Distribution and Transition of Native and Completely Unfolded Conformations in the Unfolding of Bovine Heart Cytochrome c Induced by Urea and Guanidine Hydrochloride

The unfolding of bovine heart cytochrome c induced by urea and guanidine hydrochloride was first studied through intrinsic fluorescence emission spectra and fluorescence phase diagram and the results showed that both of them separately followed a two‐state model. As the simplest sample of the unfolding of protein molecules induced by denaturants, an equation was presented to show the effect of the denaturant concentrations in denaturation solution on the residual activity ratios of bovine heart cytochrome c in their two‐state unfolding. There are two characteristic unfolding parameters K and m in this equation. The former is the thermodynamic equilibrium constant of the unfolding of bovine heart cytochrome c induced by denaturants, the latter is the number of denaturant molecules associated with a bovine heart cytochrome c molecule during the unfolding procedure, and through them the distribution and transition of native and completely unfolded bovine heart cytochrome c conformations under different concentrations of urea or guanidine hydrochloride in denaturation solution can be accurately described.     

Interactions of α-Lactalbumin and Cytochrome c with Langmuir Monolayers of Glycerophospholipids

Interaction of cytochrome c (Cyt c), α-lactalbumin III (α-La III) with Langmuir monolayers of pure and mixed glycerophospholipids was investigated using surface pressure-area (Π-A) isotherms. The general trend was that maximum interaction between protein and phospholipid is observed for mixed (1:1 molar ratio) phospholipid monolayers. Interaction between the protein and the charged phospholipid films was found to be independent of global protein charge. Our data indicate that the proteins interact with the phospholipid films by inserting themselves into the monolayer rather than anchoring to the phospholipid head groups.     

Unfolding of Bovine Heart Cytochrome c Induced by Urea and Guanidine Hydrochloride

The unfolding of bovine heart cytochrome c induced by urea and guanidine hydrochloride was studied through their intrinsic fluorescence emission spectra, fluorescence phase diagrams, fluorescence quenching, size‐exclusion chromatographies, native polyacrylamide gel electrophoreses and deactivation profiles. The results showed that during their unfolding in urea and guanidine hydrochloride solutions, bovine heart cytochrome c molecules existed only in a unimolecular form and their bi‐molecular and/or poly‐molecular aggregates and aggregate precipitates were not formed all along. When the urea and guanidine hydrochloride concentrations in denaturation solution were separately about 6.0 and 3.0 mol/L, they could be completely deactivated and almost all of the tryptophan residues originally embedded in the interior of their molecules were exposed to the surface of their molecules. Different from the unfolding of the most often used horse heart cytochrome c, that of bovine heart cytochrome c induced by urea and guanidine hydrochloride was separately a completely co‐operative procedure and followed a two‐state model.     

Mimicking Tyrosine Phosphorylation in Human Cytochrome c by the Evolved tRNA Synthetase Technique

Phosphorylation of tyrosine 48 of cytochrome c is related to a wide range of human diseases due to the pleiotropic role of the heme‐protein in cell life and death. However, the structural conformation and physicochemical properties of phosphorylated cytochrome c are difficult to study as its yield from cell extracts is very low and its kinase remains unknown. Herein, we report a high‐yielding synthesis of a close mimic of phosphorylated cytochrome c, developed by optimization of the synthesis of the non‐canonical amino acid p‐carboxymethyl‐L ‐phenylalanine (pCMF) and its efficient site‐specific incorporation at position 48. It is noteworthy that the Y48pCMF mutation significantly destabilizes the Fe?Met bond in the ferric form of cytochrome c, thereby lowering the pK_a value for the alkaline transition of the heme‐protein. This finding reveals the differential ability of the phosphomimic protein to drive certain events. This modified cytochrome c might be an important tool to investigate the role of the natural protein following phosphorylation.     

