Structural Disorder of Native Horseradish Peroxidase C Probed by Resonance Raman and Low-Temperature Optical Absorption Spectroscopy

Detecting the saddling deformations in nickel meso-phenyl substituted porphyrins using low-frequency Raman characteristic peaks

The out-of-plane (OOP) deformations of metalloporphyrins macrocycle are closely related to their biological functions, and Raman spectroscopy is a powerful tool for investigating OOP deformations. However, due to the interplay of electronic structure, substituents, porphyrin macrocycle in-plane (IP) and OOP deformations, it is challenging to measure the OOP deformations directly, or, establish a confirmative correlation between the frequency shifts of characteristic peaks and specific OOP deformation changes. In this work, we first selected the model porphyrin Ni-P and employed DFT calculations to explore the relationship between the ruffling and saddling deformation changes and their corresponding Raman spectral differences. Subsequently, we focused on nickel meso-tetraphenyl porphyrin (NiTPP), nickel meso-tetrachlorophenylporphyrin (NiTClP), and nickel meso-tetramethoxyphenyl porphyrin (NiTMeOP), which are structurally similar in nature, and investigated the relationship between their OOP deformations and Raman spectra bands based on both experiments and DFT calculations. The results indicate that the ruffling deformation magnitudes of the three nickel porphyrins are almost identical, while the saddling deformation magnitudes differ remarkably. The frequency change of the characteristic peak γ18 in relation to saddling deformation of the three porphyrins is 7.7cm-1/Å, which is close to that of the model porphyrin Ni-P 10.6cm-1/Å. Therefore, the characteristic peak γ18 can be used as a "reporter" for the change in saddling deformation. As such, this work demonstrates how to utilize the frequency shifts of low-frequency Raman characteristic peaks to identify the OOP deformation changes of the porphyrin macrocycle caused by variations in the external environment, thereby providing a theoretically assisted tool for revealing the reasons for their biological function variations.

Electronic structure and reactivity of heme bound insulin

Insulin resistance as well as insulin deficiency are said to be principal to the development of type 2 diabetes mellitus (T2Dm). Heme has also been suggested to play an important role in the disease etiology since many of the heme deficiency symptoms constitute the common pathological features of T2Dm. Besides, iron overload, higher heme iron intake and transfusion requiring diseases are associated with a higher risk of T2Dm development. In this study the interaction between these two key components i.e. heme and insulin has been studied spectroscopically under different conditions which include the effect of excess peptide as well as increasing pH. The resultant heme-insulin complexes in their reduced state are found to produce very little partially reduced oxygen species (PROS) on getting oxidized by molecular oxygen. The interaction between insulin and previously reported T2Dm relevant heme-amylin complex were also examined using absorption and resonance Raman spectroscopy. The corresponding data suggest that insulin sequesters heme from heme-amylin to form the much less cytotoxic heme-insulin.

pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes

Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.

Hemin-bound cysteinyl bolaamphiphile self-assembly as a horseradish peroxidase-mimetic catalyst

A horseradish peroxidase (HRP) mimetic catalyst was constructed by tethering hemin to the cysteinyl bolaamphiphile assembly through thiol–Fe bond. The prepared catalyst showed high catalytic activity comparable to HRP even at the high temperature.

Autoxidation of Reduced Horse Heart Cytochrome c Catalyzed by Cardiolipin-Containing Membranes

Visible circular dichroism, absorption, and fluorescence spectroscopy were used to probe the binding of horse heart ferrocytochrome c to anionic cardiolipin (CL) head groups on the surface of 1,1',2,2'-tetraoleoyl cardiolipin (TOCL)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (20%:80%) liposomes in an aerobic environment. We found that ferrocytochrome c undergoes a conformational transition upon binding that leads to complete oxidation of the protein at intermediate and high CL concentrations. At low lipid concentrations, the protein maintains a structure that is only slightly different from its native one, whereas an ensemble of misligated predominantly hexacoordinated low-spin states become increasingly populated at high lipid concentrations. A minor fraction of conformations with either high- or quantum-mixed-spin states were detected at a CL to protein ratio of 200 (the largest one investigated). The population of the non-native state is less pronounced than that found for cytochrome c-CL interactions initiated with oxidized cytochrome c. Under anaerobic conditions, the protein maintains its reduced state but still undergoes some conformational change upon binding to CL head groups on the liposome surface. Our data suggest that CL-containing liposomes function as catalysts by reducing the activation barrier for a Fe²⁺ → O₂ electron transfer. Adding NaCl to the existing cytochrome-liposome mixtures under aerobic conditions inhibits protein autoxidation of ferrocytochrome c and stabilizes the reduced state of the membrane-bound protein.

