Evidence for sub-picosecond heme doming in hemoglobin and myoglobin: a time-resolved resonance Raman comparison of carbonmonoxy and deoxy species

Franzen, Stefan; Bohn, B.; Poyart, C; Martin, Jean−Louis

doi:10.1021/bi00004a016

Cited by 112 publications

(146 citation statements)

References 59 publications

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“…very small) to those observed in Mb*CO, however, their sign is reversed. The changes in Mb structure upon photolysis can be divided conceptually into a distal and proximal component [43]. On the distal side, the protein structure must accommodate the photolyzed ligand in a docking site parallel to the heme plane.…”

Section: Spectral Changes Reflect Strain and Coupling Of Ligand And Pmentioning

confidence: 99%

Proximal ligand motions in H93G myoglobin

Franzen

Peterson

Brown

et al. 2002

European Journal of Biochemistry

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Resonance Raman spectroscopy has been used to observe changes in the iron-ligand stretching frequency in photoproduct spectra of the proximal cavity mutant of myoglobin H93G. The measurements compare the deoxy ferrous state of the heme iron in H93G(L), where L is an exogenous imidazole ligand bound in the proximal cavity, to the photolyzed intermediate of H93G(L)*CO at 8 ns. There are significant differences in the frequencies of the iron-ligand axial out-of-plane mode m(Fe-L) in the photoproduct spectra depending on the nature of L for a series of methylsubstituted imidazoles. Further comparison was made with the proximal cavity mutant of myoglobin in the absence of exogenous ligand (H93G) and the photoproduct of the carbonmonoxy adduct of H93G (H93G-*CO). For this case, it has been shown that H 2 O is the axial (fifth) ligand to the heme iron in the deoxy form of H93G. The photoproduct of H93G-*CO is consistent with a transiently bound ligand proposed to be a histidine. The data presented here further substantiate the conclusion that a conformationally driven ligand switch exists in photolyzed H93G-*CO. The results suggest that ligand conformational changes in response to dynamic motions of the globin on the nanosecond and longer time scales are a general feature of the H93G proximal cavity mutant.Keywords: resonance Raman, heme, myoglobin, hemoglobin, ligand switch.Protein structural relaxation following heme photolysis has been studied in globins as a means to obtain information on structural intermediates following diatomic ligand photolysis. In hemoglobin (Hb), time-resolved spectroscopic studies have provided information on the time scale for transition from the six-coordinate R state to the fivecoordinate T-state [1][2][3]. The proximal cavity mutant of Hb has recently demonstrated the key role of the proximal histidine in the cooperativity of quaternary structure change in response to ligand binding [4]. Strain in the covalent bond to the heme iron of Hb can be monitored by following the shift in frequency of the iron-histidine axial mode, m(FeHis), by time-resolved resonance Raman spectroscopy [5]. In myoglobin (Mb), these studies have indicated a much smaller change in structure [6]: the observed frequency shift of the iron-histidine band is c. 1.6 cm )1 on the 8 ns time scale compared to 12 cm )1 in Hb. Nonetheless, this shift in the m(Fe-His) Raman band is significant because shifts in absorption bands (the time-dependent Soret band shift and band III shift) have been attributed to iron out-of-plane displacement that should also be coupled to m(Fe-His) [7][8][9][10]. A structural interpretation of these observable phenomena helps to bridge the gap between the extensive X-ray crystallography studies and the thermodynamic and kinetic data available for Mb [7,[11][12][13][14][15][16][17][18][19][20].Histidine-ligated heme enzymes have a surprisingly large range of functions. In peroxidase, a charge relay due to hydrogen bonding of the imidazole ring of histidine permits the formation of high valent iro...

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Section: Spectral Changes Reflect Strain and Coupling Of Ligand And Pmentioning

confidence: 99%

Proximal ligand motions in H93G myoglobin

Franzen

Peterson

Brown

et al. 2002

European Journal of Biochemistry

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“…Because the CO-iron bonds in a Mb ensemble can be coherently photolysed with a laser flash within only 50 fs (4), a range of time-resolved techniques has been applied to probe various aspects of the structural dynamics after CO photodissociation, such as energy dissipation, CO dynamics, or heme doming (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). Three-dimensional movies of Mb conformational transitions were derived by means of time-resolved crystallography, which recently reached subpicosecond time resolution (16)(17)(18)(19).…”