Evaluation of thermodynamic properties of irreversible protein thermal unfolding measured by DSC

Summary We assessed the applicability of the extrapolation procedure at infinite scanning rate to differential scanning calorimetry (DSC) data related to irreversible protein unfolding. To this aim, an array of DSC curves have been simulated on the basis of the Lumry-Eyring model N↔U→F. The results obtained confirmed that when the apparent equilibrium constant K_{app (T=T1/2)} is lower than 3, the application of the extrapolation procedure provides accurate thermodynamic parameters. Although this procedure applies only to monomeric proteins for which the Lumry-Eyring model is a reasonable approximation, it will hopefully contribute to increase the potential of DSC in obtaining reliable thermodynamic information regarding the folding/unfolding equilibrium.     

Coarse-grained simulations of the conformational dynamics of proteins

The conformational dynamics of a set of proteins, cytochrome c, α-lactalbumin and barnase, is studied by an off-lattice Monte Carlo (MC)/Metropolis simulation technique. A low-resolution model (virtual bond model) for the protein structure is used with recently extracted knowledge-based potentials. The calculated root-mean-square fluctuations in the α-carbons are in good agreement with X-ray crystallographic temperature factors. The potentially yielding or non-yielding regions of the protein for unfolding, in the kinetic sense, are identified from the correlation analysis of the rotational motions of the backbone bonds. The bonds which display highly auto-correlated rotational motions, in general, belong to those regions which are experimentally identified to be highly resistant to unfolding.     

Hydrogen/deuterium exchange in parallel with acid/base induced protein conformational change in electrospray droplets

The exposure of electrospray droplets to vapors of deuterating reagents during droplet desolvation in the interface of a mass spectrometer results in hydrogen/deuterium exchange (HDX) on the sub‐millisecond time scale. Deuterated water is used to label ubiquitin and cytochrome c with minimal effect on the observed charge state distribution (CSD), suggesting that the protein conformation is not being altered. However, the introduction of deuterated versions of various acids (e.g., CD₃COOD and DCl) and bases (ND₃) induces unfolding or refolding of the protein while also labeling these newly formed conformations. The extent of HDX within a protein CSD associated with a particular conformation is essentially constant, whereas the extent of HDX can differ significantly for CSDs associated with different conformations from the same protein. In some cases, multiple HDX distributions can be observed within a given charge state (as is demonstrated with cytochrome c) suggesting that the extent of HDX and CSDs share a degree of complementarity in their sensitivities for protein conformation. The CSD is established late in the evolution of ions in electrospray whereas the HDX process presumably takes place in the bulk of the droplet throughout the electrospray process. Back exchange is also performed in which proteins are prepared in deuterated solvents prior to ionization and exposed to undeuterated vapors to exchange deuteriums for hydrogens. The degree of deuterium uptake is easily controlled by varying the identity and partial pressure of the reagent introduced into the interface. Since the exchange occurs on the sub‐millisecond time scale, the use of deuterated acids or bases allows for transient species to be generated and labeled for subsequent mass analysis. Copyright © 2014 John Wiley & Sons, Ltd.     

Crucial combinations of critical exponents for liquids–vapour and ferromagnetic second-order phase transitions

Four combinations of critical exponents pertaining to the Ising model are constructed which yield simply the dimensionality d. One of these, connecting γ and η, is shown to lead to an immediately useful estimates of the sum α + η in three dimensions, about which exponents controversy still exists. This sum in three dimensions is shown to be very near or equal to 1/8, a condition which Zhang’s predictions, for the exact solution of the 3D Ising model, satisfy with α = 0 and η = 1/8. But the pioneering work of Wilson based on renormalisation group theory gave the estimate η = 0.037, while the Perk advocates α = 0.1, without however, proceeding a proof. We therefore finally stress the current importance of further experimental measurements. The critical exponent δ may be the most favourable focus, to distinguish between Zhang’s prediction of 13/3 and a value around 4.8 following for d = 3 from Wilson’s value of η quoted above.     