Coexistence of Native-Like and Non-Native Cytochrome c on Anionic Liposomes with Different Cardiolipin Content

We employed a combination of fluorescence, visible circular dichroism, and absorption spectroscopy to study the conformational changes of ferricytochrome c upon its binding to cardiolipin-containing small unilamellar vesicles. The measurements were performed as a function of the cardiolipin concentration, the cardiolipin content of the liposomes, and the NaCl concentration of the solvent. The data were analyzed with a novel model that combines a single binding step with a conformational equilibrium between native-like and non-native-like proteins bound to the membrane surface. The equilibrium between the two conformations, which themselves are comprised of structurally slightly different subconformations, shifts to the more non-native-like conformation with increasing cardiolipin concentration. For the binding isotherms described in this paper, we explicitly considered the enthalpic and entropic contributions of molecular crowding to protein binding at low lipid concentrations and high occupancy of the liposome surface. Increasing the CL content of liposomes increases the overall binding affinity but makes the conformational distribution much more susceptible to the influence of sodium and chloride ions, which shifts the equilibrium toward the more native-like state and directly inhibits binding, particularly to liposomes with 100% cardiolipin content. Spectroscopic evidence further suggests that a fraction of the non-native conformers adopts a pentacoordinated state similar to those obtained in class C peroxidases. On the basis of our results, we propose a hypothesis that describes the balance between facilitating and impeding forces controlling the peroxidase activity of cytochrome c in the inner membrane space of mitochondria.

Cytochrome c: A Multifunctional Protein Combining Conformational Rigidity with Flexibility

Cytochrome has served as a model system for studying redox reactions, protein folding, and more recently peroxidase activity induced by partial unfolding on membranes. This review illuminates some important aspects of the research on this biomolecule. The first part summarizes the results of structural analyses of its active site. Owing to heme-protein interactions the heme group is subject to both in-plane and out-of-plane deformations. The unfolding of the protein as discussed in detail in the second part of this review can be induced by changes of pH and temperature and most prominently by the addition of denaturing agents. Both the kinetic and thermodynamic folding and unfolding involve intermediate states with regard to all unfolding conditions. If allowed to sit at alkaline pH (11.5) for a week, the protein does not return to its folding state when the solvent is switched back to neutral pH. It rather adopts a misfolded state that is prone to aggregation via domain swapping. On the surface of cardiolipin containing liposomes, the protein can adopt a variety of partially unfolded states. Apparently, ferricytochrome c can perform biological functions even if it is only partially folded.

Using spectroscopic tools to probe porphyrin deformation and porphyrin-protein interactions

The reactivity and functionality of heme proteins are to a significant extent determined by the conformation of their functional heme groups and by the interaction of axial ligands with their protein environment. This review focuses on experimental methods and theoretical concepts for elucidating symmetry lowering perturbations of the heme induced by the protein environment of the heme pocket. First, we discuss a variety of methods which can be used to probe the electric field at the heme, including spectral hole burning as well as low temperature absorption and room temperature circular dichroism spectroscopy. Second, we show how heme deformations can be described as superposition of deformations along normal coordinates, thereby using the irreducible representations of the D4h point group as a classification tool. Finally, resonance Raman spectroscopy is introduced as a tool to probe the deformations of metalloprophyrins in solution and in protein matrices by measuring and comparing intensities and depolarization properties rather than wavenumber positions.

EPR and ENDOR studies of Fe(II) hemoproteins reduced and oxidized at 77 K

gamma-irradiation of frozen solutions of Fe(II) hemoproteins at 77 K generates both electron paramagnetic resonance (EPR) active singly reduced and oxidized heme centers trapped in the conformation of the Fe(II) precursors. The reduction products of pentacoordinate (S = 2) Fe(II) globins, peroxidases and cytochrome P450cam show EPR and electron-nuclear double resonance (ENDOR) spectra characteristic of (3d 7) Fe(I) species. In addition, cryoreduced Fe(II) alpha-chains of hemoglobin and myoglobin exhibit an S = 3/2 spin state produced by antiferromagnetic coupling between a porphyrin anion radical and pentacoordinate (S = 2) Fe(II). The spectra of cryoreduced forms of Fe(II) hemoglobin alpha-chains and deoxymyoglobin reveal that the Fe(II) precursors adopt multiple conformational substates. Reduction of hexacoordinate Fe(II) cytochrome c and cytochrome b5 as well as carboxy complexes of deoxyglobins produces only Fe(II) porphyrin pi-anion radical species. The low-valent hemoprotein intermediates produced by cryoreduction convert to the Fe(II) states at T > 200 K. Cryogenerated Fe(III) cytochrome c and cytochrome b5 have spectra similar to these for the resting Fe(III) states, whereas the spectra of the products of cryooxidation of pentacoordinate Fe(II) globins and peroxidases are different. Cryooxidation of CO-Fe(II) globins generates Fe(III) hemes with quantum-mechanically admixed S = 3/2, 5/2 ground states. The trapped Fe(III) species relax to the equilibrium ferric states upon annealing at T > 190 K. Both cryooxidized and reduced centers provide very sensitive EPR/ENDOR structure probes of the EPR-silent Fe(II) state.

