Native and denatured Zn cytochrome c studied by fluorescence line narrowing spectroscopy

Hole-burning spectroscopy as a probe of nano-environments and processes in biomolecules: a review

Hole-burning spectroscopy, a high-resolution spectroscopic technique, allows details of heterogeneous nano-environments in biological systems to be obtained from broad absorption bands. Recently, this technique has been applied to proteins, nucleic acids, cells, and substructures of water to probe the electrostatic conditions created by macromolecules and the surrounding solvent. Starting with the factors that obscure the homogeneous linewidth of a chromophore within an inhomogeneously broadened absorption or emission band, we describe properties and processes in biological systems that are reflected in the measured hole spectra. The technique also lends itself to the resolution of perturbation experiments, such as temperature cycling to elucidate energy landscape barriers, applied external electric fields (Stark effect) to measure net internal electric fields, and applied hydrostatic pressure to find the volume compressibility of proteins.

Photophysical properties of Zn-substituted cytochrome c investigated by single-molecule and ensemble-averaged spectroscopy

The study of the structural reorganization and photophysical properties of Zn-Cytc using the single-molecule and ensemble-averaged spectroscopy shows that the photoblinking behaviors of single-Zn-Cytc depend on the folded and unfolded structures, whereas the fluorescence dynamics of Zn-Cytc observed in the bulk phase are hardly affected by the conformational change of a protein.

Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding

We investigate the equilibrium unfolding of Zn-cytochrome c in guanidine hydrochloride by three-pulse photon echo peak shift (3PEPS) spectroscopy. Unexpectedly, the measurements reveal that inhomogeneous broadening of the sample at the midpoint of the denaturation is larger than that of either native or unfolded states. To interpret this finding, we present simulations of the peak shift for both two-state and three-state unfolding models. Both the denaturant concentration dependence of the asymptotic peak shift (APS) and the wavelength dependence of the APS at the midpoint of the denaturation are different for the two models. Our data are consistent with two-state unfolding.

The mechanism of GroEL/GroES folding/refolding of protein substrates revisited

The thermodynamics and kinetics of zinc-cytochrome c (ZnCyt c) interactions with Escherichia coli molecular chaperone GroEL (Chaperonin 60; Cpn60) are described. Zinc(II)-porphyrin represents a flexible fluorescent probe for thermodynamic complex formation between GroEL and ZnCyt c, as well as for stopped-flow fluorescence kinetic experiments. Data suggests that GroEL and GroEL/GroES-assisted refolding of unfolded ZnCyt c takes place by a mechanism that is quite close to the Anfinsen Cage hypothesis for molecular chaperone activity. However, even in the presence of ATP, GroEL/GroES-assisted refolding of ZnCyt c takes place at approximately half the rate of refolding of ZnCyt c alone. On the other hand, there is little evidence for refolding behaviour consistent with the Iterative Annealing hypothesis. This includes a complete lack of GroEL or GroEL/GroES-assisted enhancement of refolding rate constant k(2) associated with the unfolding of a putative misfolded state I (Zn) on the pathway to the native state. Reviewing our data in the light of data from other laboratories, we observe that all forward rate enhancements or reductions could be accounted for in terms of thermodynamic coupling (adjusting positions of refolding equilibria) due to binding interactions between GroEL and unfolded protein substrates, driven by thermodynamic considerations. Therefore, we propose that passive kinetic partitioning should be considered the core mechanism of the GroEL/GroES molecular chaperone machinery, wherein the core function is to bind unfolded protein substrates leading to a blockade of aggregation pathways and to increases in molecular flux through productive folding pathway(s).

Triplet State Photosensitization of Nanocrystalline Metal Oxide Electrodes by Zinc-Substituted Cytochromec: Application to Hydrogen Evolution

The interfacing of nanostructured semiconductor photoelectrodes with redox proteins is an innovative approach to the development of artificial photosynthetic systems. In this paper, we have investigated the photoinduced electron-transfer reactions of zinc-substituted cytochrome c, ZnCyt-c, immobilized on mesoporous, nanocrystalline metal oxide electrodes. Efficient electron injection from the triplet state of ZnCyt-c is observed into TiO(2) electrodes (t(50%) approximately 100 micros) resulting in a long-lived charge-separated state (lifetime of up to 0.4 s). Further studies were undertaken as a function of electrolyte pH and metal oxide employed. Optimum yield of a long-lived charge-separated state was observed employing TiO(2) electrodes at pH 5, consistent with our previous studies of analogous dye-sensitized metal oxide electrodes. The addition of EDTA as a sacrificial electron donor to the electrolyte resulted in efficient photogeneration of molecular hydrogen, with a quantum yield per one absorbed photon of 10 +/- 5%.

