Dehydration in the folding of reduced cytochrome c revealed by the electron-transfer-triggered folding under high pressure

We determined the activation volume associated with protein folding of reduced cytochrome c from the collapsed intermediate to the native state. The folding rate was followed by a change in the absorption (420 nm) at various pressures between 0.1 and 200 MPa and at various concentrations of denaturant (guanidine hydrochloride) between 3.2 and 4.0 M. Dependence of the folding rate on both these factors revealed that the activation volume at ambient pressure in the absence of denaturant is negative (DeltaVf0 = -14 (+/-8) cm3.mol-1). Such a negative activation volume can be accounted for by a decrease in volume resulting from the dehydration of hydrophobic groups, primarily the heme group. Dehydration, which increases the entropy of the protein system, compensates for a decrease in the entropy accompanying the formation of the more compact and ordered transition state. We, therefore, propose that the positive change in the activation entropy for the folding reaction is due to the dehydration of hydrophobic groups. Furthermore, dehydration entropically promotes the protein folding reaction.     

A high-resolution probe of protein folding

Protein folding is a central problem in the biological sciences. To generate residue-specific information on the equilibrium folding of cytochrome c, we have semisynthesized the protein with specifically deuterated residues. The C-D bonds may be easily visualized in an otherwise transparent region of the IR spectra, even at high protein and denaturant concentrations. Plotted as a function of added guanidine hydrochloride denaturant, the absorption intensities reveal that the protein undergoes a conformational change at the protein-based ligand, Met80, which is then followed by a more global unfolding at 2.3 M denaturant. Deuteration and characterization of other residues in cytochrome c, or other protein of interest, should provide complete views of folding with residue specific detail that is capable of resolving even the most rapidly interconverting intermediates.     

Ruthenium bisbipyridine complexes of horse heart cytochrome c: characterization and comparative intramolecular electron-transfer rates determined by pulse radiolysis and flash photolysis

The reaction of [Ru(bpy)2L(H2O)]2+ (bpy = 2,2'-bipyridine, L = imidazole, water) with reduced horse heart cytochrome c results in coordination of [RuII(bpy)2L] at the His 33 and His 26 sites. Coordination at the His 33 site gave a diastereomeric [RuII(bpy)2L]-His-cyt c(II) mixture favoring the lambda-Ru form regardless of the substituent on the bipyridine ligands, while substitution at the more buried His 26 site gave an isomeric distribution that varies according to the substituent on the bipyridine ligands. The diastereomeric aquoproteins (L = H2O) are distinguished by their redox potentials and their conversion to the corresponding fluorescent imidazole proteins. Intramolecular electron transfer between the reduced ruthenium bipyridine and cyt c(III) in [RuII(bpy.)(bpy)L]-His33-cyt c(III) was determined by reductive pulse radiolysis using the aqueous electron as a reducing agent, kret = (2.0 +/- 0.3) x 10(5) s-1, and kret is independent of the sixth ligand L = H2O, imidazole. In addition, the rate constant for intramolecular electron transfer from cyt c(II) to the ruthenium(III) center in [RuIII(bpy)2L]-His33-cyt c(II) was determined by oxidative pulse radiolysis using azide and carbonate radicals. This rate is very sensitive to the nature of the sixth ligand. When L = H2O, the intramolecular electron-transfer rate for the major diastereomer lambda-cis-[RuIII (bpy)2(H2O)]-His33-cyt c(II) is k = 1.1 x 10(4) s-1 and is independent of pH between 5.6 and 8.3. The minor delta-cis-[RuIII(bpy)2(H2O)]-His33-cyt c(II) isomer has pH-dependent electrochemistry and a lower rate of intramolecular electron transfer. Complete conversion from L = H2O to L = imidazole is slow, requiring more than 7 days in 1 M imidazole. A lower limit (k > 2 x 10(6) s-1) for the intramolecular electron-transfer rate constant in [RuIII(bpy)2(L)]-His33-cyt c(II), L = imidazole, could be obtained by pulse radiolysis in the absence of the slower reacting aquo species. This observation is in agreement with the value of 3 x 10(6) s-1 measured by flash photolysis. Earlier pulse radiolysis experiments primarily measured the aquoligated ruthenium protein, while the flash photolysis experiments measured the imidazole-ligated fraction because it is the only species oxidatively quenched in the photoinduced reactions. Intramolecular electron-transfer reactions for a new series of ruthenium bipyridine complexes, [Ru(dabpy)2L]-His33-cyt c proteins (dabpy = 4,4'-diamino-2,2'-bipyridine) (L = imidazole, pyridine, isonicotinamide and pyrazine), proceed with lower driving force, resulting in slower rate constants amenable to measurement by oxidative pulse radiolysis. The electron-transfer rate constants for this series spanned a wide range of the Marcus log k vs delta G plot.     

