Jonathan B. Soffer

The pH Dependence of the 695 nm Charge Transfer Band Reveals the Population of an Intermediate State of the Alkaline Transition of Ferricytochrome c at Low Ion Concentrations

We have measured and analyzed the pH dependence of the 695 nm charge transfer band of horse heart ferricytochrome c as a function of pH between 7.0 and 10.5 at high (50 mM) and low (0.5 mM) phosphate ion concentrations. Our data clearly reveal that the transition from the native state (III) to the two alkaline states (IV) involves two deprotonation steps which cannot be assigned to the two different lysine ligands associated with the two alkaline states. While the respective pK values are rather similar at high phosphate concentrations (9.23 and 9.14), they are clearly different at low anion concentrations (9.65 and 8.5). Apparently, the deprotonation that can be assigned to a pK of 8.5 populates an intermediate state termed III*, in which M80 is still an axial ligand. A comparison of Soret band CD spectra suggests that III* bears some similarity with the recently characterized thermally excited state IIIh. Our data suggest that the current picture of the alkaline transition is incomplete. The obtained results might be of relevance for characterizing the structure of ferricytochrome c bound to anionic phospholipids.

Dramatic tuning of ligand donor properties in (Ttz)CuCO through remote binding of H+ (Ttz = hydrotris(triazolyl)borate)

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.

The (not completely irreversible) population of a misfolded state of cytochrome c under folding conditions.

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.

Conformational Stability of Cytochrome c Probed by Optical Spectroscopy

Over the last 50 years cytochrome c has been used as a model system for studying electron transfer and protein folding processes. Recently, convincing evidence has been provided that this protein is also involved in other biological processes such as the apoptosis and α-synuclein aggregation. Numerous lines of evidence suggest that the diversity of the functional properties of cytochrome c is linked to its conformational plasticity. This chapter introduces circular dichroism and absorption spectroscopy, as an ideal tool to explore this proteins conformational in solution. Besides assisting in distinguishing different conformations and in obtaining the equilibrium thermodynamics of the transitions between them, the two spectroscopies can also be used to explore details of heme-protein interaction, for example, the influence of the external electric field on the prosthetic heme group.

Structural Analysis of Unfolded Peptides by Raman Spectroscopy

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.

Cu(II) and Ni(II) Interactions with the Terminally Blocked Hexapeptide Ac-Leu-Ala-His-Tyr-Asn-Lys-amide Model of Histone H2B (80–85)

The N- and C-terminal blocked hexapeptide Ac-Leu-Ala-His-Tyr-Asn-Lys-amide (LAHYNK) representing the 80–85 fragment of histone H2B was synthesized and its interactions with Cu(II) and Ni(II) ions were studied by potentiometric, UV-Vis, CD, EPR, and NMR spectroscopic techniques in solution. Our data reveal that the imidazole N(3) nitrogen atom is the primary ligating group for both metal ions. Sequential amide groups deprotonation and subsequent coordination to metal ions indicated an {Nimidazole, 3Namide} coordination mode above pH∼9, in all cases. In the case of Cu(II)-peptide system, the almost exclusive formation of the predominant species CuL in neutral media accounting for almost 98% of the total metal ion concentration at pH 7.3 strongly indicates that at physiological pH values the sequence -LAHYNK- of histone H2B provides very efficient binding sites for metal ions. The imidazole pyrrole N(1) ionization (but not coordination) was also detected in species CuH−4L present in solution above pH ∼ 11.

Structure Analysis of Unfolded Peptides I: Vibrational Circular Dichroism Spectroscopy

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).

Identification of a New Charge-Transfer Transition through the Partial Unfolding of Cytochrome C under Mild Acidic Conditions

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. 338K). To unravel this enigma a variety of purification methods were employed utilizing partial unfolding-refolding protocols. The complete oxidation of cytochrome c was achieved by adjusting the pH of the sample to 11.5, neutralizing the positive patches on the protein surface. After complete oxidization, the protein was passed over a Sephadex G10 column. Subsequently, the pH of the solution was adjusted back to 8.0, which was the starting point of a titration which covered the region between 8.0 and 4.0. Surprisingly we observed a weak absorption band at 625nm, which increased with decreasing pH, reflecting the protonation of a titratable group (pK=5.2). This value strongly indicates a H33 as the involved residue. Normally, this band is indicative of the population of a ferric high spin state of the heme iron. However, in our case the 695nm band, which is an indicator of the intactness of the Fe(III)-M80 bond, remained present without any loss of intensity. Our observation suggest the stabilization of an excited charge transfer state, possibly resulting from an A2u->dπ transition by the positive charge on H33 in a heme cavity modified by the initially present TCA.