The effect of pH and hydrogen-deuterium exchange on the heme pocket structure of cytochrome c probed by resonance Raman spectroscopy

Döpner, Susanne; Hildebrandt, Peter; Heibel, George E.; Vanhecke, F.; Mauk, A. Grant

doi:10.1016/0022-2860(95)08725-b

Cited by 5 publications

(9 citation statements)

References 7 publications

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“…Preliminary SEIRA experiments monitoring the amide I band changes indicated that a complete H/D exchange requires incubation times for more than 24 h which is consistent with previous studies revealing a wide dynamic range for the substitution of the exchangeable protons [61,62]. Here we have chosen two different protocols for the H/D exchange.…”

Section: Kinetic Isotope and Viscosity Effects Of The Apparent Electrsupporting

confidence: 82%

Electric-field effects on the interfacial electron transfer and protein dynamics of cytochrome c

Wisitruangsakul

Sezer

et al. 2011

Journal of Electroanalytical Chemistry

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Section: Kinetic Isotope and Viscosity Effects Of The Apparent Electrsupporting

confidence: 82%

Electric-field effects on the interfacial electron transfer and protein dynamics of cytochrome c

Wisitruangsakul

Sezer

et al. 2011

Journal of Electroanalytical Chemistry

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“…This interpretation would imply that 15 is much more sensitive to changes of this deformation than 4 (we estimated a 'sensitivity enhancement' of 1.8 by using Eqn (18) However, the deformations derived from X-ray structures as well as from the MDS discussed below, and a comparison with earlier studies on the effect of nonplanar deformations on depolarization ratios 23,45 suggest that only the combination of the dominant deformations ruffling and saddling (B 1u and B 2u ) would have an impact, but this would give rise to antisymmetric scattering, which is detectable only with Q-band excitation. The results of Lemke et al 44 further suggest that this effect might be more likely for low-wavenumber modes and that a similar perturbation could be responsible for the large depolarization ratio variations of 15 . 17 However, this variation of the electronic perturbation is unlikely to have a big affect on depolarization ratios, which mostly reflect vibronic perturbations.…”

Section: Intensities and Depolarization Ratios Of In-plane And Periphmentioning

confidence: 94%

“…17,24 Another peculiarity of the low-wavenumber spectra of ferrocytochrome c derivatives is the rather strong intensity of the B 1g -type mode, 15 . Changes of substituent orientations can vary ip deformations, but the depolarization ratios of the 4 -mode (data not shown) of hhc (0.18) and yc (0.15) indicate that rhombic B 1g -deformations are smaller in yc than in hhc.…”

Section: Intensities and Depolarization Ratios Of In-plane And Periphmentioning

confidence: 99%

“…17,24 Another peculiarity of the low-wavenumber spectra of ferrocytochrome c derivatives is the rather strong intensity of the B 1g -type mode, 15 . These values clearly suggest that the large intensity of 15 is actually produced by Franck-Condon coupling. 49 As shown in Fig.…”

Section: Intensities and Depolarization Ratios Of In-plane And Periphmentioning

confidence: 99%

“…13 However, crystal structures are not available for all relevant ligation, spin and redox states of a given heme protein, and heme structures extracted from molecular dynamics simulations (MDS) have, accordingly, been subject to NSD analysis (e.g. 15,16 Finally, it is not yet clear whether the X-ray structure, affected by crystal packing effects or crystallization conditions, really represents the dynamic average structure in solution. 14 Moreover, the modification of heme deformations by the change of solution conditions (pH, ionic strength and viscosity) can generally not be explored by X-ray crystallography, which is a particularly important issue for ferricytochrome c, for which the structure of the heme cavity is rather pH dependent.…”

Section: Introductionmentioning

confidence: 99%

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Out‐of‐plane deformations of the heme group in different ferrocytochrome c proteins probed by resonance Raman spectroscopy

Hagarman

Wallace

Laberge

et al. 2008

J Raman Spectroscopy

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We measured the low-wavenumber polarized resonance Raman spectra of horse heart (hhc), chicken (chc) and yeastC102T (yc) ferrocytochromes c with Soret excitation. We examined the out-of-plane (oop) deformations of the heme groups by virtue of relative intensities and depolarization ratios of a variety of oop and in-plane (ip) Raman active bands. Analysis of relative Raman intensities shows differences in deviation from planarity of the heme groups of yeast, horse heart and chicken cytochromes c. The heme groups in cytochrome c proteins have been shown by normal coordinate static deformation (NSD) analysis from crystal structures to exhibit a dominant ruffling (B 1u ) deformation. As a consequence the B 1u modes, g 10 − g 12 , become resonance Raman active. We used normalized Raman intensity ratios and depolarization ratios of oop Raman active modes, whose intensities are attributable to specific nonplanar deformations, to estimate and compare their Franck-Condon-type and Jahn-Teller-type coupling magnitudes for horse heart, chicken and yeast ferrocytochrome c at neutral pH. These coupling magnitudes allow for a quantitative comparison of oop deformations between individual heme groups. Chicken ferrocytochrome was found to have the largest ruffling deformation of the three investigated proteins, followed by horse heart and yeast cytochrome c. The heme group of the former is slightly more ruffled than the corresponding active site of the latter, while saddling in both proteins is substantially larger than in chicken ferrocytochrome c. The Raman data are sensitive enough to allow a comparison of lesser deformations. Doming, which is a kinetic coordinate in many heme proteins, is largest in chicken and smallest in yeast cytochrome c. Waving is largest in yeast, followed by horse heart and chicken cytochrome c. Propellering deformations could be compared for chicken and horse heart cytochrome c and were found to be substantially larger in the latter. A comparison with heme deformations obtained from X-ray structures (for horse heart and yeast cytochrome c) and from molecular dynamics simulations (MDS) (performed for all three proteins) yields some agreement with the main ruffling and saddling deformations derived from the crystal structures, whereas the heme conformations produced by MDS seem to account better for smaller deformations like doming and propellering. The present study demonstrates the usefulness of resonance Raman spectroscopy for the analysis of nonplanar deformations in heme proteins.

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Analysis of vibrational spectra of multicomponent systems. Application to pH-dependent resonance Raman spectra of ferricytochrome c

Döpner

Hildebrandt

Mauk

et al. 1996

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

105

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The effect of pH and hydrogen-deuterium exchange on the heme pocket structure of cytochrome c probed by resonance Raman spectroscopy

Cited by 5 publications

References 7 publications

Electric-field effects on the interfacial electron transfer and protein dynamics of cytochrome c

Electric-field effects on the interfacial electron transfer and protein dynamics of cytochrome c

Out‐of‐plane deformations of the heme group in different ferrocytochrome c proteins probed by resonance Raman spectroscopy

Analysis of vibrational spectra of multicomponent systems. Application to pH-dependent resonance Raman spectra of ferricytochrome c

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