The introduction to this special section argues that the deconstruction of the city's municipal social democracy was overdetermined by shifts in the global political economy toward increased income inequality and the depoliticization of national economic management. The city's creditors forced it into an ideologically-motivated program of market discipline that cut its operating budget as the city's economy financialized, defined by Greta Krippner as the tendency for profit making in the economy to occur increasingly through financial channels rather than through productive activities. The city's leaders believed that their program would revive the city for the middle class. But financialization exacerbated income inequality. In 1970, the top 0.01 percent of earners made fifty times the average income; by 1998, that figure had increased to 250 times the average income. In 2013 Mayor Michael Bloomberg commented that: If we could get every billionaire around the world to move here, it would be a godsend that would create a much bigger income gap, which, he argued, was good for the whole city, because it would raise its tax base. The four articles of this section are part of a new and growing body of historical works about New York City since the 1970s that challenge the linear narratives of concepts such as neoliberalism, gentrification, public space, law and order, and resistance by reviewing how ordinary New Yorkers coped with declining infrastructure, services, standards of living, and increasing inequality.

Cytochrome c is a heme-protein existing in the membrane of mitochrondria which plays a pivotal role in apoptosis. Besides its important biological functions, it is a model system for protein folding and unfolding studies. Recently, Soffer et al. [Soffer et al. Biochemistry 2013, 52, 1397−1408] claimed that a meta-stable misfolded state of horse heart ferricytochreome c could be obtained after exposing the protein to the ferricyanide solution at very alkaline pH for an extended period of time, and it did not undergo any remarkable change in its secondary and tertiary structures upon adjusting the solution to folding promoting conditions at neutral pH. Yet the axial coordination of the heme iron as well as the electronic structures for the misfolded protein remained undetermined. For this purpose, in this work, electron paramagnetic resonance (EPR) spectra of the misfolded protein in the solution at different pH values were recorded, and DFT calculation was conducted to predict the EPR g-tensor at different axial ligand configurations. Our EPR data indicate that the misfolded protein at very alkaline condition exhibits a hexacoordinated low spin state, while at pH 5 the protein adapt the configuration similar to the native-like low-spin ferric heme complex which possesses a histidine/methionine coordination environment. For pH value between 6 and 7, the EPR spectra appear to be the superposition of the two species. With the aid of DFT calculation, also checked by the EPR and other spectroscopic data, the possible hexacoordinated low spin state with a hydroxyl ion as the proximal ligand and the pentacoordinated quantum mixed state of the heme iron for misfolded protein at different folding conditions were discussed. This work was partially supported by Hundred Talents Program of Chinese Academy of Sciences.

This paper reports the first quantitative analysis of the thermal transitions of all protonation states of oxidized horse heart cytochrome c at low anion concentration. Changes of secondary and tertiary structure were probed by ultraviolet (UV) as well as visible circular dichroism and absorption spectroscopy, respectively. The temperature dependence of spectra were recorded at pH values assignable to a set of different protonation states which encompass the canonical Theorell–Åkesson states and the recently discovered III* state. Our experimental data suggest a two-step process of thermal unfolding for all protonation states. The respective thermodynamic parameters were obtained from a global analysis of the temperature dependence of corresponding visible circular dichroism (CD) and absorption spectra. The results of this analysis revealed a statistically significant enthalpy–entropy compensation with different apparent compensation temperatures for the two consecutive thermal transitions (319 and 357 K). This reflects the narrow distribution of the respective folding temperatures. UVCD spectra suggest that even the thermal transitions of protonation states occupied at acidic and alkaline pH cause only a very modest unfolding of the protein’s helical structure. Our data indicate the protonation-induced unfolding at room temperatures predominantly affects the Ω-loops of the protein. The two thermal transitions involve changes of two foldons, i.e. the unfolding of two short β-strand segments (associated with the yellow foldon) followed by the unfolding of the 60′ helix (green foldon) that connects the two Ω-loops of the protein. Apparently, intra-backbone hydrogen bonding is strong enough to mostly protect the terminal N- and C-helices from unfolding even at rather extreme conditions.