The red-edge effects: 30 years of exploration

In 1970, three laboratories independently made a discovery that, for aromatic fluorophores embedded into different rigid and highly viscous media, the spectroscopic properties do not conform to classical rules. The fluorescence spectra can depend on excitation wavelength, and the excited-state energy transfer, if present, fails at the "red" excitation edge. These red-edge effects were related to the existence of excited-state distribution of fluorophores on their interaction energy with the environment and the slow rate of dielectric relaxation of this environment. In these conditions the site-selection can be provided by variation of the energy of illuminating light quanta, and the behaviour of selected species can be followed as a function of time and other variables. These observations found extensive application in different areas of research: colloid and polymer science, molecular biophysics, photochemistry and photobiology. In particular, they led to the development of very productive methods of studying the dynamics of dielectric relaxations in protein and membranes, using the tryptophan emission and the emission of a variety of probes. These studies were extended to the time domain with the observation of new site-selective effects in emission intensity and anisotropy decays. They stimulated the emergence and development of cryogenic energy-selective and single-molecular techniques that became valuable tools in their own right in chemistry and biophysics research. Site-selection effects were discovered for electron-transfer and proton-transfer reactions if they depended on the dynamics of the environment. This review is focused on the progress in the field of red-edge effects, their applications and prospects.

Fluorescence line narrowing applied to the study of proteins

Fluorescence line narrowing is a high resolution spectroscopic technique that uses low temperature and laser excitation to optically select specific subpopulations from the inhomogeneously broadened absorption band of the sample. When applied to the study of fluorescent groups in proteins one can obtain vibronically resolved spectra, which can be analyzed to give information on spectral line shapes, vibrational energies of both the ground and excited state molecule, and the inhomogeneous distribution function of the electronic transitions. These parameters reveal information about the chromophoric prosthetic group and the protein matrix and are functions of geometric strains and local electric fields imposed by the protein. Examples of the use of fluorescence line narrowing are discussed in investigations of heme proteins, photosynthetic systems and tryptophan-containing proteins.

The protein state of matter

Three ways are generally used to visualize proteins: (1) a static model in which the atomic positions are defined, (2) a dynamic model taking into account fluctuations, and (3) a reactive model that reflects the internal and external electric fields of the molecule. The properties of chromophoric prosthetic groups can be probed by optical spectroscopy, and when high resolution techniques are used, the results reveal information about the local electric fields in proteins, as influenced and determined by atomic positions and dynamics.

Zinc-substituted hemoglobins: alpha- and beta-chain differences monitored by high-resolution emission spectroscopy

The absorption and emission properties of hybrid Zn-substituted human hemoglobin (Hb) were used to monitor differences in interaction between the porphyrin and the polypeptide chain for the two subunits. Although alpha-substituted (alpha-ZnHb), beta-substituted (beta-ZnHb), or totally substituted Hb all show optical properties characteristic of Zn porphyrins, the spectra are also indicative of specific interactions between the polypeptide chain and the porphyrin. The Q0,0 absorption band of alpha-ZnHb at 5 K shows a splitting of approximately 300 cm-1, comparable to the largest split ever reported for a heme protein. This value is approximately 140 cm-1 for beta-ZnHb. The possible origin of the split is discussed in terms of the local electric field imposed by the amino acids of the respective heme pockets, different configurations of the porphyrin, and/or influences of the liganding histidine. The Zn derivatives show quasiline spectra under fluorescence line narrowing conditions, and the resolved excitation spectrum reveals differences in the vibrational levels of the Zn porphyrin in the two subunits. Broad underlying emission in the fluorescence line-narrowed emission spectrum can be accounted for, in part, by the existence of the two closely spaced electronic origins and also by the extent of phonon coupling between the porphyrin and the protein matrix.

Characterization of zinc-substituted cytochrome c by circular dichroism and resonance Raman spectroscopic methods

Iron(III) in cytochrome c is replaced with zinc(II) by a modification of a method published by others, and the procedure is described in full detail. Three forms of cytochrome c-those containing iron(III), iron(II), and zinc(II)-are examined by circular dichroism spectroscopy and resonance Raman spectroscopy. Spectra of both kinds show that introduction of zinc(II) ions does not appreciably alter the overall structure and conformation of cytochrome c. Resonance Raman spectra indicate the size of the porphyrin "core" that is inconsistent with six-coordination and consistent with five-coordination. Unlike the iron(III) and iron(II) ions, which are bound to two axial ligands (His 18 and Met 80), the zinc(II) ion in cytochrome c seems to be bound to only one, most probably His 18. Evidence pertaining to the question of axial coordination is discussed.

