Q-Band resonance Raman investigation of turnip cytochrome f and Rhodobacter capsulatus cytochrome c1

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.

Photo-induced oxidation of the uniquely liganded heme f in the cytochrome b6f complex of oxygenic photosynthesis

The ultrafast behavior of the ferrous heme f from the cytochrome b6f complex of oxygenic photosynthesis is revealed by means of transient absorption spectroscopy. Benefiting from the use of microfluidic technologies for handling the sample as well as from a complementary frame-by-frame analysis of the heme dynamics, the different relaxation mechanisms from vibrationally excited states are disentangled and monitored via the shifts of the heme α-absorption band. Under 520 nm laser excitation, about 85% of the heme f undergoes pulse-limited photo-oxidation (<100 fs), with the electron acceptor being most probably one of the adjacent aromatic amino acid residues. After charge recombination in 5.3 ps, the residual excess energy is dissipated in 3.6 ps. In a parallel pathway, the remaining 15% of the hemes directly relax from their excited state in 2.5 ps. In contrast to a vast variety of heme-proteins, including the homologous heme c1 from the cytochrome bc1 complex, there is no evidence that heme f photo-dissociates from its axial ligands. Due to its unique binding, with histidine and an unusual tyrosine as axial ligands, the heme f exemplifies a dependence of ultrafast dynamics on the structural environment.

Fe vibrational spectroscopy of myoglobin and cytochrome f

The Fe vibrational density of states (VDOS) has been determined for the heme proteins deoxymyoglobin, metmyoglobin, and cytochrome f in the oxidized and reduced states, using nuclear resonance vibrational spectroscopy (NRVS). For cytochrome f in particular, the NRVS spectrum is compared with multiwavelength resonance Raman spectra to identify those Raman modes with significant Fe displacement. Modes not seen by Raman due to optical selection rules appear in the NRVS spectrum. The mean Fe force constant extracted from the VDOS illustrates how Fe dynamics varies among these four monoheme proteins, and is correlated with oxidation and spin state trends seen in model heme compounds. The protein's contribution to Fe motion is dominant at low frequencies, where coupling to the backbone tightly constrains Fe displacements in cytochrome f, in contrast to enhanced heme flexibility in myoglobin.

CO-dependent Activity-controlling Mechanism of Heme-containing CO-sensor Protein, Neuronal PAS Domain Protein 2

Neuronal PAS domain protein 2, which was recently established to be a heme protein, acts as a CO-dependent transcription factor. The protein consists of the basic helix-loop-helix domain and two heme-containing PAS domains (PAS-A and PAS-B). In this study, we prepared wild type and mutants of the isolated PAS-A domain and measured resonance Raman spectra of these proteins. Upon excitation of the Raman spectrum at 363.8 nm, a band assignable to Fe3+-S stretching was observed at 334 cm(-1) for the ferric wild type protein; in contrast, this band was drastically weaker in the spectrum of C170A, suggesting that Cys170 is an axial ligand of the ferric heme. The Raman spectrum of the reduced form of wild type was mainly of six-coordinate low spin, and the nu11 band, which is sensitive to the donor strength of the axial ligand, was lower than that of reduced cytochrome c3, suggesting coordination of a strong ligand and thus a deprotonated His. In the reduced forms of H119A and H171A, the five-coordinate species became more prevalent, whereas no such changes were observed for C170A, indicating that His119 and His171, but not Cys170, are axial ligands in the ferrous heme. This means that ligand replacement from Cys to His occurs upon heme reduction. The nu(Fe-CO) versus nu(C-O) correlation indicates that a neutral His is a trans ligand of CO. Our results support a mechanism in which CO binding disrupts the hydrogen bonding of His171 with surrounding amino acids, which induces conformational changes in the His171-Cys170 moiety, leading to physiological signaling.

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

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 Tyr134. 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.

Role of Arg-166 in yeast cytochrome C1

A systematic screen for dominant-negative mutations of the CYT1 gene, which encodes cytochrome c(1), revealed seven mutants after testing approximately 10(4) Saccharomyces cerevisiae strains transformed with a library of mutagenized multicopy plasmids. DNA sequence analysis revealed multiple nucleotide substitutions with six of the seven altered Cyt1p having a common R166G replacement, either by itself or accompanied with other amino acid replacements. A single R166G replacement produced by site-directed mutagenesis demonstrated that this change produced a nearly nonfunctional cytochrome c(1), with diminished growth on glycerol medium and diminished respiration but with the normal or near normal level of cytochrome c(1) having an attached heme group. In contrast, R166K, R166M, or R166L replacements resulted in normal or near normal function. Arg-166 is conserved in all cytochromes c(1) and lies on the surface of Cyt1p in close proximity to the heme group but does not seem to interact directly with any of the physiological partners of the cytochrome bc(1) complex. Thus, the large size of the side chain at position 166 is critical for the function of cytochrome c(1) but not for its assembly in the cytochrome bc(1) complex.

Binding of CO at the Pro2 side is crucial for the activation of CO-sensing transcriptional activator CooA. (1)H NMR spectroscopic studies

CooA is a heme-containing transcriptional activator that anaerobically binds to DNA at CO atmosphere. To obtain information on the conformational transition of CooA induced by CO binding to the heme, we assigned ring current-shifted (1)H NMR signals of CooA using two mutants whose axial ligands of the heme were replaced. In the absence of CO, the NMR spectral pattern of H77Y CooA, in which the axial histidine (His(77)) was replaced with tyrosine, was similar to that of wild-type CooA. In contrast, the spectra of CooADeltaN5, in which the NH(2) termini including the other axial ligand (Pro(2)) were deleted, were drastically modulated. We assigned three signals of wild-type CooA at -4.5, -3.6, and -2.8 ppm to delta(1)-, alpha-, and delta(2)-protons of Pro(2), respectively. The Pro(2) signals were undetectable in the upfield region of the spectrum of the CO-bound state, which confirms that CO displaces Pro(2). Interestingly, the Pro(2) signals were observed for CO-bound H77Y CooA, implying that CO binds to the trans position of Pro(2) in H77Y CooA. The abolished CO-dependent transcriptional activity of H77Y CooA is therefore the consequence of Pro(2) ligation. These observations are consistent with the view that the movement of the NH(2) terminus triggers the conformational transition to the DNA binding form.