Nonplanar heme deformations and excited state displacements in nickel porphyrins detected by Raman spectroscopy at soret excitation

We have correlated the Raman intensities of out-of-plane modes of nickel porphyrins with the nonplanar deformations of specific symmetries, i.e., static normal coordinate deformations (SNCDs) expressed in terms of irreducible representations of the unperturbed D(4h) point group. The model porphyrins Ni(II) octaethyltetraphenylporphyrin (NiOETPP), Ni(II) tetra(isopropyl)porphyrin (NiT((i)Pr)P), Ni(II) tetra(tert-butyl)porphyrin (NiT((t)Bu)P), and Ni(II) meso-tetraphenylporphyrin (NiTPP) were chosen because they exhibit significant out-of-plane deformations of different symmetries. At B-band excitation, the Raman scattering of out-of-plane modes becomes activated mostly via the Franck-Condon mechanism. Some characteristic bands from out-of-plane modes in the spectra were identified as reliable predictors of the type and magnitude of out-of-plane deformation. The gamma(10)-gamma(13) bands are indicators of ruffling (B(1u)) deformations for porphyrins, as confirmed by data for NiTPP, NiT((i)Pr)P, and NiT((t)Bu)P, where the Raman intensity increases with the magnitude of the ruffling deformation. The gamma(15)-gamma(17) bands are indicators of saddling (B(2u)) deformations, as shown by data for NiOETPP, which is highly saddled. By comparing the relative intensities of these prominent Raman bands we estimated the vibronic coupling parameters using a self-consistent analysis, and showed that they reproduce the respective B-band absorption profiles. We also identified the deformations along the lowest wavenumber normal coordinates as the predominant reason for the Raman activity of out-of-plane modes. Our results suggest that some of the normal coordinates (gamma(10) and gamma(13)) may be used as tools to quantitatively probe the nonplanar deformations of metalloporphyrins with alkyl substituents at the meso-positions. Out-of-plane deformations also increase the vibronic coupling strength of some low frequency in-plane Raman modes, namely, nu(7) and nu(8). Generally, the Raman data suggest that the excited B-state is substantially more nonplanar than the ground state. The overall larger vibronic coupling of ruffled porphyrins yields substantially larger dipole strengths for the vibronic sidebands associated with the B-state transition, so that the relative absorptivity of the B(v) band can be used as a convenient tool to probe the nonplanarity of the porphyrin macrocycle.

Static Normal Coordinate Deformations of the Heme Group in Mutants of Ferrocytochrome c from Saccharomyces cerevisiae Probed by Resonance Raman Spectroscopy

The function of heme proteins is, to a significant extent, influenced by the ligand field probed by the heme iron, which itself can be affected by deformations of the heme macrocycle. The exploration of this field is difficult because the heme structure obtained from X-ray crystallography is not resolved enough to unambiguously identify structural changes on the scale of 10(-2) A. However, asymmetric deformations in this order of magnitude affect the depolarization ratio of the resonance Raman lines assignable to normal vibrations of the heme group. We have measured the dispersion of the depolarization ratios of four structure sensitive Raman bands (i.e., nu4, nu11, nu21, and nu28) in yeast iso-1-ferrocytochrome c and its mutants N52V, Y67F, and N52VY67F with B- and Q-band excitation. The DPR dispersion of all bands indicates the presence of asymmetric in-plane and out-of-plane deformations. The replacement of the polar tyrosine residue at position 67 by phenylalanine significantly increases the triclinic B2g deformation, which involves a distortion of the pyrrole symmetry. We relate this deformation to changes of the electronic structure of pyrrole A, which modulates the interaction between its propionate substituents and the protein environment. This specific heme deformation is eliminated in the double mutant N52VY67F. The additional substitution of N52 by valine induces a tetragonal B1g deformation which involves asymmetric changes of the Fe-N distances and increases the rhombicity of the ligand field probed by the heme iron. This heme deformation might be caused by the elimination of the water-protein hydrogen-bonding network in the heme cavity. The single mutation N52V does not significantly perturb the heme symmetry, but a small B1g deformation is consistent with our data and the heme structure obtained from a 1 ns molecular dynamics simulation of the protein.