Complexes with bulky hydrotris(triazolyl)borate (Ttz) ligands, TtzCuCO, were used to probe how acids change the donor properties of Ttz ligands. (Ttz(tBu,Me))CuCO shows four distinct protonation states and a gradual increase in the CO stretch. The increased electrophilic nature of the Cu center upon protonation leads to enhanced C-H activation catalysis.

Cytochrome c is a highly flexible heme protein known to partially unfold at a pH above 8, generally reversibly. This study reveals the unexpected conformational change that cytochrome c undergoes upon exposure to potassium ferricyanide (∼0.2 μM) at pH 11.5 for an extended period of time. A partially unfolded state was formed which is in equilibrium with an aggregated, soluble state at pH 6 to 8. UV-CD data indicate that the secondary structure remains mostly intact. The heme is hexacoordinated low spin (pH > 6), likely with two axial histidines (His18, and His33). Below pH 6, a new ligation state emerges, for which spectroscopic evidence suggests a pentacoordinated quantum mixed state of the heme iron, previously found only in ferricytochrome c' and in class 3 peroxidases. Our data indicates the population of a frustrated misfolded state, occupied as a result of an alternate folding pathway, along which the glass transition precedes folding. Gel electrophoresis revealed that the protein is predominantly monomeric at low concentration (0.05 mM), while significant amounts of soluble dimers and trimers are formed at higher concentration, where we also observed a substantial fraction of reduced cytochrome c, which we assigned to the monomeric species based on results from size exclusion chromatography. We speculate that cytochrome c might adopt a similar state on the surface of liposomes and on the inner membrane of mitochondria have been found to acquire peroxidase activity, for which this state may be a prerequisite.

This paper reports the discovery of a (meta)stable partially unfolded state of horse heart ferricytochrome c that was obtained after exposing the protein to a solution with an alkaline pH of 11.5 for 1 week. Thereafter, the protein did not undergo any detectable change in its secondary and tertiary structure upon adjusting the solution to folding promoting conditions at neutral pH. Spectroscopic data suggest that the misfolded protein exhibits a hexacoordinated low-spin state with a hydroxyl ion as the likely ligand. Below pH 6, a new ligation state emerges with the spectroscopic characteristics of a pentacoordinated quantum mixed state of the heme iron. Gel electrophoresis revealed substantial formation of soluble dimers and trimers at submillimolar concentrations, whereas monomers were dominant at lower, micromolar concentrations. Ultraviolet circular dichroism spectra indicate that oxidized monomers are pre-molten globule to globule-like with a substantial fraction of secondary (helical) structure reminiscent of alkaline state V. The oligomers contain even more helical structure, which suggests domain swapping as the underlying mechanism of their formation. A substantial fraction of the submillimolar mixture of monomers and oligomers underwent a reduction of the heme iron. Its dependence on pH suggests the coupling to a proton transfer process. Altogether, our data indicate a partially unfolded ferricytochrome c conformation with spectroscopic characteristics reminiscent of the recently discovered alkaline isomer V(b), which is stabilized under folding conditions by exposing the protein to a very alkaline pH for an extended period of time.

Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).

Raman spectroscopy has positioned itself as an invaluable tool in the study of complex biological systems, consistently being used to obtain information illustrating a vast array of fundamental properties. Of primary interest, with respect to the focus of this chapter, are conformational changes of peptide backbones. For short peptides to larger biological systems this understanding can be extended to local hydrogen bonding interactions and the probing of other structural or organizational properties. With regard to unfolded peptides Raman spectroscopy can be used as a technique complementary to infrared (IR) and vibrational circular dichroism (VCD) spectroscopy. This chapter describes how high quality polarized Raman spectra of peptide can be recorded with a Raman microspectrometer and how the structure sensitive amide I band profiles of isotropic and anisotropic Raman scattering can be analyzed in conjunction with the respective IR and VCD profiles to obtain conformational distributions of short unfolded peptides.

