Cytochrome c Structure and Redox Function in Mixed Solvents Are Determined by the Dielectric Constant

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Exploiting the unique specialty of hydrazone functionality: Synthesis of a highly sensitive UV-Vis active solvatochromic probe

The unique physico-chemical attributes of the hydrazone functionality have been extensively studied for a diverse range of chemical, biological and analytical applications. The synthesis of a highly sensitive hydrazone based UV-Vis active solvatochromic probe that exhibits excellent sensitivity toward sensing of solvent polarity, microstructural changes and onset of micellization in aqueous systems was carried out. Specifically, synthesis of 2,4-dinitrophenyl-2-(2-nitrobenzylidene)hydrazone (DNPNBH), through an easy to carry, atom economical, one-pot single step approach via use of low-cost precursors viz. ortho-nitrobenzaldehyde and 2,4-dinitrophenyl hydrazine is presented. The UV-Vis absorption features of the synthesized hydrazone exhibit excellent sensitivity toward the polarity of its immediate microenvironment. The microenvironment polarity sensing potential of DNPNBH is demonstrated for some single solvent systems and DMF-Water mixture as a model binary solvent system and the results are supported by quantum mechanical calculations. Use of the DNPNBH as a probe (at concentrations many orders lower than required for conventional probes) to precisely reflect the onset of micellization and estimation of critical micelle concentration (CMC) of amphiphilic molecules (5.25 mM for SDS, 1.53 mM for CTAB and 0.055 mM for Brij56) in aqueous solutions is also demonstrated. The results clearly qualify the synthesized hydrazone as a highly sensitive UV-Vis probe that can be employed for reliable sensing of solvent polarity, composition dependence of physicochemical attributes in mixed solvent systems and the estimation of CMC of surfactant systems via spectrophotometry.

Preservation of Protein Zwitterionic States in the Transition from Solution to Gas Phase Revealed by Sodium Adduction Mass Spectrometry

The structural characterization of proteins and their interaction network mapping in the gas phase highlights the need to preserve their most nativelike conformers in the transition from the solution to gas phase. Zwitterionic interactions in a protein are weak bonds between oppositely charged residues, which make an important contribution to protein stability. However, it is still not clear whether the native zwitterionic states of proteins can be retained or not when it is transferred from the solution to gas phase. Using the nonspecific Na⁺ adduction as a novel signature, here we show that the zwitterionic states of proteins can be preserved when a moderated droplet desolvation condition (temperature <30 °C) is used in native electrospray ionization mass spectrometry. The very low-level nonspecific metal adduction to proteins under such conditions also enables rapid and direct determination of the binding states of metal-binding proteins and sensitive detection of proteins from solutions containing highly concentrated involatile salts (e.g., 50 mM NaCl). We believe that our findings can be instructive for performing mass spectrometric analysis of proteins and useful for protein ions desalting which simply involves altering the temperature and flow rate of drying gas in the desolvation region.

Thermodynamic and kinetic properties of the outer membrane cytochrome OmcF, a key protein for extracellular electron transfer in Geobacter sulfurreducens

Gene knock-out studies on Geobacter sulfurreducens have shown that the monoheme c-type cytochrome OmcF is essential for the extracellular electron transfer pathways involved in the reduction of iron and uranium oxy-hydroxides, as well as, on electricity production in microbial fuel cells. A detailed electrochemical characterization of OmcF was performed for the first time, allowing attaining kinetics and thermodynamic data. The heterogeneous electron transfer rate constant was determined at pH 7 (0.16 ± 0.01 cm s^-1) indicating that the protein displays high electron transfer efficiency compared to other monoheme cytochromes. The pH dependence of the redox potential indicates that the protein has an important redox-Bohr effect in the physiological pH range for G. sulfurreducens growth. The analysis of the structures of OmcF allowed us to assign the redox-Bohr centre to the side chain of His⁴⁷ residue and its pK_a values in the reduced and oxidized states were determined (pK_ox = 6.73; pK_red = 7.55). The enthalpy, entropy and Gibbs free energy associated with the redox transaction were calculated, pointing the reduced form of the cytochrome as the most favourable. The data obtained indicate that G. sulfurreducens cells evolved to warrant a down-hill electron transfer from the periplasm to the outer-membrane associated cytochrome OmcF.

