Protein-Induced Changes in Nonplanarity of the Porphyrin in Nickel Cytochrome <i>c</i> Probed by Resonance Raman Spectroscopy

Ma, Jie; Laberge, Monique; Song, Xing-Zhi; Jentzen, Walter; Jia, Song‐Ling; Zhang, Jun; Vanderkooi, Jane M.; Shelnutt, John A.

doi:10.1021/bi972375b

Cited by 72 publications

(106 citation statements)

References 53 publications

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“…Despite differences of the variable "XX" residues, the CXXCH backbone structure is highly conserved, as it is defined primarily by the constraints of the covalent and coordinate bonds between the Cys and His residues with the heme (42,43). In the selected group of cyts c, this motif displays an RMSD of 0.34 Å (for backbone atoms); Ht cyt c 552 and Pa cyt c 551 have an RMSD of 0.21 Å in this region ( Figure 1C).…”

Section: Analysis Of C-heme Motif Structuresmentioning

confidence: 99%

Heme Attachment Motif Mobility Tunes CytochromecRedox Potential

et al. 2007

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Hydrogen exchange (HX) rates and midpoint potentials (E m ) of variants of cytochromes c from Pseudomonas aeruginosa (Pa cyt c 551 ) and Hydrogenobacter thermophilus (Ht cyt c 552 ) have been characterized toward developing an understanding of the impact of properties of the Cys-X-X-CysHis pentapeptide c-heme attachment motif (CXXCH) on heme redox potential. Despite structural conservation of the CXXCH motif, Ht cyt c 552 exhibits low protection from HX for amide protons within this motif relative to Pa cyt c 551 . Site-directed mutants have been prepared to determine the structural basis for and functional implications of these variations in HX behavior. The double mutant Ht-M13V/K22M displays suppressed HX within the CXXCH motif as well as decreased E m (by 81 mV), whereas the corresponding double mutant of Pa cyt c 551 (V13M/M22K) exhibits enhanced HX within the CXXCH pentapeptide and a modest increase in E m (by 30 mV). The changes in E m correlate with changes in axial His chemical shifts in the ferric proteins reflecting extent of histidinate character. Thus the mobility of the CXXCH pentapeptide is found to impact the His-Fe(III) interaction and therefore heme redox potential.Electron transfer reactions involving iron-protoporphyrin IX (heme) are central to fundamental biological processes such as respiration, redox catalysis, sensing, and signaling (1-5). A key parameter determining energetics and kinetics of electron transfer is the redox potential (1), thus, much emphasis has been placed on understanding the role of protein structure in tuning heme redox potential. Two fundamental features known to have a substantial influence on heme redox potentials are the nature of the ligands coordinated to the metal and the burial of the heme in the hydrophobic protein core. Nature alters the electron donating properties of the coordinating ligands through choice of ligands (6), modulating metal-ligand bond strength (6-12), varying coordination geometry (5), and hydrogen bonding to ligands (13)(14)(15). The encapsulation of the heme within a protein's interior also is significant for determining potential, as the hydrophobic environment favors the ferrous state over the ferric (7,8,10,16,17). Although there have been many studies of the effects of static polypeptide structure on heme-ligand interactions and on heme burial, the role of protein mobility has received less attention. Protein motions may indeed be important as they could influence metal-ligand interactions (15,18,19) and solvent exposure. † This work supported by National Institutes of Health Grant GM63170 (K.L.B.), a Fellowship from the Alfred P. Sloan Foundation (K.L.B.), and National Science Foundation Grant MCB-0546323 (S.J.E.).*To whom correspondence should be addressed: Department of Chemistry, University of Rochester, Rochester, NY 14627-0216. Telephone: (585) Here, we investigate the effects of structural fluctuations of the c-heme motif of cytochrome c (cyt c 1 ) on redox potential. The c-type heme is characterized by its covalen...

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Section: Analysis Of C-heme Motif Structuresmentioning

confidence: 99%

Heme Attachment Motif Mobility Tunes CytochromecRedox Potential

et al. 2007

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“…As shown in Figure 10, linear combinations of the main deformation modes (saddling, ruffling, doming, inverse doming, waving x , waving y , and propellering) are able to describe the nonplanar heme structures in proteins under investigation here, as well as most of the published X-ray structural data on heme proteins and synthetic metalloporphyrins. 34,[59][60][61][62] For example, an examination of the frequencies observed in the coherence spectra of the ferric samples of Mb and HRP (Table 1 and Table 2) results in an almost one-to-one correspondence (within ±5 cm −1 ), with differences appearing primarily in the relative amplitudes of the specific modes. This behavior supports the idea that symmetry-breaking deformations of the heme are induced to various degrees that are specific to each protein.…”

Section: Normal Coordinate Structural Decompositionmentioning

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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“…9) also supports this idea. Since 2 , which primarily involves C b -C b stretching, is coupled with vinyl CϭC stretching (41,42), removal of the vinyl group leads to an increase in the frequency of 2 due to decoupling of the 2 and vinyl stretching modes (41)(42)(43). In fact, horseradish peroxidase reconstituted with mesoheme, which has ethyl groups instead of vinyl groups in the 2-and 4-positions of heme, showed an upshifted 2 at 1582 cm Ϫ1 as compared with that observed at 1573 cm Ϫ1 for native horseradish peroxidase (44).…”

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The Interaction of Covalently Bound Heme with the Cytochrome c Maturation Protein CcmE

Uchida

Stevens

Daltrop

et al. 2004

Journal of Biological Chemistry

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The heme chaperone CcmE is a novel protein that binds heme covalently via a histidine residue as part of its essential function in the process of cytochrome c biogenesis in many bacteria as well as plant mitochondria. In the continued absence of a structure of the holoform of CcmE, identification of the heme ligands is an important step in understanding the molecular function of this protein and the role of covalent heme binding to CcmE during the maturation of c-type cytochromes. In this work, we present spectroscopic data that provide insight into the ligation of the heme iron in the soluble domain of CcmE from Escherichia coli. Resonance Raman spectra demonstrated that one of the heme axial ligands is a histidine residue and that the other is likely to be Tyr 134 . In addition, the properties of the heme resonances of the holo-protein as compared with those of a form of CcmE with non-covalently bound heme provide evidence for the modification of one of the heme vinyl side chains by the protein, most likely the 2-vinyl group.

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Protein-Induced Changes in Nonplanarity of the Porphyrin in Nickel Cytochrome c Probed by Resonance Raman Spectroscopy

Cited by 72 publications

References 53 publications

Heme Attachment Motif Mobility Tunes CytochromecRedox Potential

Heme Attachment Motif Mobility Tunes CytochromecRedox Potential

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

The Interaction of Covalently Bound Heme with the Cytochrome c Maturation Protein CcmE

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