The Elucidation of Peroxyl Radical Reactions in Aqueous Solution with the Help of Radiation-Chemical Methods

Whenever free radicals are formed, independent of whether this occurs thermally, is induced by UV or ionizing irradiation, or takes place in redox reactions, they are converted rapidly into the corresponding peroxyl radicals in the presence of oxygen. Peroxyl radical reactions in aqueous environments are observed not only in aquatic systems (e.g., rivers, lakes and oceans) but also in the living cell and to a considerable degree even in the atmosphere (in water droplets). The peroxyl radical chemistry occurring in this medium is often very different from that observed in the gas phase or in organic solvents. In spite of the great importance of these reactions in medicine (for example in anti-cancer irradiation therapy and ischaemia) there have been comparatively few studies of peroxyl reactions in aqueous media. Radiation-chemical techniques such as pulse radiolysis offer the best means for carrying out such studies, so that it is not surprising that the majority of the information available in this area has been obtained with the help of radiation-chemical methods. The radiation chemistry of water can be con trolled in such a manner that the main products are ^˙OH radicals (90 % yield), which react with substrate molecules to give substrate radicals and in the presence of oxygen to give substrate peroxyl radicals. The experimental conditions can also be varied in such a way that HO/O radicals can be formed in 100 % yield and caused to react with substrates. We therefore have a simple access to these intermediates, which are extremely important in biological systems. A detailed product analysis, supported by kinetic studies carried out with the help of pulse radiolysis, has been used to clarify the chemistry of a series of peroxyl radicals, so that sufficient material is now available to justify a review of the variety of the peroxyl radical reactions studied by means of radiation-chemical methods. A more general survey of the physical properties of the peroxyl radicals and their unimolecular and bimolecular reactions will be followed by a discussion of selected examples of various classes of substance. Because of the great biological importance of radical-induced DNA damage this area will also be treated briefly.     

Fluorescence lifetime distribution of folded and unfolded proteins

Time-resolved fluorescence of single tryptophan proteins have demonstrated the complexity of protein dynamic and protein structure. In particular, for some single tryptophan proteins, their fluorescence decay is best described by a distribution of fluorescence lifetimes rather than one or two lifetimes. Such results have provided further confirmation that the protein system is one which fluctuates between a hierarchy of many conformational substates. With this scenario as a theoretical framework, the correlations between protein dynamic and structure are investigated by studying the time-resolved fluorescence and anisotropy decay of holo and apo human superoxide dismutase (HSOD) at different denaturant concentrations. As a function of guanidine hydrochloride (GdHCl), the width of the fluorescence lifetime distribution of HSOD displays a maximum which is not coincident with the fully denatured form of HSOD at 6.5M GdHCl. Furthermore, the width of the fluorescence lifetime distribution for the fully denatured forms of holo and apo HSOD is greater than that of the native forms.     

Growth and reactivity of silver clusters in amino polycarboxylic acid solutions

Reduction and subsequent aggregation of silver ions in the presence of various chelating agents such as trans-1,2-diaminocyclohexanetetraacetic acid (DCTA) 1,2-propylenediaminetetraacetic acid (PDTA), diethylenetriaminepentaacetic acid (DTPA), and triethylenetetraaminehexaacetic acid (TTHA) have been studied by pulse radiolysis. Rate constants of formation and transient absorption spectra for the ligand-complexed Ag(0) and Ag(2)(+) have been determined. The redox potential of Ag(+)(L)/Ag(0)(L) becomes more negative than that of Ag(+)/Ag(0). Growth and reactivity of silver clusters were also studied in the presence of methyl viologen (MV(2+)). The kinetics of formation of the MV(+*) radical, produced by the same pulse as in the case of silver atoms, confirms the catalytic electron transfer toward super critical silver clusters in the presence of ligands. The results suggest that catalytic electron transfer activity of silver clusters depends on the ligand.     

