Anion size modulates the structure of the A state of cytochrome c

Singlet oxygen quenching as a probe for cytochrome c molten globule state formation

Singlet oxygen refers to the nonradical metastable excited state of molecular oxygen that readily oxidizes various cellular components. Its behavior in different biological systems has been studied for many years. Recently, we analyzed the effect of singlet oxygen quenching by heme cofactor in cytochrome c (cyt c). Here, we have exploited this effect in the investigation of conformational differences in the molten globule states of cyt c induced by different sodium anions, namely sulfate, chloride and perchlorate. The high efficiency of heme toward quenching singlet oxygen enabled us to use this property for the analysis of the otherwise experimentally difficult-to-determine parameter of heme upon exposure to solvents as highly similar conformational states of cyt c in the molten globule states are induced by different salts at acidic pH. Our results from singlet oxygen quenching experiments correlate well with other spectroscopic methods, such as circular dichroism and fluorescence measurements, and suggest increasing availability of heme in the order: perchlorate < chloride < sulfate. Based on our findings we propose that singlet oxygen phosphorescence measurements are useful in determining the differences in the protein conformation of their heme regions, particularly regarding the relative heme exposure to the solvent.

Characterisation of molten globule-like state of sheep serum albumin at physiological pH

Sheep serum albumin (SSA) is a 583 amino acid residues long multidomain monomeric protein which is rich in cysteine and low in tryptophan content. The serum albumins (from human, bovine and sheep) play a vital role among all proteins investigated until now, as they are the most copious circulatory proteins. We have purified SSA from sheep kidneys by a simple and efficient two-step purification procedure. Further, we have studied urea-induced denaturation of SSA by monitoring changes in the difference absorption coefficient at 287nm (Δε287), intrinsic fluorescence emission intensity at 347nm (F347) and mean residue ellipticity at 222nm ([θ]222) at pH 7.4 and 25°C. The coincidence of denaturation curves of these optical properties suggests that urea-induced denaturation is a bi-phasic process (native (N) state↔intermediate (X) state↔denatured (D) state) with a stable intermediate populated around 4.2-4.7M urea. The intermediate (X) state was further characterized by the far-UV and near-UV CD, dynamic light scattering (DLS) and fluorescence using 1-anilinonaphthalene-8-sulfonic acid (ANS) binding method. All denaturation curves were analyzed for Gibbs free energy changes associated with the equilibria, N state↔X state and X state↔D state in the absence of urea.

Heterogeneity of equilibrium molten globule state of cytochrome c induced by weak salt denaturants under physiological condition

While many proteins are recognized to undergo folding via intermediate(s), the heterogeneity of equilibrium folding intermediate(s) along the folding pathway is less understood. In our present study, FTIR spectroscopy, far- and near-UV circular dichroism (CD), ANS and tryptophan fluorescence, near IR absorbance spectroscopy and dynamic light scattering (DLS) were used to study the structural and thermodynamic characteristics of the native (N), denatured (D) and intermediate state (X) of goat cytochorme c (cyt-c) induced by weak salt denaturants (LiBr, LiCl and LiClO₄) at pH 6.0 and 25°C. The LiBr-induced denaturation of cyt-c measured by Soret absorption (Δε₄₀₀) and CD ([θ]₄₀₉), is a three-step process, N ↔ X ↔ D. It is observed that the X state obtained along the denaturation pathway of cyt-c possesses common structural and thermodynamic characteristics of the molten globule (MG) state. The MG state of cyt-c induced by LiBr is compared for its structural and thermodynamic parameters with those found in other solvent conditions such as LiCl, LiClO₄ and acidic pH. Our observations suggest: (1) that the LiBr-induced MG state of cyt-c retains the native Met80-Fe(III) axial bond and Trp59-propionate interactions; (2) that LiBr-induced MG state of cyt-c is more compact retaining the hydrophobic interactions in comparison to the MG states induced by LiCl, LiClO₄ and 0.5 M NaCl at pH 2.0; and (3) that there exists heterogeneity of equilibrium intermediates along the unfolding pathway of cyt-c as highly ordered (X1), classical (X2) and disordered (X3), i.e., D ↔ X3 ↔ X2 ↔ X1 ↔ N.

Chloride and other anions inhibit dichloroacetate-induced inactivation of human liver GSTZ1 in a haplotype-dependent manner

