Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Laberge, Monique; Vreugdenhil, Andrew J.; Vanderkooi, Jane M.; Butler, Ian S.

doi:10.1080/07391102.1998.10508999

Cited by 15 publications

(14 citation statements)

References 42 publications

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“…1 and Fig. 8, bottom), previously shown to be sensitive to pyrrole twisting (Laberge et al, 1998) and the ZN-NC-C1C-C2C and ZN-NB-C4B-C3B dihedrals (not shown), as well as other markers of out-of-plane and in-plane distortions known to be typical of the cytochrome c heme distortion (Jentzen et al, 1997). All such plots showed that the specific cytochrome c heme distortion is maintained throughout the trajectories.…”

Section: Discussionmentioning

confidence: 61%

Sampling Field Heterogeneity at the Heme of c-Type Cytochromes by Spectral Hole Burning Spectroscopy and Electrostatic Calculations

Laberge

Köhler

Vanderkooi

et al. 1999

Biophysical Journal

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We report on a comparative investigation of the heme pocket fields of two Zn-substituted c-type cytochromes-namely yeast and horse heart cytochromes c-using a combination of hole burning Stark spectroscopy and electrostatic calculations. The spectral hole burning experiments are consistent with different pocket fields experienced at the hemes of the respective cytochromes. In the case of horse heart Zn-cytochrome c, two distinguishable electronic origins with different electrostatic properties are observed. The yeast species, on the other hand, displays a single electronic origin. Electrostatic calculations and graphics modeling using the linearized finite-difference Poisson-Boltzmann equation performed at selected time intervals on nanosecond-molecular dynamics trajectories show that the hemes of the respective cytochromes sample different potentials as they explore conformational space. The electrostatic potentials generated by the protein matrix at the heme show different patterns in both cytochromes, and we suggest that the cytochromes differ by the number of "electrostatic substates" that they can sample, thus accounting for the different spectral populations observed in the two cytochromes.

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Section: Discussionmentioning

confidence: 61%

Sampling Field Heterogeneity at the Heme of c-Type Cytochromes by Spectral Hole Burning Spectroscopy and Electrostatic Calculations

Laberge

Köhler

Vanderkooi

et al. 1999

Biophysical Journal

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“…Essentially, as the solvent matrix freezes, it is expected that a greater number of subconformations will be frozen out, and thus there will be significant inhomogeneous broadening at low temperatures. We also mention that it has been suggested in resonance Raman and molecular dynamics studies that a sixth ligand to Fe in MP-11 is water . Any axial ligand with a large permanent dipole moment might be expected to act together with the axial histidine to produce a large electric field gradient across the heme.…”

Section: Discussionmentioning

confidence: 93%

“…We point out that the absence of any splitting in the Q(0,0) band of MP-11 may still be consistent with a significant heme distortion. Studies have shown that the distortion in MP-11 is similar to that of the parent HH cyt c , although there is a greater degree of motional freedom. It is thus possible that as the temperature is lowered, a random distribution of many heme conformations is “frozen” in place.…”

Section: Influence Of Heme Distortion On the Q(00) Splittingmentioning

confidence: 97%

The Effects of Protein Environment on the Low Temperature Electronic Spectroscopy of Cytochrome c and Microperoxidase-11

1999

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Low temperature UV-visible spectra of cytochrome c and microperoxidase-11 are studied experimentally and theoretically using quantum chemical and Poisson−Boltzmann electrostatics models. Spectral splitting in the Q(0,0) visible absorption band is observed at low temperature (<180 K) in all cytochromes c studied. The Q-band is also found to be blue-shifted with decreasing temperature for cytochrome c and microperoxidase-11. Variations in the energy and splitting of the Q-band are interpreted in terms of heme distortions and interactions of the heme charge distribution with the internal electric field of the heme pocket, generated by charged and polar groups in the protein. The temperature dependence of the spectra is interpreted in terms of coupling of the heme electronic transitions to low frequency vibrational modes and thermal expansion/contraction of the protein−solvent lattice.

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“…Since in this case the proximal His is present but other His or Met are absent, it was postulated that the sixth ligand might be provided by the terminal amino groups of the same molecule or via aggregation of different molecules (21,22). To obtain model spectra for the four-, five-and six-coordinate protoheme in the reduced state, the prosthetic group was dissolved in 5% SDS in the presence of different types of ligands (Fig.…”

Section: Resultsmentioning

confidence: 99%

Fast Coordination Changes in Cytochrome c Do Not Necessarily Imply Folding

Arcovito

Gianni

Brunori

et al. 2001

Journal of Biological Chemistry

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Folding of globular proteins occurs with rates that range from microseconds to minutes; consequently, it has been necessary to develop new strategies to follow the faster processes that exceed stopped-flow capabilities. Rapid photochemical methods have been employed to study the rate of folding of reduced cytochrome c. In this protein, the iron of the covalently bound heme binds a His and a Met, proximal and distal. Unfolding by guanidine or urea weakens the Fe-Met bond, and the reduced unfolded cytochrome c easily binds CO and other heme ligands, which would react slowly or not at all with the native protein. Therefore in the presence of CO, reduced cytochrome c unfolds at lower denaturant concentrations than in the absence of this ligand, and rapid photochemical removal of CO from unfolded cytochrome c, is expected to trigger at least an incomplete refolding. This approach is complicated by the breakage of the proximal His-Fe bond that may occur as a consequence of CO photodissociation in the unfolded cytochrome c because of the so-called base elimination mechanism. Rebinding of CO to the four-coordinate heme yields kinetic intermediates unrelated to folding. Our hypothesis is supported by parallel observations carried out with protoheme and microperoxidase.

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Microperoxidase-11: Molecular Dynamics and Q-Band Excited Resonance Raman of the Oxidized, Reduced and Carbonyl Forms

Cited by 15 publications

References 42 publications

Sampling Field Heterogeneity at the Heme of c-Type Cytochromes by Spectral Hole Burning Spectroscopy and Electrostatic Calculations

Sampling Field Heterogeneity at the Heme of c-Type Cytochromes by Spectral Hole Burning Spectroscopy and Electrostatic Calculations

The Effects of Protein Environment on the Low Temperature Electronic Spectroscopy of Cytochrome c and Microperoxidase-11

Fast Coordination Changes in Cytochrome c Do Not Necessarily Imply Folding

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