A biofuel cell in non-aqueous solution

We report the first example of a biofuel cell operating in organic solvents.

Electrooxidation of homogentisic acid in aqueous and mixed solvent solutions: experimental and theoretical studies

Electrochemical behavior of homogentisic acid (HGA) has been studied in both aqueous and mixed solvent solution of water-acetonitrile. Physicochemical parameters of the electrochemical reaction of HGA in these solutions are obtained experimentally by cyclic voltammetry method and are also calculated theoretically using accurate ab initio calculations (G3MP2//B3LYP). Solvation energies are calculated using the available solvation model of CPCM. The pH dependence of the redox activity of HGA in aqueous and the mixture solutions at different temperatures was used for the experimental determination of the standard reduction potential and changes of entropy, enthalpy, and Gibbs free energy for the studied reaction. The experimental standard redox potential of the compound in aqueous solution was obtained to be 0.636 V versus the standard hydrogen electrode. There is a good agreement between the theoretical and experimental values (0.702 and 0.636 V) for the standard electrode potential of HGA. The changes of thermodynamic functions of solvation are also calculated from the differences between the solution-phase experimental values and the gas-phase theoretical values. Finally, using the value of solvation energy of HGA in water and acetonitrile solvents which calculated by the CPCM model of energy, we proposed an equation for calculating the standard redox potential of HGA in mixture solution of water and acetonitrile. A good agreement between the result of electrode potential calculated by the proposed equation and the experimental value confirms the validity of the theoretical models used here and the accuracy of experimental methods.

Single-walled carbon nanotubes alter cytochrome c electron transfer and modulate mitochondrial function

Single-walled carbon nanotubes (SWCNTs) are broadly used for various biomedical applications such as drug delivery, in vivo imaging, and cancer photothermal therapy due to their unique physiochemical properties. However, once they enter the cells, the effects of SWCNTs on the intracellular organelles and macromolecules are not comprehensively understood. Cytochrome c (Cyt c), as a key component of the electron transport chain in mitochondria, plays an essential role in cellular energy consumption, growth, and differentiation. In this study, we found the mitochondrial membrane potential and mitochondrial oxygen uptake were greatly decreased in human epithelial KB cells treated with SWCNTs, which accompanies the reduction of Cyt c. SWCNTs deoxidized Cyt c in a pH-dependent manner, as evidenced by the appearance of a 550 nm characteristic absorption peak, the intensity of which increased as the pH increased. Circular dichroism measurement confirmed the pH-dependent conformational change, which facilitated closer association of SWCNTs with the heme pocket of Cyt c and thus expedited the reduction of Cyt c. The electron transfer of Cyt c is also disturbed by SWCNTs, as measured with electron spin resonance spectroscopy. In conclusion, the redox activity of Cyt c was affected by SWCNTs treatment due to attenuated electron transfer and conformational change of Cyt c, which consequently changed mitochondrial respiration of SWCNTs-treated cells. This work is significant to SWCNTs research because it provides a novel understanding of SWCNTs' disruption of mitochondria function and has important implications for biomedical applications of SWCNTs.

Fluorescence and circular dichroism spectroscopy of cytochrome c in alkylammonium formate ionic liquids

The structural stability of cytochrome c has been studied in alkylammonium formate (AAF) ionic liquids such as methylammonium formate (MAF) and ethylammonium formate (EAF) by fluorescence and circular dichroism (CD) spectroscopy. At room temperature, the native structure of cytochrome c is maintained in relatively high ionic liquid concentrations (50-70% AAF/water or AAF/phosphate buffer pH 7.0) in contrast with denaturation of cytochrome c in similar solutions of methanol or acetonitrile with water or buffer cosolvents. Fluorescence and CD spectra indicate that the conformation of cytochrome c is maintained in 20% AAF-80% water from 30 to 50 °C. No such temperature stability is found in 80% AAF-20% water. About one-third of the enzyme activity of cytochrome c in 80% AAF-20% water can be maintained as compared with phosphate buffer, and this is greater than the activities measured in corresponding methanol and acetonitrile aqueous solutions. This biophysical study shows that AAFs have potential application as organic solvent replacements at moderate temperature in the mobile phase for the separation of proteins in their native form by reversed phase liquid chromatography.

