Investigations of Coherent Vibrational Oscillations in Myoglobin

Rosca, Florin; Kumar, Anand T. N.; Xiong, Yue; Sjodin, Theodore; Demidov, A.M.; Champion, P. M.

doi:10.1021/jp993617f

Cited by 101 publications

(167 citation statements)

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“…(9), using the masses of Cl or Br for m 2 . We use the appropriately averaged masses of two most abundant isotopes of Cl and Br: 35 Cl, 37 Cl, 79 Br, and 81 Br (all predictions for halide compounds considered in this paper depend very little on which of the above isotopes to use for halide). Similarly, the 0.79 frequency ratio observed for these features slightly exceeds the 0.65 ratio predicted 78 for the two-body oscillator.…”

Section: Experimental Analysis Of Porphine Halide Vibrationsmentioning

confidence: 99%

“…42,93 In particular, VCS reveals oscillations below 200 cm −1 strongly coupled to ligand dissociation reactions in heme proteins. 35,[37][38][39]42 Some of these have been plausibly associated with heme doming, but there is no direct evidence for involvement of the Fe. The VCS measurements on porphine halides reveal a 77 cm −1 oscillation whose frequency downshifts by 15 cm −1 upon substitution of Br for Cl, 42 similar to the 19 cm −1 shift of γ 9 determined using NRVS.…”

Section: B Characterization Of Reactive Modesmentioning

confidence: 99%

“…1) long believed to control biologically important reactions in heme proteins, such as cooperative oxygen binding in hemoglobin. [31][32][33] Far infrared measurements find vibrational signals in the frequency range expected for heme doming in iron porphyrins 34 and vibrational coherence spectroscopy (VCS) reveals low frequency molecular oscillations coupled to ligand binding reactions in heme proteins [35][36][37][38][39][40] and porphyrin model compounds. 41,42 However, these measurements do not exclude other vibrations that may appear in this frequency range, such as the FeCO distortion mode (in-phase bend/tilt) in iron carbonyl porphyrins [43][44][45] or other heme distortions that may control redox reactions.…”

Section: Introductionmentioning

confidence: 99%

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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: Experimental Analysis Of Porphine Halide Vibrationsmentioning

confidence: 99%

Section: B Characterization Of Reactive Modesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Spectroscopic identification of reactive porphyrin motions

Barabanschikov

Demidov

Kubo

et al. 2011

The Journal of Chemical Physics

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“…This kind of measurement integrates over all frequencies and results in better fidelity for the detection of low-frequency modes. 21,37 The "detuned" or "dispersed" detection scheme, on the other hand, leads to stronger relative enhancement of the higher frequency regions of the coherent signal. 21,[37][38][39] In this latter case, a photomultiplier tube (PMT) coupled to a monochromator was employed for detection, resulting in increased amplitude and superior detection of the higher frequency components of the third order polarization signal.…”

Section: Laser Systemmentioning

confidence: 99%

Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

et al. 2008

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Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm −1 ) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the lowfrequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above ~50 cm −1 and very weak activity below ~50 cm −1 . Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm −1 , while HRPCN displays a strong oscillation at higher frequency (96 cm −1 ) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays lowfrequency coherence spectra that contain strong modes near 30 and 80 cm −1 , probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm −1 that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T ≲ 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.

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“…Because of the advance of laser technology, there have been many experimental studies of VER in proteins (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). These experimental works are impressive, but it is difficult to derive detailed information from the experimental data alone.…”

mentioning

confidence: 99%

Vibrational energy relaxation in proteins

Fujisaki

Straub

2005

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

121

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An overview of theories related to vibrational energy relaxation (VER) in proteins is presented. VER of a selected mode in cytochrome c is studied by using two theoretical approaches. One approach is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach, which describes the protein as an ensemble of normal modes interacting through nonlinear coupling elements. Both methods result in similar estimates of the VER time (subpicoseconds) for a CD stretching mode in the protein at room temperature. The theoretical predictions are in accord with previous experimental data. A perspective on directions for the detailed study of time scales and mechanisms of VER in proteins is presented.W hen a protein is excited by ligand binding, ATP attachment, or laser pulses, vibrational energy relaxation (VER) occurs. Energy initially ''injected'' into a localized region flows to the rest of the protein and surrounding solvent. VER in large molecules (including proteins) is an important problem for chemical physics (1,2). Even more significant is the challenge to relate VER to fundamental reaction processes, such as a conformational change or electron transfer of a protein, associated with protein functions. The development of an accurate understanding of VER in proteins is an essential step toward the goal of controlling protein dynamics (3).Because of the advance of laser technology, there have been many experimental studies of VER in proteins (4-17). These experimental works are impressive, but it is difficult to derive detailed information from the experimental data alone. Theoretical approaches, including atomic-scale simulations, can provide more detailed information. In turn, experimental data can be used to refine simulation methods and empirical force fields. This combination of experimental and theoretical studies of protein structures and dynamics has begun to blossom. As experimental methods develop further and theoretical approaches grow in accuracy, the relationship will become fruitful.There have been many theoretical tools (see Theories) developed to analyze VER in proteins. Some aspects of VER in proteins can be explained by perturbative formulas based on the equilibrium condition of the bath (see Cyt c), but the use of the perturbative formulas may be too restrictive to describe protein dynamics generally at room temperature. In this article, we not only discuss the success of such established methods but also present a perspective on the study of VER in proteins. TheoriesIn this section, we present a selective overview of theories appropriate for the study of VER in proteins. For the most part, these theories have been developed to deal with VER in liquids, solids, or glasses. For recent reviews, see refs. 18-20. We refer to two distinct categories; one is based on equilibrium dynamics and Fermi's golden rule, whereas the other is based on nonequilibrium dynamical models.Fermi's Golden Rule. If (i) there is a clear separation between the system and bath, (...

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Investigations of Coherent Vibrational Oscillations in Myoglobin

Cited by 101 publications

References 77 publications

Spectroscopic identification of reactive porphyrin motions

Spectroscopic identification of reactive porphyrin motions

Coherence Spectroscopy Investigations of the Low-Frequency Vibrations of Heme: Effects of Protein-Specific Perturbations

Vibrational energy relaxation in proteins

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