The adsorption of cytochromes on a modified surface of gold electrodes

The adsorption of cytochromes b ₅ and c on the surface of gold electrodes, including the surface modified with cysteine, was studied. The quartz crystal microbalance method with parallel dissipation energy measurements, microcontact printing, and atomic-force microscopy were used to show that the special features of the structure and morphology of two-component cytochrome b ₅ and c films were determined by the nature of the proteins themselves and the influence of the modifying “sublayer.” The largest changes in the weight of films and dissipation energy were observed in the adsorption of cytochrome b ₅ on a cytochrome c film deposited on a cysteine sublayer. Atomic-force microscopy measurements showed that strong interaction between cytochrome c and b ₅ molecules on the surface of gold modified with cysteine could be related to the formation of the corresponding protein complex.     

Electrochemical probing into cytochrome c modification with homocysteine-thiolactone

Homocysteine thiolactone modification is a unique process of posttranslational protein modification as well as a significant clinical indicator of cardiovascular and neurovascular diseases, so we report a new method in this paper to sensitively monitor such a modification using horse heart cytochrome c as a model protein. After the modification has been confirmed by UV–vis spectroscopy and ESI-MS, N-linked cytochrome c is then covalently assembled onto the surface of a gold electrode via the resulted homocysteine thiol group, thus electrochemical techniques, especially differential pulse voltammetry, have been employed and proven to provide an efficient way to probe into the modification of the protein. While the immobilized protein can exhibit well-defined voltammetric response, the signal of the modified cytochrome c is positively correlated to the concentration of homocysteine-thiolactone. The detectable electrochemical signal can be attained with the minimum concentration of 5 × 10⁻⁵ M homocysteine-thiolactone. Furthermore, screening of N-homocysteinylation inhibitors can be also feasible since the electrochemical waves linearly decrease with the concentration of an inhibitor pyridoxal 5-phosphate. The limit of detection for the inhibitors can be about 1 × 10⁻⁵ M.     

Thermodynamic Insight into Protein Aggregation Using a Kinetic Ising Model

In this work, we present a kinetic analysis for protein aggregation using the kinetic Ising model, which serves as a new application of a previously proposed model [Liang et al., J. Chin. Chem. Soc.­ 2003 , 50, 335]. Considering protein as a single spin unit, we map two states of a unit to the aggregation‐prone (AP) and the fibril (F) states. This work shows that the model can successfully capture the nucleation‐growth features of protein aggregation from experiments, which offers thermodynamic interpretations of aggregation properties, such as lag‐time and fibril stability.     

A Thermodynamic Model of Auto-regulated Protein Assembly by a Supramolecular Scaffold

Ligand-mediated regulation of protein assembly occurs frequently in different cellular contexts. Auto-regulated assembly, where a ligand acts as its own competitive inhibitor, provides a mechanism for exquisite control of assembly. Unlike simple protein-ligand systems a quantification of the binding thermodynamics is not straightforward. Here, we characterize the interactions of a recently identified model system in which the oligomerization of cytochrome c is controlled by sulfonato-calix[8]arene, an anionic supramolecular scaffold. Isothermal titration calorimetry and thermodynamic modelling, in combination with Bayesian fitting, were used to quantify the ligand binding and assembly equilibria for this system. The approach and variations of this model may prove useful for the analysis of auto-regulated protein assembly in general.     

Direct determination of the primary binding site of cisplatin on cytochrome c by mass spectrometry