Kinetic model for the radical degradation of tri-halonitromethane disinfection byproducts in water

The halonitromethanes (HNMs) are byproducts of the ozonation and chlorine/chloramine treatment of drinking waters. Although typically occurring at low concentrations HNMs have high cytotoxicity and mutagenicity, and may therefore represent a significant human health hazard. In this study, we have investigated the radical based mineralization of fully-halogenated HNMs in water using the congeners bromodichloronitromethane and chlorodibromonitromethane. We have combined absolute reaction rate constants for their reactions with the hydroxyl radical and the hydrated electron as measured by electron pulse radiolysis and analytical measurements of stable product concentrations obtained by ⁶⁰Co steady-state radiolysis with a kinetic computer model that includes water radiolysis reactions and halide/nitrogen oxide radical chemistry to fully elucidate the reaction pathways of these HNMs. These results are compared to our previous similar study of the fully chlorinated HNM chloropicrin. The full optimized computer model, suitable for predicting the behavior of this class of compounds in irradiated drinking water, is provided.     

Ultrafast heme dynamics in ferrous versus ferric cytochrome c studied by time-resolved resonance Raman and transient absorption spectroscopy

Cytochrome c (Cyt c) is a heme protein involved in electron transfer and also in apoptosis. Its heme iron is bisaxially ligated to histidine and methionine side chains and both ferric and ferrous redox states are physiologically relevant, as well as a ligand exchange between internal residue and external diatomic molecule. The photodissociation of internal axial ligand was observed for several ferrous heme proteins including Cyt c, but no time-resolved studies have been reported on ferric Cyt c. To investigate how the oxidation state of the heme influences the primary photoprocesses, we performed a comprehensive comparative study on horse heart Cyt c by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We found that in ferric Cyt c, in contrast to ferrous Cyt c, the photodissociation of an internal ligand does not take place, and relaxation dynamics is dominated by vibrational cooling in the ground electronic state of the heme. The intermolecular vibrational energy transfer was found to proceed in a single phase with a temperature decay of approximately 7 ps in both ferric and ferrous Cyt c. For ferrous Cyt c, the instantaneous photodissociation of the methionine side chain from the heme iron is the dominant event, and its rebinding proceeds in two phases, with time constants of approximately 5 and approximately 16 ps. A mechanism of this process is discussed, and the difference in photoinduced coordination behavior between ferric and ferrous Cyt c is explained by an involvement of the excited electronic state coupled with conformational relaxation of the heme.     

One-electron oxidations of ferrocenes: A pulse radiolysis study

Using the pulse radiolysis technique we have studied the oxidation by various inorganic radicals of four water soluble ferrocene derivatives, hydroxyethyl, dimethylaminomethyl, monocarboxylic acid and dicarboxylic acid. We report the second order rate constants for these reactions, the stabilities and spectral properties of the ferrocinium products, and the electrochemically determined ferrocinium/ferrocene redox potentials. We also present preliminary estimates of tyrosine and tryptophan radical redox potentials obtained with the dicarboxylic acid ferrocene derivative as reference, and we discuss the relationship between redox potential differences and the reactivities of the ferrocenes with the inorganic radicals.     

细胞色素c在硒代胱氨酸修饰电极上的直接电化学

采用电化学和接触角实验方法研究了硒代胱氨酸自组装膜修饰金电极(SeCys SAMs/Au)和十六烷基三甲基溴化铵(CTAB)-硒代胱氨酸自组装复合膜修饰金电极(CTAB-SeCys SAMs/Au)的特性. 探讨了细胞色素c(Cyt c)在SeCys SAMs/Au电极和CTAB-SeCys SAMs/Au电极上的电化学行为. 实验证明SeCys可促进Cyt c在电极上的氧化还原反应, 加入CTAB后其与SeCys之间的协同作用可在Cyt c与电极之间形成一个开放的通道, 促进作用更加明显, 且在一定浓度范围内, 随CTAB浓度(1×10^-5-1×10^-4 mol·L^-1)的增大, Cyt c在CTAB-SeCys SAMs/Au电极上的氧化还原电流增大, 在接近临界胶束浓度处出现极大值. 在CTAB-SeCys SAMs/Au电极上Cyt c产生一对氧化还原峰, 其峰电位分别为0.305和0.235 V, 其电化学过程受扩散控制. 光谱实验证实SeCys对Cyt c电化学过程的促进作用是由于SeCys与Cyt c中赖氨酸残基的结合.     