The in vivo elimination rate of dichloroacetate (DCA), an investigational drug; is determined by the rate of its biotransformation to glyoxylate, catalyzed by glutathione transferase ζ1 (GSTZ1). DCA is a mechanism-based inactivator of GSTZ1, thus elimination of DCA is slowed with repeated dosing. We observed that chloride, a physiologically important anion, attenuated DCA-induced GSTZ1 inactivation in human liver cytosol in a concentration and GSTZ1 haplotype-dependent way. In the absence of chloride, incubation with 0.5mM DCA resulted in inactivation of GSTZ1 with a half-life of 0.4h (samples with the KRT haplotype) to 0.5h (EGT haplotype). At the hepatic physiological chloride concentration, 38mM, samples with the EGT haplotype retained more activity (80%) following a 2-h incubation with 0.5mM DCA than those possessing the KRT haplotype (55%). The chloride concentration that protected 50% of the GSTZ1 activity following 2-h incubation with 0.5mM DCA (EC50) was 15.0±3.1mM (mean±S.D., n=3) for EGT samples and 36.2±2.2mM for KRT samples. Bromide, iodide and sulfite also protected GSTZ1 from inactivation by DCA, however fluoride, sulfate, carbonate, acetate, cyanide did not. Protection by bromide varied by GSTZ1 haplotype: EC50 was 1.3±0.3mM for the EGT haplotype and 5.0±0.60mM for the KRT haplotype. The EC50 values for iodide and sulfite in liver cytosol samples with EGT haplotype were respectively 0.14±0.06mM and 9.6±1.1mM (mean±S.D., n=3). Because the in vivo half-life of DCA is determined by the fraction of active GSTZ1 in the liver, identifying factors that regulate GSTZ1 activity is important in determining appropriate DCA dosing in humans.

The role of key residues in structure, function, and stability of cytochrome-c

Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.

Role of lysines in cytochrome c-cardiolipin interaction

Cytochrome c undergoes structural variations during the apoptotic process; such changes have been related to modifications occurring in the protein when it forms a complex with cardiolipin, one of the phospholipids constituting the mitochondrial membrane. Although several studies have been performed to identify the site(s) of the protein involved in the cytochrome c-cardiolipin interaction, to date the location of this hosting region(s) remains unidentified and is a matter of debate. To gain deeper insight into the reaction mechanism, we investigate the role that the Lys72, Lys73, and Lys79 residues play in the cytochrome c-cardiolipin interaction, as these side chains appear to be critical for cytochrome c-cardiolipin recognition. The Lys72Asn, Lys73Asn, Lys79Asn, Lys72/73Asn, and Lys72/73/79Asn mutants of horse heart cytochrome c were produced and characterized by circular dichroism, ultraviolet-visible, and resonance Raman spectroscopies, and the effects of the mutations on the interaction of the variants with cardiolipin have been investigated. The mutants are characterized by a subpopulation with non-native axial coordination and are less stable than the wild-type protein. Furthermore, the mutants lacking Lys72 and/or Lys79 do not bind cardiolipin, and those lacking Lys73, although they form a complex with the phospholipid, do not show any peroxidase activity. These observations indicate that the Lys72, Lys73, and Lys79 residues stabilize the native axial Met80-Fe(III) coordination as well as the tertiary structure of cytochrome c. Moreover, while Lys72 and Lys79 are critical for cytochrome c-cardiolipin recognition, the simultaneous presence of Lys72, Lys73, and Lys79 is necessary for the peroxidase activity of cardiolipin-bound cytochrome c.

Cytochrome c folding / unfolding: a unifying picture

Recent NMR structural and dynamical data on partially folded forms of mono-heme cytochrome c provide a unifying picture of the behavior of the protein far from the native conditions and suggest useful hints to explain the redox dependent stability of the protein. A fragile hinge in the structure of mitochondrial cytochrome c is identified, which may not have correspondents in smaller type-1 cytochromes. Former spectroscopic and kinetic data are here discussed in terms of this new view.

Thermodynamic and structural properties of the acid molten globule state of horse cytochrome C

To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high salt concentrations was evaluated by solution X-ray scattering (SXS), dynamic light scattering, and circular dichroism measurements. MG1 was globular and slightly (3%) larger than the native state, N. Calorimetric methods, such as differential scanning calorimetry and isothermal acid-titration calorimetry, were used to evaluate the thermodynamic parameters in the transitions of N to MG1 and MG1 to denatured state D of horse cytochrome c. The heat capacity change, ΔC(p), in the N-to-MG1 transition was determined to be 2.56 kJ K(-1) mol(-1), indicating the increase in the level of hydration in the MG1 state. Moreover, the intermediate state on the thermal N-to-D transition of horse cytochrome c at pH 4 under low-salt conditions showed the same structural and thermodynamic properties of the MG1 state in both SXS and calorimetric measurements. The Gibbs free energy changes (ΔG) for the N-to-MG1 and N-to-D transitions at 15 °C were 10.9 and 42.2 kJ mol(-1), respectively.

A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration

To understand the stabilization mechanism of the transient intermediate state in protein folding, it is very important to understand the structure and stability of the molten globule state under a native condition, in which the native state exists stably. The thermal transitions of horse cytochrome c were thermodynamically evaluated by highly precise differential scanning calorimetry (DSC) at pH 3.8-5.0. The heat capacity functions were analyzed using double deconvolution and the nonlinear least-squares method. An intermediate (I) state is clearly confirmed in the thermal native (N)-to-denatured (D) transition of horse cytochrome c. The mole fraction of the intermediate state shows the largest value, 0.4, at nearly 70 degrees C at pH 4.1. This intermediate state was also detected by the circular dichroism (CD) method and was found to have the properties of the molten globule-like structure by three-state analysis of the CD data. The Gibbs free-energy change between N and I, DeltaG(NI), and that between N and D, DeltaG(ND), were evaluated to be 9-22 kJ mol(-1) and 41-45 kJ mol(-1), respectively at 15( ) degrees C and pH 4.1.