Cytochrome c, a model protein, has been isolated from a wide variety of prokaryotic and eukaryotic sources. It is commonly believed that proteins behave identically if it is extracted from the same source. This investigation illustrates the unexpected conformational change on the exposure of oxidized equine heart cytochrome c to TCA, as opposed to the preparation from acetic acid, both obtained from Sigma-Aldrich and dissolved at a concentration of 0.5 mM in 1.0 mM monobasic phosphate buffer. Without further purification an earlier unfolding event was obtained with the TCA exposed protein (pH 7.0, Temp.

Cytochrome_c, in its oxidized state, adopts a multitude of conformations depending on solution conditions. Some of these conformations are relevant for the protein's functions in the electron transport process and in apoptosis. As frequently as cytochrome_c has been investigated limited experiments have been carried out under low ionic conditions, which is of significant biological importance since it's required for Apaf-1 complex formation and anionic lipids. This investigation explores the energy landscape of cytochrome_c under well-defined thermodynamic conditions. A comparison of CD and absorption of the Soret band region of both the native and non-native states of ferricytochrome c adopted between pH1-13, and temperatures between 278-353K at ionic strengths below 0.1mM was performed. Avoiding the binding of anions to positive patches on the proteins surface. State-I shows the protein unfolded with the iron in a high spin state, as the protein environment was acidified a Cotton band emerges in the CD spectra, the intensity of the bands decreased, starting around pH4. Approaching state-III, the iron enters a low spin state, a stronger couplet emerges reflecting band-splitting, predominantly caused by a combination of electronic and vibronic perturbations, maintained below 343K. Suggesting a conformational transition from the native state, into a thermally activated intermediate state, affecting the internal electric field causing moderate rearrangements of the heme, until it enters a thermally unfolded state. This state of the protein consistently becomes populated at higher temperatures across the pH range. This couplet remains into pH9 possible reflecting an intermediate transition of state III-IV, moving more alkaline this couplet disappears. Using Kuhn anisotropy, Δɛ/ε vs temperature, the population of intermediates is indicated as temperature increased. Characterization of ferricytochrome_c transitions at low ionic strength showed significant heterogeneity of the protein throughout the pH range.

We determined the dispersion of the depolarization ratio (DPR) of several Raman bands of ferricytochrome c at different pH values using low-ionic-strength conditions. The experimental data predominantly cover the pre-resonance and resonance region of Q-band excitation. The selected pH values 7.5, 9.0, 10.0 and 11.0 correspond to the conformational states III, III*, IV, and V of the protein. While the existence of the states III, IV, and V is known for nearly 70 years, the nativelike state III* has only recently been obtained from optical measurements at low ionic strength [D. Verbaro, A. Hagarman, J. B. Soffer and R. Schweitzer-Stenner, Biochemistry, 48, 2990, 2009]. We used group-theoretical arguments to obtain in-plane symmetry-lowering deformations from the obtained DPRs of various Raman bands in the high-wavenumber region of the obtained spectra. Thus, we found that a comparatively strong rhombic deformation along the B-1g mode, nu(18), is maintained at all pH values investigated. It most likely arises from static Jahn-Teller distortion of the E-symmetry ground state. While this distortion depends on the existence of a strong sixth ligand, its occurrence is rather independent of the nature of this ligand as long as a low-spin configuration is maintained. The III -> III* transition was found to modify A(1g)-type perturbations of the heme macrocycle. This is likely to reflect a decrease in nonplanar distortions such as ruffling and saddling. This drop in nonplanarity is slightly reversed by the subsequent transitions into states IV and V. Circular dichroism (CD) spectra of the Q-band region suggest that the III -> III* transition reduces the electronic contribution to the Q-band splitting, which could reflect either a weakening or a reorientation of the internal electric field in the heme pocket. Our results underscore the relevance of state III* as a thermodynamic intermediate of the alkaline transition between states III and IV. Copyright (C) 2010 John Wiley & Sons, Ltd.