Enzymatic activity and thermal stability of metallo proteins in hydrated ionic liquids

Hydrated choline dihydrogen phosphate (Hy[ch][dhp]) containing 30 wt% water was investigated as a novel protein solvent. The Hy[ch][dhp] dissolved some metallo proteins (cytochrome c, peroxidase, ascorbate oxidase, azurin, pseudoazurin and fructose dehydrogenase) without any modification. These proteins retained the surroundings of the active site after dissolution in Hy[ch][dhp]. Some metallo proteins were found to retain their activity in the Hy[ch][dhp].

Binding of imidazole to the heme of cytochrome c1 and inhibition of the bc1 complex from Rhodobacter sphaeroides: II. Kinetics and mechanism of binding

The kinetics of imidazole (Im) and N-methylimidazole (MeIm) binding to oxidized cytochrome (cyt) c(1) of detergent-solubilized bc(1) complex from Rhodobacter sphaeroides are described. The rate of formation of the cyt c(1)-Im complex exhibited three separated regions of dependence on the concentration of imidazole: (i) below 8 mM Im, the rate increased with concentration in a parabolic manner; (ii) above 20 mM, the rate leveled off, indicating a rate-limiting conformational step with lifetime approximately 1 s; and (iii) at Im concentrations above 100 mM, the rate substantially increased again, also parabolically. In contrast, binding of MeIm followed a simple hyperbolic concentration dependence. The temperature dependences of the binding and release kinetics of Im and MeIm were also measured and revealed very large activation parameters for all reactions. The complex concentration dependence of the Im binding rate is not consistent with the popular model for soluble c-type cytochromes in which exogenous ligand binding is preceded by spontaneous opening of the heme cleft, which becomes rate-limiting at high ligand concentrations. Instead, binding of ligand to the heme is explained by a model in which an initial and superficial binding facilitates access to the heme by disruption of hydrogen-bonded structures in the heme domain. For imidazole, two separate pathways of heme access are indicated by the distinct kinetics at low and high concentration. The structural basis for ligand entry to the heme cleft is discussed.

Direct label-free electrochemical detection of proteins using the polarized oil/water interface

Voltammetric behaviors of various globular proteins, including cytochrome c, ribonuclease A, lysozyme, albumin, myoglobin, and alpha-lactalbumin, were studied at the polarized 1,2-dichloroethane/water (DCE/W) interface in the presence of four different anionic surfactants, that is, dinonylnaphthalenesulfonate (DNNS), bis(2-ethylhexyl)sulfosuccinate (Aerosol-OT; AOT), bis(2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl)sulfosuccinate (BDFHS), and bis(2-ethylhexyl)phosphate (BEHP). When the W phase was acidic (pH = approximately 3.4), the surfactants (except for BEHP) added to DCE facilitated the adsorption of the above proteins to the DCE/W interface and gave a well-developed voltammetric wave due to the adsorption/desorption of the proteins. This voltammetric wave, which we here call "protein wave", is promising for direct label-free electrochemical detection of proteins. The current for the adsorption of a protein to the interface showed a linear dependence on the protein concentration in the presence of excess surfactant. The foot potential at which the protein wave appeared in cyclic voltammetry showed different values depending on the natures of the protein and surfactant. Multivariate analysis for the foot potentials determined for different proteins with different surfactants revealed that the protein selectivity should depend on the charged, polar, and nonpolar surface areas of a protein molecule. On the basis of these voltammetric studies, it was shown in principle that online electrochemical separation/determination of proteins could be performed using a two-step oil/water-type flow-cell system.