mentioning

confidence: 99%

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Brinkmann

Hub

2016

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

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"Protein quake" denotes the dissipation of excess energy across a protein, in response to a local perturbation such as the breaking of a chemical bond or the absorption of a photon. Femtosecond timeresolved small-and wide-angle X-ray scattering (TR-SWAXS) is capable of tracking such ultrafast protein dynamics. However, because the structural interpretation of the experiments is complicated, a molecular picture of protein quakes has remained elusive. In addition, new questions arose from recent TR-SWAXS data that were interpreted as underdamped oscillations of an entire protein, thus challenging the long-standing concept of overdamped global protein dynamics. Based on molecular-dynamics simulations, we present a detailed molecular movie of the protein quake after carbon monoxide (CO) photodissociation in myoglobin. The simulations suggest that the protein quake is characterized by a single pressure peak that propagates anisotropically within 500 fs across the protein and further into the solvent. By computing TR-SWAXS patterns from the simulations, we could interpret features in the reciprocalspace SWAXS signals as specific real-space dynamics, such as CO displacement and pressure wave propagation. Remarkably, we found that the small-angle data primarily detect modulations of the solvent density but not oscillations of the bare protein, thereby reconciling recent TR-SWAXS experiments with the notion of overdamped global protein dynamics.time-resolved SAXS/WAXS | free-electron laser | molecular dynamics F unctional protein dynamics occur on various timescales, ranging from tens of femtoseconds for bond breaking, up to milliseconds and seconds for large-scale conformational transitions or protein folding. Observing and explaining such transitions, if possible in a time-resolved manner, has remained a central goal of molecular biophysics. A popular model system used to study proteins dynamics has been the 18-kDa protein myoglobin (Mb), the protein of first known tertiary structure (1). Mb contains an iron-porphyrin heme group that reversibly binds small gas molecules such as molecular oxygen (O 2 ) or carbon monoxide (CO). Mb is abundant in the muscle tissue of vertebrates, where it plays an important role in the transport and storage of O 2 and in the biochemistry of nitric oxide (2, 3).Because the CO-iron bonds in a Mb ensemble can be coherently photolysed with a laser flash within only 50 fs (4), a range of time-resolved techniques has been applied to probe various aspects of the structural dynamics after CO photodissociation, such as energy dissipation, CO dynamics, or heme doming (5-15). Three-dimensional movies of Mb conformational transitions were derived by means of time-resolved crystallography, which recently reached subpicosecond time resolution (16-19). These experimental studies were complemented by several pioneering molecular-dynamics (MD) simulations that revealed the Mb dynamics with atomic detail, with some focus on heat dissipation, vibrational dynamics, as well as ligand migration (20-28).Time-re...

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“…In the vicinity of an optical resonance the refractive index of the crystal is strongly frequency-dependent, causing a femtosecond light pulse (not monochromatic through the Heisenberg uncertainty principle) to broaden as it propagates through the crystal, a phenomenon encountered in near-femtosecond spectroscopy experiments (19)(20)(21)(22)(23)(24)(25)(26) that is compensated for optically by focusing the minimum pulse duration at the center of the sample. Hence, dispersion of the laser pulse should not significantly limit the potential temporal resolution in x-ray diffraction experiments.…”

Section: Physical Crystalmentioning

confidence: 99%

“…With the advent of the femtosecond pulsed laser, several beautiful ultra-fast spectroscopy experiments have been performed on small molecules (19)(20)(21) as well as on biologically important macromolecules (22)(23)(24)(25)(26). These experiments have opened a window through which the behavior of chemical and biological systems can be studied at time scales characteristic of transition-state life times.…”

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confidence: 99%

Femtosecond time resolution in x-ray diffraction experiments

Neutze

Hajdu

1997

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

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This paper presents the theoretical background for a synthesis of femtosecond spectroscopy and x-ray diffraction. When a diffraction quality crystal with 0.1-0.3 mm overall dimensions is photoactivated by a femtosecond laser pulse (physical length ‫؍‬ 0.3 m), the evolution of molecules at separated points in the crystal will not be simultaneous because a finite time is required for the laser pulse to propagate through the body of the crystal. Utilizing this lack of global crystal synchronization, topographic x-ray diffraction may enable femtosecond temporal resolution to be achieved from ref lection profiles in the diffraction pattern with x-ray exposures of picosecond or longer duration. Such x-ray pulses are currently available, and could be used to study femtosecond reaction dynamics at atomic resolution on crystals of both small-and macromolecules. A general treatment of excitation and diffraction geometries in relation to spatial and temporal resolution is presented.

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Evidence for sub-picosecond heme doming in hemoglobin and myoglobin: a time-resolved resonance Raman comparison of carbonmonoxy and deoxy species

Cited by 112 publications

References 59 publications

Proximal ligand motions in H93G myoglobin

Proximal ligand motions in H93G myoglobin

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Femtosecond time resolution in x-ray diffraction experiments

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