Protein—cisplatin interactions lie at the heart of both the effectiveness of cisplatin as a therapeutic agent and side effects associated with cisplatin treatment. Because a greater understanding of the protein—cisplatin interactions at the molecular level can inform the design of cisplatin-like agents for future use, mass spectrometric determination of the binding site of cisplatin on a model protein, cytochrome c, was undertaken in this paper. The monoadduct cytochrome c—Pt(NH₃)₂(H₂O) is found to be the primary adduct produced by the cytochrome c—cisplatin interactions under native conditions. To locate the primary binding site of cisplatin, both free cytochrome c and the cytochrome c adducts underwent trypsin digestion, followed by Fourier transform mass spectrometry (FT-MS) to identify unique fragments in the adduct digest. Four such fragments were found in the adduct digest. Tandem mass spectrometry (MS/MS and MS³ indicates that two fragments are Pt(NH₃)₂(H₂O) bound peptides (Gly56-Glu104 and Asn54-Glu104) with one water associated at the peptide bond Lys79∼Met80, and the other two fragments are heme containing peptides (acety1-Gly1-Lys53 and acety1-Gly1-Lys55). The product-ion spectra of the four fragments reveal that Met65 is the primary binding site of cisplatin on cytochrome c.     

Design of Maleimide‐Functionalised Electrodes for Covalent Attachment of Proteins through Free Surface Cysteine Groups

Mixed two‐component monolayers on glassy carbon are prepared by electrochemical oxidation of N‐(2‐aminoethyl)acetamide and mono‐N‐Boc‐hexamethylenediamine in mixed solution. Subsequent N‐deprotection, amide coupling and solid‐phase synthetic steps lead to electrode‐surface functionalisation with maleimide, with controlled partial coverage of this cysteine‐binding group at appropriate dilution for covalent immobilisation of a model redox‐active protein, cytochrome c, with high coverage (≈7.5 pmol cm^?2).     

Hierarchical self-assembly in diblock copolypeptides of poly(γ-benzyl-l-glutamate) with poly poly(l-leucine) and poly(O-benzyl-l-tyrosine)

Block copolypeptides with their inherent nanometer length scale of phase separation, provide means of manipulating the type (α-helices, β-strands) and persistence of peptide secondary structures. Two such examples are employed based on the α-helical poly(γ-benzyl-l-glutamate) (PBLG) polypeptide as one block and poly(l-leucine) (α-helical) or poly(O-benzyl-l-tyrosine) (POBT) (β-strands) as the second block. Although both secondary structures are present in the copolypeptides the effect of nano-scale confinement is to induce folding in the POBT β-sheets and to maintain the defected α-helices of PBLG and PLEU with a limited lateral coherence.     

How to Turn an Electron Transfer Protein into a Redox Enzyme for Biosensing

Cytochrome c is a small globular protein whose main physiological role is to shuttle electrons within the mitochondrial electron transport chain. This protein has been widely investigated, especially as a paradigmatic system for understanding the fundamental aspects of biological electron transfer and protein folding. Nevertheless, cytochrome c can also be endowed with a non-native catalytic activity and be immobilized on an electrode surface for the development of third generation biosensors. Here, an overview is offered of the most significant examples of such a functional transformation, carried out by either point mutation(s) or controlled unfolding. The latter can be induced chemically or upon protein immobilization on hydrophobic self-assembled monolayers. We critically discuss the potential held by these systems as core constituents of amperometric biosensors, along with the issues that need to be addressed to optimize their applicability and response.     

Temperature-time duality exemplified by Ising magnets and quantum-chemical many electron theory

In this work, we first present a detailed analysis of temperature-time duality in the 3D Ising model, by inspecting the resemblance between the density operator in quantum statistical mechanics and the evolution operator in quantum field theory, with the mapping β = (k _B T)⁻¹ → it. We point out that in systems like the 3D Ising model, for the nontrivial topological contributions, the time necessary for the time averaging must be infinite, being comparable with or even much larger than the time of measurement of the physical quantity of interest. The time averaging is equivalent to the temperature averaging. The phase transitions in the parametric plane (β, it) are discussed, and a singularity (a second-order phase transition) is found to occur at the critical time t _c , corresponding to the critical point β _c (i.e, T _c ). It is necessary to use the 4-fold integral form for the partition function for the 3D Ising model. The time is needed to construct the (3 + 1)D framework for the quaternionic sequence of Jordan algebras, in order to employ the Jordan-von Neumann-Wigner procedure. We then turn to discuss quite briefly temperature-time duality in quantum-chemical many-electron theory. We find that one can use the known one-dimensional differential equation for the Slater sum S(x, β) to write a corresponding form for the diagonal element of the Feynman propagator, again with the mapping β → it.     