Salt-induced formation of the A-state of ferricytochrome c--effect of the anion charge on protein structure

Structural information on partially folded forms is important for a deeper understanding of the folding mechanism(s) and the factors affecting protein stabilization. The non-native compact state of equine cytochrome c stabilized by salts in an acidic environment (pH 2.0-2.2), called the A-state, is considered a suitable model for the molten globule of cytochrome c, as it possesses a native-like alpha-helix conformation but a fluctuating tertiary structure. In this article, we extend our knowledge on anion-induced protein stabilization by determining the effect of anions carrying a double negative charge; unlike monovalent anions (which are thought to exert an 'ionic atmosphere' effect on the macromolecule), divalent anions are thought to bind to the protein at specific surface sites. Our data indicate that divalent anions, in comparison to monovalent ions, have a greater tendency to stabilize the native-like M-Fe(III)-H coordinated state of the protein. The possibility that divalent anions may bind to the protein at the same sites previously identified for polyvalent anions was evaluated. To investigate this issue, the behavior of the K88E, K88E/T89K and K13N mutants was investigated. The data obtained indicate that the mutated residues, which contribute to form the binding sites of polyanions, are important for stabilization of the native conformation; the mutants investigated, in fact, all show an increased amount of the misligated H-Fe(III)-H state and, with respect to wild-type cytochrome c, appear to be less sensitive to the presence of the anion. These residues also modulate the conformation of unfolded cytochrome c, influencing its spin state and the coordination to the prosthetic group.

Comparative study of effects of polyols, salts, and alcohols on trichloroacetic acid-induced state of cytochrome c

A systematic investigation of the effect of polyethylene glycols, salts, and alcohols on the trichloroacetic acid (TCA)-induced state of ferricytochrome c was made using various spectroscopic techniques. Native cytochrome c (Cyt c) has a fluorescence maximum at 335 nm, whereas the TCA-induced state of Cyt c has a red shift of 7 nm with enhanced fluorescence intensity. The near- and far-UV CD spectra showed a significant loss of tertiary and secondary structure, although the protein is relatively less unfolded as compared with a conformation at pH 2.0. Addition of 70% (v/v) polyols to TCA (3.3 mM)-induced state of Cyt c resulted in increased 1-anilino-8-naphthalene sulfonate binding and increased mean residue ellipticity at 222 nm, indicating increase in compactness with enhanced exposure of hydrophobic surface area. Also, the stabilizing effect of salts and alcohols on the TCA-induced state was studied and compared with their effect on trifluoroacetic acid-unfolded state of Cyt c. Among all the polyols, salts, and alcohols studied, PEG-400, K3[Fe(CN)6], and butanol were the most efficient in inducing secondary structure in TCA-induced state as examined by the above-mentioned spectroscopic techniques. For salts, the efficiency in inducing the secondary structure followed the order K3[Fe(CN)6] > KClO4 > K2SO4 > KCl. For alcohols, this order was found to be as follows: butanol > propanol > ethanol > methanol.

Kinetic, Thermodynamic, and Mechanistic Patterns for Free (Unbound) Cytochromec at Au/SAM Junctions: Impact of Electronic Coupling, Hydrostatic Pressure, and Stabilizing/Denaturing Additives

Combined kinetic (electrochemical) and thermodynamic (calorimetric) investigations were performed for an unbound (intact native-like) cytochrome c (CytC) freely diffusing to and from gold electrodes modified by hydroxyl-terminated self-assembled monolayer films (SAMs), under a unique broad range of experimental conditions. Our approach included: 1) fine-tuning of the charge-transfer (CT) distance by using the extended set of Au-deposited hydroxyl-terminated alkanethiol SAMs [-S-(CH(2))(n)-OH] of variable thickness (n=2, 3, 4, 6, 11); 2) application of a high-pressure (up to 150 MPa) kinetic strategy toward the representative Au/SAM/CytC assemblies (n=3, 4, 6); 3) complementary electrochemical and microcalorimetric studies on the impact of some stabilizing and denaturing additives. We report for the first time a mechanistic changeover detected for "free" CytC by three independent kinetic methods, manifested through 1) the abrupt change in the dependence of the shape of the electron exchange standard rate constant (k(o)) versus the SAM thickness (resulting in a variation of estimated actual CT range within ca. 15 to 25 A including ca. 11 A of an "effective" heme-to-omega-hydroxyl distance). The corresponding values of the electronic coupling matrix element vary within the range from ca. 3 to 0.02 cm(-1); 2) the change in activation volume from +6.7 (n=3), to approximately 0 (n=4), and -5.5 (n=6) cm(3) mol(-1) (disclosing at n=3 a direct pressure effect on the protein's internal viscosity); 3) a "full" Kramers-type viscosity dependence for k(o) at n=2 and 3 (demonstrating control of an intraglobular friction through the external dynamic properties), and its gradual transformation to the viscosity independent (nonadiabatic) regime at n=6 and 11. Multilateral cross-testing of "free" CytC in a native-like, glucose-stabilized and urea-destabilized (molten-globule-like) states revealed novel intrinsic links between local/global structural and functional characteristics. Importantly, our results on the high-pressure and solution-viscosity effects, together with matching literature data, strongly support the concept of "dynamic slaving", which implies that fluctuations involving "small" solution components control the proteins' intrinsic dynamics and function in a highly cooperative manner as far as CT processes under adiabatic conditions are concerned.

Nature of the cytochrome c molten globule

We have employed fluorescence energy transfer (FET) kinetics to probe unfolded and molten globule states of five dansyl (Dns) variants of Saccharomyces cerevisiae iso-1 cytochrome c. The covalently bound Fe(III) heme group quenches Dns fluorescence by energy transfer; measurements of FET kinetics yielded distributions of D-A distances (P(r)) for these states. The P(r) distributions and corresponding mean force potentials (U(r)) show that the cytochrome c molten globule is a highly structured state with a substantial number of native interactions. Wide P(r) distributions directly reflect the dynamic nature and conformational diversity of this molten globule. P(r) distributions for the "burst-phase" refolding intermediate suggest that the equilibrium cytochrome c molten globule is not a suitable model for early intermediates formed during protein refolding.

Unusual effect of salts on the homodimeric structure of NADH oxidase from Thermus thermophilus in acidic pH

The unusual salt-dependent behavior of the homodimeric flavoenzyme NADH oxidase from Thermus thermophilus in acidic pH has been studied using circular dichroism (CD) and sedimentation velocity. The native-like secondary and quaternary structures in acidic low ionic strength conditions were significantly perturbed by the addition of salts. The peptide region of the CD spectra showed a major salt-induced conformational change in the protein secondary structure. Sedimentation velocity experiments showed dissociation of the homodimeric structure of NADH oxidase in the presence of salt (>1 M). The new acidic conformation of the protein was stabilized by high ionic strength as indicated by a salt-induced increase in the melting temperature of the protein, and by a shift in the apparent pK(a) values of the conformational transition to a less acidic pH. Distortion of the dominant alpha-helical signal was expressed as the disappearance of the parallel polarized Moffitt exciton band at 208 nm without an accompanying loss of amplitude of n-->pi* electronic transitions at 222 nm. The unusual CD spectra correlated qualitatively with the theoretically calculated CD spectra of short alpha-helical structures and/or twisted beta-sheets. Differences between the experimentally obtained CD spectra and theoretical calculations (AGADIR) of the alpha-helical content of NADH oxidase indicate a role for non-local interactions in the protein conformation at high ionic strength and low pH. These findings indicate the importance of the homodimeric interface and electrostatic interactions for maintaining the structural integrity of this thermophilic protein.

Conformational Transitions of Ferricytochrome c in Strong Inorganic Acids

Conformational transitions of horse heart ferricytochromec(ferricytc) have been investigated in the presence of strong inorganic acids and their salts by optical absorption spectroscopy, magnetic circular dichroism and circular dichroism. In the presence of acids (HClO4or H2SO4, pH 2) or their salts (1 M NaClO4or Na2SO4, pH 2, 25 °C), the three ligation states of ferricytcheme were identified. One is the high-spin state: His18-Fe-H2O (40-50%), and two are the low-spin states: His18-Fe-Met80 (30-25%) and His18-Fe-His (30-25%). Under these conditions low temperatures facilitate native heme coordination of ferricytc. Transition from low-spin to high-spin heme coordination of ferricytcis complete in 1 M HClO4or 3 M H2SO4. At the concentration of HClO4and H2SO4above 3 M, different behavior in spectral transitions of ferricytcnear the heme is observed. High-spin pentacoordinated ferricytcwith the heme ligand of His18-Fe is formed in 8 M H2SO4. This state is unstable at higher concentration of H2SO4and porphyrin ferricytcis formed. At HClO4concentration higher than 3 M, the new, until this time not observed heme coordination structure of ferricytcoriginates.

Insights into the role of the histidines in the structure and stability of cytochrome c

In this paper we investigate the role played by each histidine in the amino acid sequence of yeast iso-1-cytochrome c (with the exception of H18, the residue axially coordinated to the heme iron) in determining the protein structure and stability. To this end, we have generated and characterized the double mutants H26Y/H33Y, H26Y/H39K and H33Y/H39K obtained from the C102T variant of the protein, which retain only one histidine side chain in the amino acid sequence. In particular, the H39K mutation inserts a lysine at position 39 as in the sequence of equine cytochrome c. The H26Y/H33Y/H39K triple mutant, which lacks all three histidines, was also produced and its spectroscopic properties are compared with those of the double mutants. The data highlight the critical role played by H26 in determining protein stability. Recombinant horse cytochrome c and the corresponding H26Y mutant were also generated and characterized. Since equine cytochrome c exhibits higher stability than the yeast protein, this provides a valuable opportunity to understand the role played by the invariant H26 residue in determining structure and stability.

Cytochrome c Superstructure Biocomposite Nucleated by Gold Nanoparticle: Thermal Stability and Voltammetric Behavior

The thermal stability of cytochrome c (cyt c) after Au-nanoparticle-directed association has been studied by various spectroscopic (electronic absorption, resonance Raman, and circular dichroism) and electrochemical methods. The results show that the thermal stability of the Au-cyt c superstructure biocomposite formed by the electrostatic and hydrophobic interactions among the associated proteins increases significantly. It is mainly caused by strong hydrophobicity of the associated cyt c in Au-cyt c superstructure at high temperature, which results from the compact secondary structure and the packing of hydrophobic side chains around the Trp 59 and heme. In addition, the formation of bis-His configuration of heme is facilitated by the tightly self-associated state of cyt c in the Au-cyt c superstructure. The electrostatic coupling of the opposite charges among shells of the adsorbed proteins due to the formation of the superstructure biocomposite can reduce repulsions among the same charges in protein. These factors are also important for enhancing the stability of the associated cyt c. Furthermore, the voltammetric behavior of Au-cyt c at DNA modified glassy carbon electrode has been investigated for extending the application of Au-cyt c.

Direct observation of the enthalpy change accompanying the native to molten-globule transition of cytochrome c by using isothermal acid-titration calorimetry

The enthalpy change accompanying the reversible acid-induced transition from the native (N) to the molten-globule (MG) state of bovine cytochrome c was directly evaluated by isothermal acid-titration calorimetry (IATC), a new method for evaluating the pH dependence of protein enthalpy. The enthalpy change was 30 kJ/mol at 30 degrees C, pH 3.54, with 500 mM KCl. The results of the global analysis of the temperature dependence of the excess enthalpy from 20 to 35 degrees C demonstrated that the N to MG transition is a two-state transition with a small heat capacity change of 1.1 kJ K(-1) mol(-1). The present findings were also indicative of the pH dependence of the enthalpy and the heat capacity of the MG state, -13 kJ mol(-1) pH(-1) and -1.0 kJ K(-1) mol(-1) pH(-1), respectively, at 30 degrees C within a pH range from 2 to 3.

Electrochemistry of unfolded cytochrome c in neutral and acidic urea solutions

The present investigation reports the first experimental measurements of the reorganization energy of unfolded metalloprotein in urea solution. Horse heart cytochrome c (cyt c) has been found to undergo reversible one-electron transfer reactions at pH 2 in the presence of 9 M urea. In contrast, the protein is electrochemically inactive at pH 2 under low-ionic strength conditions in the absence of urea. Urea is shown to induce ligation changes at the heme iron and lead to practically complete loss of the alpha-helical content of the protein. Despite being unfolded, the electron-transfer (ET) kinetics of cyt c on a 2-mercaptoethanol-modified Ag(111) electrode remain unusually fast and diffusion controlled. Acid titration of ferric cyt c in 9 M urea down to pH 2 is accompanied by protonation of one of the axial ligands, water binding to the heme iron (pK(a) = 5.2), and a sudden protein collapse (pH < 4). The formal redox potential of the urea-unfolded six-coordinate His18-Fe(III)-H(2)O/five-coordinate His18-Fe(II) couple at pH 2 is estimated to be -0.083 V vs NHE, about 130 mV more positive than seen for bis-His-ligated urea-denatured cyt c at pH 7. The unusually fast ET kinetics are assigned to low reorganization energy of acid/urea-unfolded cyt c at pH 2 (0.41 +/- 0.01 eV), which is actually lower than that of the native cyt c at pH 7 (0.6 +/- 0.02 eV), but closer to that of native bis-His-ligated cyt b(5) (0.44 +/- 0.02 eV). The roles of electronic coupling and heme-flattening on the rate of heterogeneous ET reactions are discussed.

ATP specifically drives refolding of non-native conformations of cytochrome c

An increasing body of evidence ascribes to misfolded forms of cytochrome c (cyt c) a role in pathophysiological events such as apoptosis and disease. Here, we examine the conformational changes induced by lipid binding to horse heart cyt c at pH 7 and study the ability of ATP (and other nucleotides) to refold several forms of unfolded cyt c such as oleic acid-bound cyt c, nicked cyt c, and acid denatured cyt c. The CD and fluorescence spectra demonstrate that cyt c unfolded by oleic acid has an intact secondary structure, and a disrupted tertiary structure and heme environment. Furthermore, evidence from the Soret CD, electronic absorption, and resonance Raman spectra indicates the presence of an equilibrium of at least two low-spin species having distinct heme-iron(III) coordination. As a whole, the data indicate that binding of cyt c to oleic acid leads to a partially unfolded conformation of the protein, resembling that typical of the molten globule state. Interestingly, the native conformation is almost fully recovered in the presence of ATP or dATP, while other nucleotides, such as GTP, are ineffective. Molecular modeling of ATP binding to cyt c and mutagenesis experiments show the interactions of phosphate groups with Lys88 and Arg91, with adenosine ring interaction with Glu62 explaining the unfavorable binding of GTP. The finding that ATP and dATP are unique among the nucleotides in being able to turn non-native states of cyt c back to native conformation is discussed in the light of cyt c involvement in cell apoptosis.

Characterization of molten globule state of cytochrome c at alkaline, native and acidic pH induced by butanol and SDS

In our earlier communications, we had studied the acid induced unfolding of stem bromelain, glucose oxidase and fetuin [Eur. J. Biochem. 269 (2002) 47; Biochem. Biophys. Res. Comm. 303 (2003) 685; Biochim. Biophys. Acta 1649 (2003) 164] and effect of salts and alcohols on the acid unfolded state of alpha-chymotrypsinogen and stem bromelain [Biochim. Biophy. Acta 1481 (2000) 229; Arch. Biochem. Biophys. 413 (2) (2003) 199]. Here, we report the presence of molten globule like equilibrium intermediate state under alkaline, native and acid conditions in the presence of SDS and butanol. A systematic investigation of sodium dodecyl sulphate and butanol induced conformational alterations in alkaline (U(1)) and acidic (U(2)) unfolded states of horse heart ferricytochrome c was examined by circular dichroism (CD), tryptophan fluorescence and 1-anilino-8-napthalene sulfonate (ANS) binding. The cytochrome c (cyt c) at pH 9 and 2 shows the loss of approximately 61% and 65% helical secondary structure. Addition of increasing concentrations of butanol (0-7.2 M) and sodium dodecyl sulphate (0-5 mM) led to an increase in ellipticity value at 208 and 222 nm, which is the characteristic of formation of alpha-helical structure. Cyt c is a heme protein in which the tryptophan fluorescence is quenched in the native state by resonance energy transfer to the heme group attached to cystines at positions 14 and 17. At alkaline and acidic pH protein shows enhancement in tryptophan fluorescence and quenched ANS fluorescence. Addition of increasing concentration of butanol and SDS to alkaline or acid unfolded state leads to decrease in tryptophan and increase in ANS fluorescence with a blue shift in lambda(max), respectively. In the presence of 7.2 M butanol and 5 mM SDS two different intermediate states I(1) and I(2) were obtained at alkaline and acidic pH, respectively. States I(1) and I(2) have native like secondary structure with disordered side chains (loss of tertiary structure) as predicted from tryptophan fluorescence and high ANS binding. These results altogether imply that the butanol and SDS induced intermediate states at alkaline and acid pH lies between the unfolded and native state. At pH 6, in the presence of 7.2 M butanol or 5 mM SDS leads to the loss of CD bands at 208 and 222 nm with the appearance of trough at 228 nm also with increase in tryptophan and ANS fluorescence in contrast to native protein. This partially unfolded intermediate state obtained represents the folding pathway from native to unfolded structure. To summarize; the 7.2 M butanol and 5 mM SDS stabilizes the intermediate state (I(1) and I(2)) obtained at low and alkaline pH. While the same destabilizes the native structure of protein at pH 6, suggesting a difference in the mechanism of conformational stability.

Cytochrome c?dimyristoylphosphatidylglycerol interactions studied by asymmetrical flow field-flow fractionation

Lipid membranes are well recognized ligands that bind peripheral and integral proteins in a specific manner and regulate their function. Cytochrome c (cyt c) is one of the partner peripheral protein that binds to the lipid membranes via electrostatic and hydrophobic interactions. In this study, asymmetrical flow field-flow fractionation (AsFlFFF) was used to compare the interactions of cyt c with the acidic phospholipid 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG), oleic acid (OA), and sodium dodecyl sulfate (SDS). The influence of pH and the cyt c-lipid molar mass ratios were evaluated by monitoring the diffusion coefficients and particle diameter distributions obtained for the free and lipid-bound protein. The hydrodynamic particle diameter of cyt c (pI 10) was 4.1 nm at pH 11.4 and around 4.2 nm at pH 7.0 and 8.0. Standard molar mass marker proteins were used for calibration to obtain the molar masses of free cyt c and its complexes with lipids. AsFlFFF revealed the binding of cyt c to DMPG and to OA to be mainly electrostatic. In the absence of electrostatic interactions, minor complex formation occurred, possibly due to the extended lipid anchorage involving the hydrophobic cavity of cyt c and the hydrocarbon chains of DMPG or SDS. The possibility of the formation of the molten globule state of cyt c, induced by the interaction between cyt c and lipids, is discussed.

Effect of Colloidal Gold Size on the Conformational Changes of Adsorbed Cytochrome c: Probing by Circular Dichroism, UV−Visible, and Infrared Spectroscopy

The conformational changes of bovine heart cytochrome c (cyt c) induced by the adsorption on gold nanoparticles with different sizes have been investigated by electronic absorption, circular dichroism (CD), and Fourier transform infrared spectra. The combination of these techniques can give complementary information about adsorption-induced conformational changes. The results show that there are different conformational changes for cyt c adsorbed on gold nanoparticles with different sizes due to the different interaction forces between cyt c and gold nanoparticles. The colloidal gold concentration-dependent conformation distribution curves of cyt c obtained by analysis of CD spectra using the singular value decomposition least-squares method show that the coverage of cyt c on the gold nanoparticles surface also affects the conformational changes of the adsorbed cyt c.

The 40s ?-loop plays a critical role in the stability and the alkaline conformational transition of cytochrome c

The structural and redox properties of a non-covalent complex reconstituted upon mixing two non-contiguous fragments of horse cytochrome c, the residues 1-38 heme-containing N-fragment with the residues 57-104 C-fragment, have been investigated. With respect to native cyt c, the complex lacks a segment of 18 residues, corresponding, in the native protein, to an omega (Omega)-loop region. The fragment complex shows compact structure, native-like alpha-helix content but a less rigid atomic packing and reduced stability with respect to the native protein. Structural heterogeneity is observed at pH 7.0, involving formation of an axially misligated low-spin species and consequent partial displacement of Met80 from the sixth coordination position of the heme-iron. Spectroscopic data suggest that a lysine (located in the Met80-containing loop, namely Lys72, Lys73, or Lys79) replaces the methionine residue. The residues 1-38/57-104 fragment complex shows an unusual biphasic alkaline titration characterized by a low (p K(a1)=6.72) and a high p K(a)-associated state transition (p K(a2)=8.56); this behavior differs from that of native cyt c, which shows a monophasic alkaline transition (p K(a)=8.9). The data indicate that the 40s Omega-loop plays an important role in the stability of cyt c and in ensuring a correct alkaline conformational transition of the protein.

pH-dependent conformational changes of ferricytochrome c induced by electrode surface microstructure

pH-dependent processes of bovine heart ferricytochrome c have been investigated by electronic absorption and circular dichroism (CD) spectra at functionalized single-wall carbon nanotubes (SWNTs) modified glass carbon electrode (SWNTs/GCE) using a long optical path thin layer cell. These methods enabled the pH-dependent conformational changes arising from the heme structure change to be monitored. The spectra obtained at functionalized SWNTs/GCE reflect electrode surface microstructure-dependent changes for pH-induced protein conformation, pK(a) of alkaline transition and structural microenvironment of the ferricytochrome c heme. pH-dependent conformational distribution curves of ferricytochrome c obtained by analysis of in situ CD spectra using singular value decomposition least square (SVDLS) method show that the functionalized SWNTs can retain native conformational stability of ferricytochrome c during alkaline transition.

Hydrophobic effect of trityrosine on heme ligand exchange during folding of cytochrome c

Effect of a hydrophobic peptide on folding of oxidized cytochrome c (cyt c) is studied with trityrosine. Folding of cyt c was initiated by pH jump from 2.3 (acid-unfolded) to 4.2 (folded). The Soret band of the 2-ms transient absorption spectrum during folding decreased its intensity and red-shifted from 397 to 400 nm by interaction with trityrosine, whereas tyrosinol caused no significant effect. The change in the transient absorption spectrum by interaction with trityrosine was similar to that obtained with 100 mM imidazole, which showed that the population of the intermediate His/His coordinated species increased during folding of cyt c by interaction with trityrosine. The absorption change was biphasic, the fast phase (82+/-9s(-1)) corresponding to the transition from the His/H(2)O to the His/Met coordinated species, whereas the slow phase (24+/-3s(-1)) from His/His to His/Met. By addition of trityrosine, the relative ratio of the slow phase increased, due to increase of the His/His species at the initial stage of folding. According to the resonance Raman spectra of cyt c, the high-spin 6-coordinate and low-spin 6-coordinate species were dominated at pH 2.3 and 4.2, respectively, and these species were not affected by addition of trityrosine. These results demonstrated that the His/His species increased by interaction with trityrosine at the initial stage of cyt c folding, whereas the heme coordination structure was not affected by trityrosine when the protein was completely unfolded or folded. Hydrophobic peptides thus may be useful to study the effects of hydrophobic interactions on protein folding.

Anion concentration modulates the conformation and stability of the molten globule of cytochrome c

Anions induce collapse of acid-denatured cytochrome c into a compact state, the A-state, showing molten globule character. Since structural information on partially folded forms of proteins is important for a deeper understanding of folding mechanisms and of the factors affecting protein stabilization, in this paper we have investigated in detail the effects of anions on the tertiary conformation of the A-state. We have found that the salt-induced collapse of acid-denatured cytochrome c leads to a number of equilibria between high-spin and low-spin heme states and between two types of low-spin states. The two latter states are characterized by conformations leading to a native-like Met-Fe-His axial coordination and a bis-His configuration. The equilibrium between these two A-states is dependent on the concentration and/or size of the anions (i.e. the bigger the anion, the greater its effect). Further, on the basis of fast kinetic data, a kinetic model of the folding process from the acid-unfolded protein to the A-state (at low and high anion concentration) is described.

Structural features of the cytochrome C molten globule revealed by fluorescence energy transfer kinetics

Nonnative states of proteins are involved in a variety of cellular processes, including translocation of proteins across membranes and formation of amyloid fibrils. Probes that report on the structural heterogeneity of a polypeptide ensemble could resolve ambiguities in the classification of these states. Employing fluorescence energy transfer kinetics, we have shown that added anions shift the equilibrium between the compact and extended polypeptide structures that are present during refolding of Saccaromyces cerevisiae iso-1 cytochrome c. Specifically, at high salt concentrations (>/=700 mM), all of the polypeptides are compact with a mean C-terminal fluorophore-heme separation quite close to that in the native protein (25 A).

Molten-globule and other conformational forms of zinc cytochrome C. Effect of partial and complete unfolding of the protein on its electron-transfer reactivity

To test the effect of protein conformation on reactivity, we use laser flash photolysis to compare the electron-transfer properties of the triplet state of zinc-substituted cytochrome c, designated (3)Zncyt, in the folded forms at low (F(low)) and high (F(high)) ionic strength, molten-globule (MG) form, and the forms unfolded by acid (U(acid)) and urea (U(urea)) toward the following four oxidative quenchers: Fe(CN)(6)(3-), Co(acac)(3), Co(phen)(3)(3+), and iron(III) cytochrome c. We characterize the conformational forms of Zncyt on the basis of the far-UV circular dichroism, Soret absorption, and rate constant for natural decay of the triplet state. This rate constant in the absence of quencher increases in the order F(high) < F(low) < MG < U(acid) < U(urea) because the exposure of porphyrin to solvent increases as Zncyt unfolds. Bimolecular rate constants for the reaction of (3)Zncyt with the four quenchers show significant effects on reactivity of electrostatic interactions and porphyrin exposure to solvent. This rate constant at the ionic strength of 20 mM increases upon unfolding by urea and acid, respectively, as follows: 1340-fold and 466-fold when the quencher is Co(phen)(3)(3+) and 168-fold and 36-fold when the quencher is cyt(III). To compare reactivity of (3)Zncyt in the F(low), F(high), MG, U(acid), and U(urea) forms without complicating effects of electrostatic interactions, we used the electroneutral quencher Co(acac)(3). Indeed, reactivity of folded (3)Zncyt with Co(acac)(3) was independent of ionic strength. Reactivity of (3)Zncyt with Co(acac)(3) upon partial and complete unfolding increases 10-fold, 54-fold, and 64-fold in the molten-globule, urea-unfolded, and acid-unfolded forms.

Glycerol-induced formation of the molten globule from acid-denatured cytochrome c: implication for hierarchical folding

At high concentration (98% or higher, v/v), glycerol induces collapse of acid-denatured cytochrome c into a compact state, the G(U) state, showing a molten globule character. The G(U) state possesses a nativelike alpha-helix structure but a tertiary conformation less packed with respect to the native state. The spectroscopic properties of the G(U) state closely resemble those of the molten globule stabilized by the organic solvent from the native protein (called the G(N) state), indicating that glycerol can stabilize the molten globule of cytochrome c either from the native or the acid-denatured protein. The G(U) and the G(N) states show spectroscopic (and, thus, structural) properties and stabilities comparable to those of molten globules stabilized by different effectors, despite the fact that the mechanisms involved in the molten globule formation may significantly differ. This implies in cytochrome c a hierarchy for the rupture (native-to-molten globule) or the formation (unfolded-to-molten globule) of intramolecular interactions leading to the stabilization of the molten globule state of the protein, independently from the effector responsible for the structural transition, in accord with the sequential model proposed by Englander and collaborators.

Cytochrome c reconstituted from two peptide fragments displays native-like redox properties

Recombination of two fragments of horse cytochrome c (the heme-containing N-fragment, residues 1-56, and the C-fragment, residues 57-104), which are substantially unstructured at neutral pH, gives rise to a 1:1 fragment complex with a compact conformation, in which the alpha helical structure and the native Met80-Fe(III) axial bond are recovered. With respect to the native protein, the ferric complex shows a less rigid atomic packing and a decreased stability [Delta(DeltaG(o))D = 14.7 kJ.mol(-1)], ascribed to perturbations involving the Trp59 microenvironment and, to a lower extent, the heme pocket region. The redox potential, E1/2 = 234 +/- 5 mV vs. normal hydrogen electrode at 25 degrees C, is close to that of the intact protein, consistent with recovery of the native Met80-heme Fe(III) axial bond. Furthermore, the fragment complex shows reactivity similar to intact cytochrome c, in the reaction with cytochrome c oxidase. We conclude that the absence in the complex of some native cross-links and interlocked packing important for protein rigidity and stability is not as relevant for maintaining the native redox properties of the protein, provided that some structural requirements (i.e. recovering of the native-like alpha helical structure) are fulfilled and coordination of Met80 to the heme-iron is restored.