theory (DFT) geometry and force field studies (15)(16)(17)(18)(19), calculated resonance Raman (18), and IR intensities (19).…”

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confidence: 99%

Doming modes and dynamics of model heme compounds

Klug

Zgierski

Tse

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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Synchrotron far-IR spectroscopy and density-functional calculations are used to characterize the low-frequency dynamics of model heme FeCO compounds. The ''doming'' vibrational mode in which the iron atom moves out of the porphyrin plane while the periphery of this ring moves in the opposite direction determines the reactivity of oxygen with this type of molecule in biological systems. Calculations of frequencies and absorption intensities and the measured pressure dependence of vibrational modes in the model compounds are used to identify the doming and related normal modes.

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Determination of the phonon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation

Cited by 50 publications

References 15 publications

Spectroscopic identification of reactive porphyrin motions

Spectroscopic identification of reactive porphyrin motions

Vibrational dynamics of biological molecules: Multi-quantum contributions

Doming modes and dynamics of model heme compounds

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