Fluorescence line narrowing spectroscopy: a tool for studying proteins

Perhaps the most important contribution of FLN is that it provides an experimental approach to relate physical changes in the protein to predicted dynamical behavior. It is clear that the sample is inhomogeneously broadened in a continuous manner, consistent with the damped motion of proteins. At the same time configurational substates can be selected, suggesting that there is indeed a hierarchy of protein motion and structure. As yet, identification of the structure, and relating it to the spectra, has not been achieved. It is clear that the electric field exerted by neighboring atoms shifts the electronic transition, and the inhomogeneity is greater when the surrounding disorder is greater. The inhomogeneity for the chromophore in the protein is dependent on the protein conformation and is intermediate between that of a crystal and a glass. The phonon coupling also depends on the chromophore and the protein. Fluorescence line narrowing provides in addition ground- and excited-state vibrational frequencies, thereby allowing for structural differences between the excited-state and the ground-state molecule to be detected.

Spectral splitting in the alpha (Q0,0) absorption band of ferrous cytochrome c and other heme proteins

The alpha or Q0,0 absorption band of horse iron(II) cytochrome c splits and shifts to the blue as temperature decreases over the temperature range of 290-10 K. At room temperature, its maximum is at 18 150 cm-1 and the spectral width is 273 cm-1, whereas at 10 K, the two bands of the Q0,0 transition occur at 18 364 and 18 253 cm-1 and the width of the lowest-energy band is 96 cm-1. Temperature dependent splitting also occurs for zinc cytochrome c, a derivative in which Fe has been replaced by Zn; at 10 K, the peaks in the Q0,0 band region occur at 17 106 and 16 996 cm-1. The peak positions are independent of the cryosolvent (aqueous ethylene glycol or glycerol mixtures). The splitting of the Q0,0 band seen in the protein (approximately 110 cm-1 for iron and zinc cytochrome c) is comparable to the crystal field splitting observed for metalloporphyrins in mixed crystals. In contrast, the Q0,0 band of zinc coproporphyrin III in a glassy solvent (dimethylformamide/ethylene glycol) or in poly(vinyl chloride) shows a blue shift with temperature decrease but no evidence of Q0,0 splitting. Available spectral data show that the Q0,0 band is composed of two nearly degenerate electronic transitions and the split is due to the asymmetry in the heme pocket of the protein that arises from the surrounding polypeptide chain. This asymmetry results in the stabilization of one form of the excited state over the other, according to a Jahn-Teller mechanism.

Electron paramagnetic resonance of the excited triplet state of metal-free and metal-substituted cytochrome c

The photoactivated metastable triplate states of the porphyrin (free-base, i.e., metal-free) zinc and tin derivatives of horse cytochrome c were investigated using electron paramagnetic resonance. Zero-field splitting parameters, line shape, and Jahn-Teller distortion in the temperature range 3.8-150 K are discussed in terms of porphyrin-protein interactions. The zero-field splitting parameters D for the free-base, Zn and Sn derivatives are 465 x 10(-4), 342 x 10(-4) and 353 x 10(-4) cm-1, respectively, and are temperature invariant over the temperature ranges studied. AN E value at 4 K of 73 x 10(-4) cm-1 was obtained for Zn cytochrome c, larger than any previously found for Zn porphyrins derivatives of hemeproteins, showing that the heme site of cytochrome c imposes an asymmetric field. Though the E value for Zn cytochrome c is large, the geometry of the site appears quite constrained, as indicated by a spectral line shape showing a single species. Intersystem crossing occurred predominantly to the T2 > zero-field spin sublevel. EPR line shape changes with respect to temperature of Zn cyt c are interpreted in terms of vibronic coupling, and a maximum Jahn-Teller crystal-field splitting of approximately 180 cm-1 is obtained. Sn cytochrome c in comparison with the Zn protein exhibits a photoactivated triplet line shape that is less well resolved in the X-Y region. The magnitude of E value is approximately 60 x 10(-4) cm-1 at 4 K; its value rapidly tends toward zero with increasing temperature, from which a value for the Jahn-Teller crystal-field splitting of > or = 40 cm-1 is estimated. In contrast to those for the metal cytochromes, the magnitude of E value for the free-base derivative was essentially zero at all temperatures studied. This finding is discussed as a consequence of an excited-state tautomerization process that occurs even at 4 K.