A laser flash photolysis and pulse radiolysis study of primary photochemical processes of flumequine

The 355 nm laser flash photolysis of argon-saturated pH 8 phosphate buffer solutions of the fluoroquinolone antibiotic flumequine produces a transient triplet state with a maximum absorbance at 575 nm where the molar absorptivity is 14,000 M(-1) cm(-1). The quantum yield of triplet formation is 0.9. The transient triplet state is quenched by various Type-1 photodynamic substrates such as tryptophan (TrpH), tyrosine, N-acetylcysteine and 2-deoxyguanosine leading to the formation of the semireduced flumequine species. This semireduced form has been readily identified by pulse radiolysis of argon-saturated pH 8 buffered aqueous solutions by reaction of the hydrated electrons and the CO2*- radicals with flumequine. The absorption maximum of the transient semireduced species is found at 570 nm with a molar absorptivity of 2,500 M(-1) cm(-1). In argon-saturated buffered solutions, the semireduced flumequine species formed by the reaction of the flumequine triplet with TrpH stoichiometrically reduces ferricytochrome C (Cyt Fe3+) under steady state irradiation with ultraviolet-A light. In the presence of oxygen, O2*- is formed but the photoreduction of Cyt Fe3+ by O2*- competes with an oxidizing pathway which involves photo-oxidation products of TrpH.     

Radiolytically generated benzene triplets as sensitizers for energy and combined electron/proton transfer processes

Pulse radiolysis technique has been employed to investigate energy and electron transfer reactions involving triplets of naphthols and hydroxybiphenyls. The transient absorption spectra obtained on pulse radiolysis of N₂-saturated solution of naphthols and hydroxybiphenyls in benzene are assigned to triplet–triplet absorption. It was found that biphenyl triplets undergo energy transfer to naphthols and hydroxybiphenyls forming the acceptor triplets. On the other hand, benzophenone triplets, favor electron transfer followed by H⁺ transfer reaction forming benzophenone ketyl radical and phenoxyl radical of the acceptor. An analogous sequence mimics with 2-naphthol triplets and using benzophenone, acetophenone or chloranil as electron acceptor.     

Probing photocatalytic reactions in semiconductor systems: Study of the chemical intermediates in 4 -chlorophenol degradation by a variety of methods

The photocatalytic transformation of 4-chlorophenol (4-CP) has been studied in aqueous slurries, on powders and on immobilized particulate films of TiO₂. These results are compared to those obtained using gamma and pulse radiolysis in order to establish a comprehensive picture of the 4-CP reaction pathway in TiO₂ systems. The disappearance of 4-CP and its reaction intermediates in TiO₂ slurries involves a combination of hydroxyl radical oxidation, direct electron transfer and surface chemical reactions.     

Breaking time-resolution limits in pulse radiolysis

Pulse radiolysis, which is a time-resolved stroboscopic method based on ultrashort electron pulse and ultrashort analyzing light, is widely used for the study of the chemical kinetics and radiation primary processes or reactions. Although it has become possible to use femtosecond-pulse electron beam and femtosecond laser light in pulse radiolysis, the resolution is limited by the difference in group velocities of the electrons and the light in sample. In this contribution, we introduce a concept of equivalent velocity spectroscopy (EVS) into pulse radiolysis and demonstrate the methodology experimentally. In EVS, both the electron and the analyzing light pulses precisely overlap at every point in the sample and throughout the propagation time by rotating the electron pulse. The advance allows us to overcome the resolution degradation due to the different group velocity. We also present a method for measuring the rotated angle of the electron pulse and a technique for rotating the electron pulse with a deflecting cavity.     

Early events in radiation chemistry and in photoionization

Real-time studies of aliphatic and aromatic hydrocarbons by pulse radiolysis and laser photoionization reveal the chemistry of the ionic species in the condensed phase. The occurrence of radical cation reactions with solvent molecules provides the core mechanism capable of explaining a wide range of observations in photoionization and radiation chemistry. The study of products and transients in photoionization of aromatic solutes in hydrocarbon and alcohol solvents illustrates several details of this “high-energy” chemistry. A reaction pathway involving ion-molecule reaction of excited ions is indicated for a series of polycyclic aromatic hydrocarbons photoionized using intense excimer laser (248 and 308 nm) pulses in hydrocarbon and alcohol solutions. We have found that condensed-phase ion-molecule reactions in radiolysis are ubiquitous and we speculate on their overall role in hydrocarbon radiolysis.     

