Differences in the dynamics of oxidized and reduced cytochrome c measured by Mössbauer spectroscopy

Frolov, E. N.; Gvosdev, R.; Gol’danskii, V.I.; Parak, F.

doi:10.1007/pl00010647

Cited by 23 publications

(37 citation statements)

References 15 publications

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“…Recalling some literature data, a wide band width of AEx 2 v ae slopes is found, e.g. iron in a heme plane yields values from 0.31·10 -4 Å 2 K -1 in reduced and 0.55·10 -4 Å 2 K -1 in oxidized cytochrome c [44] to 0.93·10 -4 Å 2 K -1 in deoxyhemoglobin [57]. Deoxymyoglobin is characterized by the value 0.94·10 -4 Å 2 K -1 [58].…”

Section: Discussionmentioning

confidence: 96%

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Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP

et al. 2002

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The temperature dependence of the mean square displacement of the (57)Fe nuclei due to motion faster than 100 ns are measured by temperature-dependent Mössbauer spectroscopy for oxidized and reduced HiPIPs from Ectothiorhodospira halophila, Chromatium vinosum WT and a Cys77Ser mutant. The behaviour is interpretable in the frame of the general model of protein dynamics distinguishing two temperature intervals. The character of harmonic and quasi-diffusional modes in HiPIPs is discussed. Dynamic information obtained from Mössbauer spectroscopy and Fe K-edge EXAFS are compared. Structure dynamics of the iron-sulfur cluster in the partially unfolded reduced HiPIP from C. vinosum was investigated by Mössbauer spectroscopy and EXAFS, indicating an intact metal centre and a protein backbone with a largely collapsed secondary structure. The role of the cofactor during protein folding is discussed. Differences in the dynamics between the native protein and the molten globule are found at physiological temperatures only. The structure and dynamic behaviour of the [Fe(4)S(4)]Cys(3)Ser cluster in the Cys77Ser mutant of the HiPIP from C. vinosum are analysed. The temperature dependence of electron relaxation in oxidized HiPIPs is investigated by Mössbauer spectroscopy and analysed theoretically, considering spin-spin and spin-lattice relaxation. The latter consists of contributions from direct phonon bottleneck and Orbach mechanisms. The data agree with former pulsed EPR results. Orbach relaxation is interpreted as due to transitions between electronic isomers of oxidized HiPIPs. With this interpretation, the energetic difference between both isomers equals the energy gap estimated from the temperature dependence of the Orbach relaxation.

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Section: Discussionmentioning

confidence: 96%

“…Above a characteristic temperature T C , a dramatic increase of AEx 2 ae has been found. This behaviour is typical for proteins [33,43,44,45]. In this temperature regime, additional broad lines have to be taken into account in order to obtain a satisfactory fit.…”

Section: Mo¨ssbauer Experimentsmentioning

confidence: 96%

Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP

et al. 2002

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“…Mössbauer spectroscopy may be used to measure the values of the electron density, the electric field gradient, and magnetic field of the iron atom in heme proteins, which can provide information about the symmetry and strength of the covalent bonds with the iron atom. (33,(73)(74)(75)(76)(77)(78)(79)(80)(81)(82) Previously published investigations (22,32,(83)(84)(85) also used Mössbauer spectroscopy to determine the Fe MSD…”

Section: Mean-squared Displacementsmentioning

confidence: 99%

“…Recent measurements yield varying results regarding the influence of oxidation state on the vibrational dynamics of cyt c. Mössbauer measurements on a bacterial cyt c suggest an increased Fe MSD upon oxidation (22), and THz measurements reveal increased absorption in the oxidized state (23). On the other hand, methyl C-D vibrations of the Met-80 ligand provide no indication that Fe oxidation affects the vibrational dynamics of the active site (24).…”

Section: Introductionmentioning

confidence: 99%

Resilience of the Iron Environment in Heme Proteins

Leu

Zhang

et al. 2008

Biophysical Journal

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Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.

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“…x 2 for the reduced state of Cyt-c. The points are experimental data36 and the solid lines are calculations according to Eqs. (1),(16), and(17).…”

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confidence: 99%

Ergodicity breaking of iron displacement in heme proteins

Seyedi

Matyushov

2017

Soft Matter

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We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.

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Differences in the dynamics of oxidized and reduced cytochrome c measured by Mössbauer spectroscopy

Cited by 23 publications

References 15 publications

Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP

Dynamics of wild-type HiPIPs: a Cys77Ser mutant and a partially unfolded HiPIP

Resilience of the Iron Environment in Heme Proteins

Ergodicity breaking of iron displacement in heme proteins

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