Electrochemistry of nanozeolite-immobilized cytochrome c in aqueous and nonaqueous solutions

The electrochemical properties of cytochrome c (cyt c) immobilized on multilayer nanozeolite-modified electrodes have been examined in aqueous and nonaqueous solutions. Layers of Linde type-L zeolites were assembled on indium tin oxide (ITO) glass electrodes followed by the adsorption of cyt c, primarily via electrostatic interactions, onto modified ITO electrodes. The heme protein displayed a quasi-reversible response in aqueous solution with a redox potential of +324 mV (vs NHE), and the surface coverage (Gamma*) increased linearly for the first four layers and then gave a nearly constant value of 200 pmol cm(-2). On immersion of the modified electrodes in 95% (v/v) nonaqueous solutions, the redox potential decreased significantly, a decrease that originated from changes in both the enthalpy and entropy of reduction. On reimmersion of the modified electrode in buffer, the faradic response immediately returned to its original value. These results demonstrate that nanozeolites are potential stable supports for redox proteins and enzymes.

Spectroscopic Characterization and Electrochemistry of Poly(ethylene oxide)-Modified Myoglobin in Organic Solvents

Myoglobin (Mb) was chemically modified with activated poly(ethylene oxide) (PEO) (average molecular weight of 2000) to solubilize it in various organic solvents. UV-vis, circular dichroism, and Raman spectroscopy were used to characterize the structure correlated with the electron-transfer reactions of PEO-modified Mb (PEO-Mb). Spectroscopic data indicated changes in heme coordination geometry for PEO-Mb in various organic solvents that are different from that in water. The Raman spectrum showed the characteristics of PEO-Mb in PEO oligomer (average MW of 200) in the five-coordinate high-spin state, which facilitates fast electron-transfer reactions between protein and the glassy carbon electrode. These results suggest heme environment effects on the properties of proteins in organic solvents.

A sensor for superoxide in aqueous and organic/aqueous media based on immobilized cytochrome c on binary self-assembled monolayers

A method for the electrochemical detection of superoxide radical was developed, based on cytochrome c (cyt c) immobilized on the binary self-assembled monolayers (SAMs) of thioctic acid (T-COOH) and thioctic amide (T-NH2) on gold electrode. The sensor works by electrochemically detecting cyt c reduced by the superoxide radical generated by a xanthine-XOD system. The electrochemical properties of immobilized cyt c were investigated in aqueous buffer and in a mixture of aqueous and organic solvents. The interaction of superoxide radical with the modified electrode was characterized in phosphate buffer solution (PBS) and in the mixtures of both PBS and dimethyl sulfoxide (DMSO) and PBS and glycerol (Gly). The results showed that the sensors responded immediately to superoxide radical in PBS and gave a steady-state anodic current within 10s during the generation of superoxide radical. In 40% DMSO and in 30% Gly solution, the current response reached a steady-state anodic current within 20s. The sensor could also be used to estimate superoxide dismutase (SOD).

Calixarene-Assisted Protein Refolding via Liquid−Liquid Extraction

In this paper we report on protein refolding by means of a liquid-liquid transfer technique using a calixarene. We have found that a calix[6]areneacetic acid derivative forms a supramolecular complex with urea-denatured cytochrome c at the oil-water interface, which enables quantitative transfer of the protein from an 8 M urea aqueous solution into an organic phase through a proton-exchange mechanism. Denatured cytochrome c is completely separated from the denaturant and is isolated from other denatured cytochrome c molecules to suppress the generation of aggregates due to protein-protein interactions. The recovery of cytochrome c from the organic phase is successfully achieved under acidic conditions using an appropriate amount of 1-butanol. UV-vis, CD, and fluorescence spectroscopic characterizations demonstrate that cytochrome c transferred into a denaturant-free aqueous solution regains its native structure. The reduction kinetics of refolded cytochrome c using ascorbic acid indicates that the protein provides approximately 72% of native activity as an electron-transfer protein.