Redox and Conformational Equilibria and Dynamics of Cytochrome c at High Electric Fields

Cytochrome c (Cyt‐c) adsorbed in the electrical double layer of the Ag electrode/electrolyte interface has been studied by stationary and time‐resolved surface‐enhanced resonance Raman spectroscopy to analyse the effect of strong electric fields on structure and reaction equilibria and dynamics of the protein. In the potential range between +0.1 and ?0.55 V (versus saturated calomel electrode), the adsorbed Cyt‐c forms a potential‐dependent reversible equilibrium between the native state B1 and a conformational state B2. The redox potentials of the bis‐histidine‐coordinated six‐coordinated low‐spin and five‐coordinated high‐spin substates of B2 were determined to be ?0.425 and ?0.385 V, respectively, whereas the additional six‐coordinated aquo‐histidine‐coordinated high‐spin substate was found to be redox‐inactive. The redox potential for the conformational state B1 was found to be the same as in solution in agreement with the structural identity of the adsorbed B1 and the native Cyt‐c. For all three redox‐active species, the formal heterogeneous electron transfer rate constants are small and of the same order of magnitude (3–13 s^?1), which implies that the rate‐limiting step is largely independent of the redox‐site structure. These findings, as well as the slow and potential‐dependent transitions between the various conformational (sub‐)states, can be rationalized in terms of an electric field‐induced increase of the activation energy for proton‐transfer steps linked to protein structural reorganisation. Further increasing the electric field strength by shifting the electrode potential above +0.1 V leads to irreversible structural changes that are attributed to an unfolding of the polypeptide chain.     

Pulse radiolysis study of the initial steps of the polymerization of cyclohexyl acrylate and cyclohexyl methacrylate

Pulse radiolysis with kinetic spectroscopic detection was applied to study the kinetics of the first steps of radiation induced polymerization of cyclohexyl acrylate and cyclohexyl methacrylate in cyclohexane solvent. The reactions were initiated by cyclohexyl radicals produced in the radiolysis of the solvent. The transient absorption spectra of the -carboxyalkyl type radicals produced in addition reaction show maxima around 300 nm. This shifts to longer wavelength with time after the pulse. This phenomenon was explained by the oligomerization reaction. From the kinetic curves average rate coefficients of termination for the oligomer radicals (2k_t) were determined as a function of time elapsed after the electron pulse. The values obtained were compared with those calculated for other (acrylate and methacrylate type) monomers.     

A Pulse Radiolysis Study of the Dynamics of Ascorbic Acid Free Radicals within a Liposomal Environment

The dynamics of free‐radical species in a model cellular system are examined by measuring the formation and decay of ascorbate radicals within a liposome with pulse radiolysis techniques. Upon pulse radiolysis of an N₂O‐saturated aqueous solution containing ascorbate‐loaded liposome vesicles, ascorbate radicals are formed by the reaction of OH^. radicals with ascorbate in unilamellar vesicles exclusively, irrespective of the presence of vesicle lipids. The radicals are found to decay rapidly compared with the decay kinetics in an aqueous solution. The distinct radical reaction kinetics in the vesicles and in bulk solution are characterized, and the kinetic data are analyzed.     

Electron transfer in SAM/cytochrome/polyelectrolyte hybrid systems on electrodes: a time-resolved surface-enhanced resonance Raman study

Silver electrodes were covered with mixed self-assembled monolayers (SAMs) of 11-mercaptoundecanoic acid (MUA) and 11-mercaptoundecanol (MU) and subsequently coated with alternating layers of cytochrome c (Cyt) and poly(anilinesulfonic acid) (PASA). The immobilized protein is electroactive and retains its native structure. Compared to the case of systems on gold electrodes, the stability of the assembly was found to be decreased. The redox process of Cyt is accompanied by reversible oxidation-reduction of PASA as revealed by the comparative surface-enhanced resonance Raman (SERR) analysis of assemblies including Cyt and the redox-inactive apo-cytochrome c. Time-resolved SERR experiments show a fast electron exchange between the protein and the polyelectrolyte that may play a supporting role in the electric communication of thicker multilayer assemblies employed as sensors.     

The study of stabilizer action modes by means of time-resolved techniques: Intermediate radical cations

In organic systems, radiation- and photo-induced electron transfer reactions result in the first step in the formation of radical cations. With pulse radiolysis and laser photolysis experiments radical cations of phenols could be indirectly characterized whereas radical cations of sterically hindered amines (HALS compounds) could be directly observed.