Time-resolved resonance Raman spectroscopy of cytochrome c reduced by pulse radiolysis

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

Activation mechanism of the CO sensor CooA. Mutational and resonance Raman spectroscopic studies

CooA is a CO-dependent heme protein transcription factor of the bacterium Rhodospirillum rubrum. CO binding to its heme causes CooA to bind DNA and activate expression of genes for CO metabolism. To understand the nature of CO activation, several CooA mutational variants have been studied by resonance Raman spectroscopy, in vivo activity measurements, and DNA binding assays. Analysis of the Fe-C and C-O stretching Raman spectroscopy bands permits the conclusion that when CO displaces the Pro2 heme ligand, the protein forms a hydrophobic pocket in which the C-helix residues Gly117, Leu116, and Ile113 are close to the bound CO. The displaced Pro2 terminus is expelled from this pocket, unless the pH is raised above the pKa, in which case the terminus remains in H-bond contact. The pKa for this transition is 8.6, two units below that of aqueous proline, reflecting the hydrophobic nature of the pocket. The proximal Fe-His bond in Fe[II]CooA is as strong as it is in myoglobin but is weakened by CO binding, an effect attributable to loss of an H-bond from the proximal His77 ligand to the adjacent Asn42 side chain. A structural model is proposed for the position of the CO-bound heme in the active form of CooA, which has implications for the mechanism of CO activation.

Regulation of interprotein electron transfer by residue 82 of yeast cytochrome c

Yeast iso-1-cytochrome c (Cc) mutants have been constructed with Phe, Tyr, Gly, Ser, Leu, and Ile at position 82, each with Thr substituted for Cys at position 102. Their long-range electron transfer with zinc-substituted cytochrome c peroxidase (ZnCcP) has been studied by two kinetic techniques. The charge-separated complex, [(ZnCcP)+,FeIICc] converts to [ZnCcP,FeIIICc] by a single, intracomplex electron transfer step that is not governed by "gating" through possible rapid dissociation of the complex or isomerization (for example, heme-ligand) by FeIICc subsequent to its formation from FeIIICc. In every variant with an aliphatic residue at position 82 of Cc, the rate of this electron transfer process is approximately 10(4) slower at approximately 0 degrees C than for the two variants with aromatic residues.

Resonance Raman spectra of chlorophylls dissolved in liquid crystal matrices. I. The interaction between chlorophylls and a liquid crystalline MBBA + EBBA mixture

The resonance Raman (RR) spectra of chlorophyll (Chl) a, Chl b and pheophytin a dissolved in a liquid-crystalline MBBA + EBBA mixture were measured. The RR frequencies of chlorophylls in the liquid crystal (LC) are compared with those of solutions of various chlorophyll monomers and aggregates taken from the literature. It is concluded that Chl a and Chl b in LC exist largely as the solvated monomers, even at high concentration. The magnesium atoms in both Chl a and Chl b are pentacoordinated.

Resonance Raman spectroscopy as a probe of heme protein structure and dynamics

Our understanding of metalloporphyrin resonance Raman spectra has advanced to the point where it is possible to obtain detailed information about the structure of the heme group in situ in heme proteins. The porphyrin skeletal mode frequencies can be analyzed in terms of the ligation and spin state of the heme and may provide information about protein-induced stresses. The high-frequency region of the spectrum also contains bands due to vibrations of the porphyrin peripheral substituents, which are potentially monitors of the protein contacts. In the low-frequency region, it is possible to locate bands, at least in some states of the heme protein, which are associated with vibrations of the axial ligands. They give direct information about the nature of the bonding to exogenous ligands or to the proximal protein residue. Thus, a variety of evidence is potentially available in the resonance Raman spectra from which a fairly complete picture of the heme site can be assembled for a particular protein in its various functional states. Detailed studies have been pursued for paradigmatic heme proteins, including myoglobin, hemoglobin, cytochrome c, horseradish peroxidase, and cytochrome oxidase. These studies provide a substantial data base from which the exploration of lesser known systems can be launched. Another extension of current knowledge to new frontiers is in the time domain, since pulsed lasers now make it feasible to carry out time-resolved resonance Raman studies on heme protein reactions. Time-resolved resonance Raman spectroscopy is capable of elucidating the temporal evolution of heme structure and provides a link between heme chemistry and protein dynamics. This link is being elucidated for hemoglobin and cytochrome c, where specific heme intermediates have been identified following ligand photodissociation or electron transfer.

Intermediate and stable redox states of cytochrome c studied by low temperature resonance Raman spectroscopy

Stabilized intermediate redox states of cytochrome c are generated by radiolytic reduction of initially oxidized enzyme in glass matrices at liquid nitrogen temperature. In the intermediate states the heme group is reduced by hydrated electrons, whereas the protein conformation is restrained close to its oxidized form by the low-temperature glass matrix. The intermediate and stable redox states of cytochrome c at neutral and alkaline pH are studied by low-temperature resonance Raman spectroscopy using excitations in resonance with the B (Soret) and Q1 (beta) optical transitions. The assignments of the cytochrome c resonance Raman bands are discussed. The observed spectral characteristics of the intermediate states as well as of the alkaline transition in the oxidized state are interpreted in terms of oxidation-state marker modes, spin-state marker modes, heme iron--axial ligand stretching modes, totally symmetric in-plane porphyrin modes, nontotally symmetric in-plane modes, and out-of-plane modes.

Continuous flow-resonance Raman spectroscopy of an intermediate redox state of cytochrome C

An intermediate redox state of cytochrome c at alkaline pH, generated upon rapid reduction by sodium dithionite, has been observed by resonance Raman (RR) spectroscopy in combination with the continuous flow technique. The RR spectrum of the intermediate state is reported for excitation both in the (alpha, beta) and the Soret optical absorption band. The spectra of the intermediate state are more like those of the stable reduced form than those of the stable oxidized form. For excitation of 514.5 nm, the most prominent indication of an intermediate state is the wave-number shift of one RR band from 1,562 cm-1 in the stable oxidized state through 1,535 cm-1 in the intermediate state to 1,544 cm-1 in the stable reduced state. For excitation at 413.1 nm, a band, present at 1,542 cm-1 in the stable reduced state but not present in the stable oxidized state, is absent in the intermediate state. We interpret the intermediate species as the state where the heme iron is reduced but the protein remains in the conformation of the oxidized state, with methionine-80 displaced as sixth ligand to the heme iron, before relaxing to the conformation of the stable reduced state, with methionine-80 returned as sixth ligand.