Extractive solubilization, structural change, and functional conversion of cytochrome c in ionic liquids via crown ether complexation

This article reports on the extraction behavior of heme proteins from an aqueous phase into ionic liquids (ILs) with dicyclohexano-18-crown-6 (DCH18C6), and the structure-function relationship of cytochrome c (Cyt-c) dissolved in ILs. We have found that DCH18C6 enables transfer of Lys-rich proteins into ILs via supramolecular complexation. The hydrophobicity and functional groups of ILs have a great influence on protein partitioning, and a hydroxyl group-containing IL with DCH18C6 is capable of the quantitative partitioning of Cyt-c. On the other hand, protein transfer using conventional organic solvents is negligibly small. UV-visible, CD, and resonance Raman spectroscopic characterizations indicate that the sixth ligand Met 80 in the heme group of the Cyt-c-DCH18C6 complex in IL is replaced by other amino acid residues of the peptide chain and that a non-natural, six-coordinate, low-spin ferric heme structure is induced in IL. Solubilization of Cyt-c in IL causes the environmental change of the heme vicinity of Cyt-c, which triggers the functional conversion of Cyt-c from an electron-transfer protein to peroxidase. The Cyt-c-DCH18C6 complex in IL provides remarkably high peroxidase activity compared with native Cyt-c, because of enhancement of the affinity for H2O2.

Electrochemical extraction of proteins by reverse micelle formation

The transfer of proteins by the anionic surfactant bis(2-ethylhexyl) sulfosuccinate (AOT) at a polarized 1,2-dichloroethane/water (DCE/W) interface was investigated by means of ion-transfer voltammetry. When the tetrapentylammonium salt of AOT was added to the DCE phase, the facilitated transfer of certain proteins, including cytochrome c (Cyt c), ribonuclease A, and protamine, could be controlled electrochemically, and a well-defined anodic wave for the transfer was obtained. At low pH values (e.g., pH 3.4), the anodic wave was usually well-separated from the wave for the formation of protein-free (i.e., unfilled) reverse micelles. The anodic wave for the protein transfer was analyzed by applying the theory for facilitated transfer of ions by charged ligands and then supplying information regarding the number of AOT anions reacting with one protein molecule and the total charge carried by the protein transfer. However, controlled-potential electrolyses performed for the transfer of Cyt c, which is red, revealed that the protein-AOT complexes were unstable in DCE and liable to aggregate at the interface when the pH of the W phase was 3.4. At pH 7.0, when formation of unfilled reverse micelles occurred simultaneously, the protein-AOT complexes appeared to be stabilized, probably via fusion with unfilled reverse micelles.

Temperature-dependent studies of NO recombination to heme and heme proteins

The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.

Bioelectrocatalysis in ionic liquids. Examining specific cation and anion effects on electrode-immobilized cytochrome c

Cytochrome c immobilized on alkylthiol self-assembled monolayers exhibits a characteristic Fe(II)/Fe(III) redox signal that is lost when exposed to ionic liquids composed of a butylimidazolium cation combined with either hexafluorophosphate or bis(trifluoromethylsulfonyl)imide anion. In this study it was shown that exposure to the aqueous solubilized ionic liquid components, butyl-, hexyl-, and octyl-imidazolium cations and hexafluorophosphate, tetrafluoroborate, and bis(trifluoromethylsulfonyl)imide anions, resulted in partial electrochemical signal loss. Absorbance and fluorescence measurements showed that signal loss due to the cationic ionic liquid component followed a different mechanism than that of the anionic component. Although a portion of the signal was recoverable, irreversible signal loss also occurred in both cases. The source of the irreversible component is suggested to be the loss of protein secondary structure through complexation between the ionic liquid components and the protein surface residues. The reversible electrochemical signal loss is likely due to interfacial interactions imposed between the electrode and the cytochrome heme group. The influence of the amount of exposed surface residues was explored with a simplified model protein, microperoxidase-11.