On the Temperature–Pressure Free‐Energy Landscape of Proteins

We studied the thermodynamic stability of a small monomeric protein, staphylococcal nuclease (Snase), as a function of both temperature and pressure, and expressed it as a 3D free‐energy surface on the p,T‐plane using a second‐order Taylor expansion of the Gibbs free‐energy change ΔG upon unfolding. We took advantage of a series of different techniques (small‐angle Xray scattering, Fourier‐transform infrared spectroscopy, differential thermal analysis, pressure perturbation calorimetry and densitometry) in the evaluation of the conformation of the protein and in evaluating the changes in the thermodynamic parameters upon unfolding, such as the heat capacity, enthalpy, entropy, volume, isothermal compressibility and expansivity. The calculated results of the free‐energy landscape of the protein are in good agreement with experimental data of the p,T‐stability diagram of the protein over a temperature range from 200 to 400 K and at pressures from ambient pressure to 4000 bar. The results demonstrate that combined temperature–pressure‐dependent studies can help delineate the free‐energy landscape of proteins and hence help elucidate which features and thermodynamic parameters are essential in determining the stability of the native conformational state of proteins. The approach presented may also be used for studying other systems with so‐called re‐entrant or Tamman loop‐shaped phase diagrams.     

Interpreting conformational effects in protein nano-ESI-MS spectra

Nano-electrospray-ionization mass spectrometry (nano-ESI-MS) is employed here to describe equilibrium protein conformational transitions and to analyze the influence of instrumental settings, pH, and solvent surface tension on the charge-state distributions (CSD). A first set of experiments shows that high flow rates of N₂ as curtain gas can induce unfolding of cytochrome c (cyt c) and myoglobin (Mb), under conditions in which the stability of the native protein structure has already been reduced by acidification. However, it is possible to identify conditions under which the instrumental settings are not limiting factors for the conformational stability of the protein inside ESI droplets. Under such conditions, equilibrium unfolding transitions described by ESI-MS are comparable with those obtained by other established biophysical methods. Experiments with the very stable proteins ubiquitin (Ubq) and lysozyme (Lyz) enable testing of the influence of extreme pH changes on the ESI process, uncoupled from acid-induced unfolding. When HCl is used for acidification, Ubq and Lyz mass spectra do not change between pH~7 and pH 2.2, indicating that the CSD is highly characteristic of a given protein conformation and not directly affected by even large pH changes. Use of formic or acetic acid for acidification of Ubq solutions results in major spectral changes that can be interpreted in terms of protein unfolding as a result of the increased hydrophobicity of the solvent. On the other hand, Lyz, cyt c, and Mb enable direct comparison of protein CSD (corresponding to either the folded or the unfolded protein) in HCl or acetic acid solutions at low pH. The values of surface tension for these solutions differ significantly. Confirming indications already present in the literature, we observe very similar CSD under these solvent conditions for several proteins in either compact or disordered conformations. The same is true for comparison between water and water–acetic acid for folded cyt c and Lyz. Thus, protein CSD from water–acetic solutions do not seem to be limited by the low surface tension of acetic acid as previously suggested. This result could reflect a general lack of dependence of protein CSD on the surface tension of the solvent. However, it is also possible that the effect of acetic acid on the precursor ESI droplets is smaller than generally assumed.     

Effects of Select Anions from the Hofmeister Series on the Gas-Phase Conformations of Protein Ions Measured with Traveling-Wave Ion Mobility Spectrometry/Mass Spectrometry

The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and α-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and α-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H₂SO₄ molecules than HClO₄ or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No significant change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO₄, HI, or H₂SO₄ to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations.