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).     

Calorimetric indication of the molten globule-like state of cytochrome c induced by n-alkyl sulfates at low concentrations

The molten globule state has been proposed as a major intermediate of protein folding. However it has proven difficult to obtain thermodynamic data characterizing this state. To explore an alternative approach for characterization of the molten globule state, n-alkyl sulfates induced formation of the molten globule state of horse cytochrome c at pH 2 was studied by isothermal titration calorimetry (ITC). Titration of the acid unfolded state of cytochrome c with sodium octyl sulfate, sodium dodecyl sulfate or sodium tetradecyl sulfate, generated an exothermic reaction for formation of the molten globule state. The effects of various n-alkyl sulfates on the acid unfolded state of cytochrome c demonstrated that the increased alkyl chain length enhanced the exothermic values of calorimetric enthalpy and induced a more compact molten globule states. The heat contents agreed well with the conformational transition measured by molar ellipticity at 222 nm ([θ]₂₂₂) and Stoke radius (Rs) values. These results emphasize that isothermal titration calorimetry provides a reasonable alternative method for characterization of the molten globule state.     

Spectroscopic study on acid-induced unfolding and refolding of apo-neuroglobin

pH-induced unfolding and refolding of apo-neuroglobin (apo-Ngb) were investigated by UV, fluorescence, circular dichroism (CD) spectra and light scattering measurements. Results revealed that apo-Ngb became partially unfolded at around pH 5.0, with evidences from a red shift in the fluorescence spectra, a decrease in the far-UV CD and a sharp peak in the light scattering intensity. Further lowering of the pH reversed these effects, suggesting that apo-Ngb folds back to a compact state. At pH 2.0, the apo-Ngb forms a folding intermediate known as molten globule (MG), which is possessed of native-like secondary structure and almost complete loss of tertiary structure. Based on these results, the acid-induced denaturation pathway of apo-Ngb can be illustrated from the native state (N), via a partially unfolded state (U_A) to the molten globule state (MG).     

Electrochemical and Spectroscopic Study on the Interaction of Cytochrome c with Anionic Lipid Vesicles

The structure and the electron-transfer of cytochrome c binding on the anionic lipid vesicles wrer analyzed by electrochemical and various spectroscopic methods.It was found that upon binding to anionic lipid membrane,the formal potential of cytochrome c shifted 30 mV negtively indicating an easier redox interaction than that in its native state.This is due to the local alteration of the coordination and the heme crevice.The structural perturbation in which a molten globule-like state is formed during binding to anionic lipid vesicles is more important.This study may help to understand the mechanism of the electron-transfer reactions of cytochrome c at the mitochondrial membrane.     

Dynamic spectroelectrochemical measurement for the conformational transition of cytochrome c induced by bromopyrogal red

The conformational transition of horse heart cytochrome c induced by bromopyrogal red (BPR) in very low concentration has been firstly investigated by dynamic spectroelectrochemical technique, both at the BPR adsorbed platinum gauze electrode and at a bare platinum gauze electrode in a solution containing BPR. The effect of BPR on the structure of cytochrome c was studied by UV-visible and Fourier transform IR spectroscopy. The unfolded cytochrome c behaves simply as an electron transfer protein with a formal potential of −142 mV vs. a normal hydrogen electrode. The difference between the formal potentials of the native and unfolded cytochrome c is coupled to a difference in conformational energy of the two states of about 40 kJ mol⁻¹, which agrees well with the result reported. The stability and slow refolding of the unfolded cytochrome c are discussed.     

2,2,2-trifluoroethanol-induced molten globule state of concanavalin a and energetics of 8-anilinonaphthalene sulfonate binding: calorimetric and spectroscopic investigation

The interaction of 2,2,2-trifluoroethanol (TFE) with concanavalin A has been investigated by using a combination of differential scanning calorimetry, isothermal titration calorimetry (ITC), circular dichroism (CD), and fluorescence spectroscopy at pH 2.5 and 5.2. All of the calorimetric transitions at both the pH values were found to be irreversible. In the presence of 4 mol kg(-1) TFE at pH 2.5, concanavalin A is observed to be in a partially folded state with significant loss of native tertiary structure. The loss of specific side chain interactions in the transition from native to the TFE-induced partially folded state is demonstrated by the loss of cooperative thermal transition and reduction of the CD bands in the aromatic region. Acrylamide quenching, 8-anilinonaphthalene sulfonate (ANS) binding, and energy transfer also suggest that in the presence of 4 mol kg(-1) TFE at pH 2.5 concanavalin A is in a molten globule state. ITC has been used for the first time to characterize the energetics of ANS binding to the molten globule state. ITC results indicate that the binding of ANS to the molten globule state and acid-induced state at pH 2.5 displays heterogeneity with two classes of non-interacting binding sites. The results provide insights into the role of hydrophobic and electrostatic interactions in the binding of ANS to concanavalin A. The results also demonstrate that ITC can be used to characterize the partially folded states of the protein both qualitatively and quantitatively.     

Solvent-induced modulation of collective photophysical processes in fluorescent silica nanoparticles

In this paper we show how it is possible to control the nature and the efficiency of collective photophysical processes in a network composed of two different fluorescent units organized on the surface of silica nanoparticles. Such a structure is obtained by covering nanoparticles with a layer of dansyl moieties (Dns) and by partially protonating them in solution. The two fluorophores Dns and Dns.H(+) have very different photophysical properties and can be selectively excited and detected. The interaction between the two units Dns and Dns.H(+) has been first investigated in a reference compound obtained by derivatizing 1,6-hexanediamine with two dansyl units. The photophysical characterization of this compound (absorption spectra, fluorescence spectra, quantum yield, and lifetime) showed that the two moieties can be involved both in energy and electron-transfer processes. Dansylated nanoparticles were prepared by modifying preformed silica nanoparticles with dansylated (3-aminopropyl)trimethoxysilane. Photophysical studies indicated that protonation has a dramatic effect on the fluorescence of the nanoparticles, leading to the quenching of both the protonated units and the surrounding nonprotonated ones. This amplified response to protonation, due to charge-transfer interactions, is solvent-dependent and is less efficient in pure chloroform with respect to acetonitrile/chloroform (5/1 v/v) mixtures. The reduced efficiency of the electron-transfer processes responsible for the quenching makes energy transfer competitive to such an extent that in pure chloroform excitation energy migration takes place from Dns.H(+) to Dns with great efficiency.     

Temperature dependent free energy surface of polymer folding from equilibrium and quench studies

Langevin dynamics simulation studies have been employed to calculate the temperature dependent free energy surface and folding characteristics of a 500 monomer long linear alkane (polyethylene) chain with a realistic interaction potential. Both equilibrium and temperature quench simulation studies have been carried out. Using the shape anisotropy parameter (S) of the folded molecule as the order parameter, we find a weakly first order phase transition between the high-temperature molten globule and low-temperature rodlike crystalline states separated by a small barrier of the order of k(B)T. Near the melting temperature (580 K), we observe an intriguing intermittent fluctuation with pronounced "1/f noise characteristics" between these two states with large difference in shape and structure. We have also studied the possibilities of different pathways of folding to states much below the melting point. At 300 K starting from the all-trans linear configuration, the chain folds stepwise into a very regular fourfold crystallite with very high shape anisotropy. Whereas, when quenched from a high temperature (900 K) random coil regime, we identify a two step transition from the random coiled state to a molten globulelike state and, further, to a anisotropic rodlike state. The trajectory reveals an interesting coupling between the two order parameters, namely, radius of gyration (R(g)) and the shape anisotropy parameter (S). The rodlike final state of the quench trajectory is characterized by lower shape anisotropy parameter and significantly larger number of gauche defects as compared to the final state obtained through equilibrium simulation starting from all-trans linear chain. The quench study shows indication of a nucleationlike pathway from the molten globule to the rodlike state involving an underlying rugged energy landscape.     

Thermodynamic analysis of partially folded states of myoglobin in presence of 2,2,2-trifluoroethanol

The thermal denaturation of myoglobin was studied in the presence of 2,2,2-trifluoroethanol (TFE) at various pH values using differential scanning calorimetry and UV–visible spectroscopy. The most obvious effect of TFE was lowering the transition temperature up to 1.5 mol · kg⁻¹, beyond which no thermal transitions were observed. The protein conformation was analysed by fluorescence and circular dichroism measurements. Quantitative binding of ANS to the TFE induced molten globule state of myoglobin was studied by using isothermal titration calorimetry. The results enable quantitative estimation of the binding strength of ANS with the molten globule state of myoglobin along with the enthalpic and entropic contributions to the binding process. The results suggest occurrence of common structural features of the molten globule states of proteins offering two types of binding sites to ANS molecules which are a widely used fluorescence probe to characterise partially folded states of proteins.     

Mapping the cytochrome C folding landscape

The solution to the riddle of how a protein folds is encoded in the conformational energy landscape for the constituent polypeptide. Employing fluorescence energy transfer kinetics, we have mapped the S.cerevisiae iso-1 cytochrome c landscape by monitoring the distance between a C-terminal fluorophore and the heme during folding. Within 1 ms after denaturant dilution to native conditions, unfolded protein molecules have evolved into two distinct and rapidly equilibrating populations: a collection of collapsed structures with an average fluorophore-heme distance (r) of 27 A and a roughly equal population of extended polypeptides with r > 50 A. Molecules with the native fold appear on a time scale regulated by heme ligation events ( approximately 300 ms, pH 7). The experimentally derived landscape for folding has a narrow central funnel with a flat upper rim on which collapsed and extended polypeptides interchange rapidly in a search for the native structure.     

An electrospray ionization mass spectrometry investigation of 1-anilino-8-naphthalene-sulfonate (ANS) binding to proteins

The binding of 1-anilino-8-naphthalene-sulfonic acid (ANS) to various globular proteins at acidic pH has been investigated by electrospray ionization mass spectrometry (ESI-MS). Maximal ANS binding is observed in the pH range 3-5. As many as seven species of dye-bound complexes are detected for myoglobin. Similar studies were carried out with cytochrome c, carbonic anhydrase, triosephosphate isomerase, lysozyme, alpha-lactalbumin, and bovine pancreatic trypsin inhibitor (BPTI). Strong ANS binding was observed wherever molten globule states were postulated in solution. ANS binding is not observed for lysozyme and BPTI, which have tightly folded structures in the native form. Alpha-lactalbumin, which is structurally related to lysozyme but forms a molten globule at acidic pH, exhibited ANS binding. Reduction of disulfide bonds in these proteins leads to the detection of ANS binding even at neutral pH. Binding was suppressed at very low pH (<2.5), presumably due to neutralization of the charge on the sulfonate moiety. The distribution of the relative intensities of the protein bound ANS species varies with the charge state, suggesting heterogeneity of gas phase conformations. The binding strength of these complexes was qualitatively estimated by dissociating them using enhanced nozzle skimmer potentials. The skimmer voltages also affected the lower and higher charge states of these complexes in a different manner.     

Charge recombination fluorescence in photosystem I reaction centers from Chlamydomonas reinhardtii

The fluorescence kinetics of photosystem I core particles from Chlamydomonas reinhardtii have been measured with picosecond resolution in order to test a previous hypothesis suggesting a charge recombination mechanism for the early electron-transfer steps and the fluorescence kinetics (Müller et al. Biophys. J. 2003, 85, 3899-3922). Performing global target analyses for various kinetic models on the original fluorescence data confirms the "charge recombination" model as the only acceptable one of the models tested while all of the other models can be excluded. The analysis allowed a precise determination of (i) the effective charge separation rate constant from the equilibrated reaction center excited state (438 ns(-1)) confirming our previous assignment based on transient absorption data (Müller et al. Biophys. J. 2003, 85, 3899-3922), (ii) the effective charge recombination rate constant back to the excited state (52 ns(-1)), and (iii) the intrinsic secondary electron-transfer rate constant (80 ns(-1)). The average energy equilibration lifetime core antenna/RC is about 1 ps in the "charge recombination" model, in agreement with previous transient absorption data, vs the 18-20 ps energy transfer lifetime from antenna to RC within "transfer-to-the-trap-limited" models. The apparent charge separation lifetime in the recombination model is about three times faster than in the "transfer-to-the-trap-limited" model. We conclude that the charge separation kinetics is trap-limited in PS I cores devoid of red antenna states such as in C. reinhardtii.     

Energy Transfer between Flavin and Cytochrome c

Energy transfer between photoexcited flavin and cytochrome c has been investigated in order to estimate intermolecular forces between flavin and cytochrome c. The quenching of the fluorescence of flavin by cytochrome c excited at 372 nm was found to be much greater than that excited at 465 nm. This dependence of the quenching on the exciting wavelength is considered to be due to the “prerelaxational” fast energy transfer. From the analysis of the quenching of the fluorescence of FMN and lumiflavin by cytochrome c excited at 465 nm, it was concluded that 1) the quenching is mainly controlled by resonance energy transfer, and 2) the heterogeneous dispersion state of molecules due to electrostatic forces makes the critical transfer distance, R ₀, of the resonance process longer than the real distance. For the quenching of the fluorescence of flavodoxin by cytochrome c, it was found that complex formation is a dominant process and is controlled to a great extent by electrostatic forces. Furthermore, fluorescence decay curves were measured by a single-photon counting method in order to estimate the dynamic processes of flavin fluorescence. The results also showed that the resonance process exists in the energy transfer between flavin and cytochrome c.     

Peptide and glycopeptide dendrimer apple trees as enzyme models and for biomedical applications

Solid phase peptide synthesis (SPPS) provides peptides with a dendritic topology when diamino acids are introduced in the sequences. Peptide dendrimers with one to three amino acids between branches can be prepared with up to 38 amino acids (MW ~ 5,000 Da). Larger peptide dendrimers (MW ~ 30,000) were obtained by a multivalent chloroacetyl cysteine (ClAc) ligation. Structural studies of peptide dendrimers by CD, FT-IR, NMR and molecular dynamics reveal molten globule states containing up to 50% of α-helix. Esterase and aldolase peptide dendrimers displaying dendritic effects and enzyme kinetics (k(cat)/k(uncat) ~ 10(5)) were designed or discovered by screening large combinatorial libraries. Strong ligands for Pseudomonas aeruginosa lectins LecA and LecB able to inhibit biofilm formation were obtained with glycopeptide dendrimers. Efficient ligands for cobalamin, cytotoxic colchicine conjugates and antimicrobial peptide dendrimers were also developed showing the versatility of dendritic peptides. Complementing the multivalency, the amino acid composition of the dendrimers strongly influenced the catalytic or biological activity obtained demonstrating the importance of the "apple tree" configuration for protein-like function in peptide dendrimers.     

Thermodynamic insights into the binding of ANS with the salt induced molten globule states of cytochrome c

The molten globule (MG) state or the A-state of cytochrome c (cyt c) has been induced by addition of salts sodium perchlorate (NaClO₄), sodium thiocyanate (NaSCN), and sodium sulphate (Na₂SO₄) at pH 2.0. Isothermal titration calorimetry (ITC) has been used for determining the energetics of binding of 8-anilino naphthalene sulphonate (ANS) to the salt induced A-state of cyt c, and the accompanying thermodynamic parameters have been analyzed to elucidate the nature of the interactions between ANS and the A-state of cyt c. Temperature dependent studies of the binding process reveal that the binding is not a two state process and there are more than a single type of interactions involved. Addition of a bulky salt tetraethylammonium bromide (TEAB) increases the stoichiometry of binding significantly, with a reduction in the binding affinity at a higher concentration. The results provide quantitative information on the binding of ANS to the salt induced molten globule states of cyt c. It is further inferred that the binding involves a combination of hydrophobic and electrostatic interactions.     

Rotational and vibrational energy transfer in vibrationally excited acetylene at energies near 6560 cm(-1)

Collisional energy transfer kinetics of vibrationally excited acetylene has been examined for states with internal energies near 6560 cm(-1). Total population removal rate constants were determined for selected rotational levels of the (1,0,1,0(0),0(0)) and (0,1,1,2(0),0(0)) states. Values in the range of (10-18) × 10(-10) cm(3) s(-1) were obtained. Measurements of state-to-state rotational energy transfer rate constants were also carried out for these states. The rotational energy transfer kinetics was found to be consistent with simple energy gap models for the transfer probabilities. Vibrational transfer out of the (0,1,1,2(0),0(0)) state accounted for no more than 16% of the total removal process. Transfer from (1,0,1,0(0),0(0)) to the u-symmetry (0,2,0,3(1),1(-1)), (0,1,1,2(0),0(0)), and (1,1,0,1(1),1(-1)) states was observed. Applying the principle of detailed balance to these data indicated that vibrational transfer to (1,0,1,0(0),0(0)) accounted for ~0.1% of the population loss from (0,2,0,3(1),1(-1)) or (0,1,1,2(0),0(0)), and 3% of the loss from (1,1,0,1(1),1(-1)). Relative rotational transfer probabilities were obtained for transfer to the g-symmetry (1,1,0,2(0),0(0))∕(0,0,2,0(0),0(0)) dyad. These results are related to recent studies of optically pumped acetylene lasers.     

Solvation dynamics of a protein in the pre molten globule state

The nature of solvent molecules around proteins in native and different non-native states is crucial for understanding the protein folding problem. We have characterized two compact denatured states of glutaminyl-tRNA synthetase (GlnRS) under equilibrium conditions in the presence of a naturally occurring osmolyte, l-glutamate. The solvation dynamics of the compact denatured states and the fully unfolded state has been studied using a covalently attached probe, acrylodan, near the active site. The solvation dynamics progressively becomes faster as the protein goes from the native to the molten globule to the pre molten globule to the fully unfolded state. Anisotropy decay measurements suggest that the pre-molten-globule intermediate is more flexible than the molten globule although the secondary structure is largely similar. Dynamic light scattering studies reveal that both the compact denatured states are aggregated under the measurement conditions. The implications of solvation dynamics in aggregated compact denatured states have been discussed.     

Fluorescence resonance energy transfer from a bio-active imidazole derivative 2-(1-phenyl-1H-imidazo[4,5-f][1,10]phenanthrolin-2-yl)phenol to a bioactive indoloquinolizine system

Novel donor imidazole derivative, 2-(1-phenyl-1H-imidazo [4,5-f][1,10]phenanthrolin-2-yl)-phenol (PIPP) was screened as highly sensitive chemisensor for transition metal ions and it can be used as a "multi-way" optically switchable material. Solvatochromic effects on the fluorescence behaviour of PIPP were studied in different solvents. The fluorescence of PIPP was highly sensitive to both the polarity as well as protic nature of the solvent. Fluorescence (Forster) resonance energy transfer (FRET) process from PIPP to a potent bioactive indoloquinolizine molecule was studied and it is argued that long-range dipole-dipole interaction is operating for the energy transfer mechanism. The energy transfer efficiency (E) and the distance between the acceptor and the donor (r(0)) have been determined.     

Semiflexible polymers confined in soft tubes

We discuss various conformations for a polymer (of persistent length l(p)) confined into a deformable tube (the wall being a lipid bilayer with a certain surface tension sigma and curvature energy K). Our study assumes that there is no adsorption of the chain on the wall. Three states are compared: (a) an unperturbed tube, plus a confined chain, (b) a tube swollen in all the region surrounding the chain (similar to a snake eating a sausage), (c) a globule, a roughly spherical coil surrounded by a strongly deformed tube. We construct a (qualitative) phase diagram for these systems with two variables: the surface tension sigma and the degree of polymerization N. Our main conclusion is that "globules" usually win over "snakes".