Shifts in protein charge state distributions with varying redox reagents in nanoelectrospray triple quadrupole mass spectrometry

The influence of a number of redox reagents on the charge state distribution in nanoelectrospray mass spectrometry was examined using cytochrome c and ubiquitin. The redox active species investigated were: 1,4-benzoquinone, quinhydrone, tetracyanoquinodimethane (TCNQ), hydroquinone, and ascorbic acid. The redox active species was mixed with the protein sample before injection into the nanoelectrospray emitter, and mass spectra were acquired using a triple quadrupole mass spectrometer. Under the same experimental conditions, the charge state distribution of cytochrome c was observed to shift from a weighted average charge state of 14.25 (in the absence of redox species) to 7.10 in the presence of 1,4-benzoquinone. When quinhydrone was mixed with cytochrome c, the charge state distribution of the protein also shifted to lower charge states (weighted average charge state = 9.43), indicative of less charge state reduction for quinhydrone than with 1,4-benzoquinone. Addition of the redox reagent had little effect on the conformation of cytochrome c, as indicated by far ultraviolet circular dichroism spectra. In contrast, the reagents TCNQ, hydroquinone, and ascorbic acid exhibited negligible effects on the observed charge state distribution of the protein. The differing results for these redox reagents can be rationalized in terms of the redox half reactions involving these species. The results observed with ubiquitin upon adding quinhydrone were analogous to those observed with cytochrome c.

Electrochemistry of cytochrome C in aqueous and mixed solvent solutions: thermodynamics, kinetics, and the effect of solvent dielectric constant

The solvent dielectric constant is considered an important factor in determining the redox potential of the heme-containing protein cytochrome c in solution. In this study, we investigate the electrochemical response of cytochrome c in aqueous/organic solvent mixtures (100% aqueous buffer, 30% acetonitrile, 40% dimethyl sulfoxide, and 50% methanol), reporting the redox potential (E degrees'), enthalpy, and entropy of reduction. The temperature dependence of the solvent dielectric constant (epsilon) was also measured. The results show that epsilon alone cannot regulate the E degrees' of cytochrome c in mixed solvent systems. The implications of the temperature dependence of epsilon on the validity of the thermodynamic data are also discussed. The effect of solvent and temperature on the electron-transfer rate constant, k(s), was determined in each solvent mixture. A substantial increase in the activation energy for electron transfer was observed in 40% DMSO.

A simple relationship between dielectric constant of mixed solvents with solvent composition and temperature

A simple computational method for calculating dielectric constants of solvent mixtures based on Redlich-Kister extension was proposed. The model was applied to the experimental dielectric constant of binary and ternary solvent mixtures at fixed and/or various temperatures and showed accurate results. Overall average percentage deviation (OAPD) between calculated and experimental dielectric constants was calculated as an accuracy criterion. The OAPDs for correlative and predictive analyses of dielectric constants in binary solvents at a fixed temperature were 0.56 and 1.42%, respectively. The corresponding values for binary solvents at different temperatures were 1.29 and 1.92%, respectively. The OAPDs for correlative and predictive analyses of dielectric constants of a nonaqueous ternary solvent mixture at various temperatures were 1.61 and 3.05%. The accuracy of the proposed models has also been compared with those of previously published models and results showed that the proposed models were superior and capable of providing more accurate results.

Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C

The vibrational energy relaxation of a selected vibrational mode in cytochrome c--a C-D stretch in the terminal methyl group of Met80--has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. As demonstrated in the pioneering work of Romesberg and co-workers, isotopic labeling of the C-H (to C-D) stretch in alkyl side chains shifts the stretching frequency to the transparent region of the protein's density of states, making it an effective and versatile probe of protein structure and dynamics. Molecular dynamics trajectories of solvated cytochrome c were run at 300 K, and vibrational population relaxation times were estimated using the classical Landau-Teller-Zwanzig model and a number of semiclassical theories of resonant and two-phonon vibrational relaxation processes. The C-D stretch vibrational population relaxation time is estimated to be T(1) = 14-40 ps; the relatively close agreement between various semiclassical estimates of T(1) lends support to the applicability of those expressions. Normal mode calculations were used to identify the dominant coupling between the protein and C-D oscillator. All bath modes strongly coupled to the C-D stretch are in close proximity. Angle bending modes in the terminal methyl group of Met80 appear to be the most likely acceptor modes defining the mechanism of population relaxation of the C-D vibration.

Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution

The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.