The importance of vibronic perturbations in ferrocytochrome c spectra: a reevaluation of spectral properties based on low-temperature optical absorption, resonance Raman, and molecular-dynamics simulations

We have measured and analyzed the low-temperature (T=10 K) absorption spectrum of reduced horse heart and yeast cytochrome c. Both spectra show split and asymmetric Q(0) and Q(upsilon) bands. The spectra were first decomposed into the individual split vibronic sidebands assignable to B(1g) (nu15) and A(2g) (nu19, nu21, and nu22) Herzberg-Teller active modes due to their strong intensity in resonance Raman spectra acquired with Q(0) and Q(upsilon) excitations. The measured band splittings and asymmetries cannot be rationalized solely in terms of electronic perturbations of the heme macrocycle. On the contrary, they clearly point to the importance of considering not only electronic perturbations but vibronic perturbations as well. The former are most likely due to the heterogeneity of the electric field produced by charged side chains in the protein environment, whereas the latter reflect a perturbation potential due to multiple heme-protein interactions, which deform the heme structure in the ground and excited states. Additional information about vibronic perturbations and the associated ground-state deformations are inferred from the depolarization ratios of resonance Raman bands. The results of our analysis indicate that the heme group in yeast cytochrome c is more nonplanar and more distorted along a B(2g) coordinate than in horse heart cytochrome c. This conclusion is supported by normal structural decomposition calculations performed on the heme extracted from molecular-dynamic simulations of the two investigated proteins. Interestingly, the latter are somewhat different from the respective deformations obtained from the x-ray structures.

Functionally Relevant Electric-Field Induced Perturbations of the Prosthetic Group of Yeast Ferrocytochrome c Mutants Obtained from a Vibronic Analysis of Low-Temperature Absorption Spectra

We have measured the low temperature (T = 20 K) absorption spectra of the N52A, N52V, N52I, Y67F, and N52AY67F mutants of ferrous Saccharomyces cerevisiae (baker's yeast) cytochrome c. All the bands in the Q0- and Q(v)-band region are split, and the intensity distributions among the split bands are highly asymmetric. The spectra were analyzed by a decomposition into Voigtian profiles. The spectral parameters thus obtained were further analyzed in terms of the vibronic coupling model of Schweitzer-Stenner and Bigman (Schweitzer-Stenner, R.; Bigman, D. J. Phys. Chem. B 2001, 7064-7073) to identify parameters related to electronic and vibronic perturbations of the heme macrocycle. We report that the electronic perturbation is of B(1g) symmetry and reflects the heterogeneity of the electric field at the heme, that is, the difference between the gradients along the perpendicular N-Fe-N axis of the heme core. We found that all the investigated mutations substantially increase this electronic perturbation, so that the spectral properties become similar to those of horse heart cytochrome c. Moreover, the electronic perturbation was found to correlate nonlinearly with the enthalpy changes associated with the reduction of the heme iron. Group theoretical arguments are invoked to propose a simple model which explains how a perturbation of the obtained symmetry can stabilize the reduced state of the heme iron. Finally, vibronic coupling parameters obtained from the analysis of the Q(v)-band region suggest that the investigated mutations decrease the nonplanar deformations of the heme group. This finding was reproduced by a normal mode structural decomposition (NSD) analysis of the N52V and N52VY67F heme conformations obtained from a 1 ns molecular dynamics simulation. We argue that the reduced nonplanarity contributes to the stabilization of the reduced state.

Normal mode analysis of the horseradish peroxidase collective motions: Correlation with spectroscopically observed heme distortions

Horseradish peroxidase C is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme and significantly affect the spectroscopically detectable properties of the heme, such as the spin state of the iron, heme normal modes, and distortions from planarity. In this work, we report on normal mode analysis (NMA) performed on models subjected to 2 ns of molecular dynamics simulations to describe the effect of calcium removal on protein collective motions and to investigate the correlation between active site (heme) and protein matrix fluctuations. We show that in the native peroxidase model, heme fluctuations are correlated to matrix fluctuations while they are not in the calcium-depleted model.

The charge transfer band in horseradish peroxidase correlates with heme in-plane distortions induced by calcium removal

Horseradish peroxidase C (HRPC) is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme. The spin state of the iron, a mixture of high spin (HS) and mixed quantum spin state (QS) consisting of intermediate spin (IS) 3/2 + (HS) 5/2, is also significantly affected by calcium removal, going from a predominant QS component to a predominant HS component upon removal of one calcium. Removal of both calcium ions, however, results in the appearance of a significant LS contribution, easily monitored in the charge transfer (CT) band region by low-T absorption. Normal structural decomposition (NSD) calculations of the in-plane (ip) modes of the heme extracted from HRPC native and Ca(2+)-depleted models show that removal of the proximal calcium is associated with perturbed E(u) and increased A(1g) ip distortions of the heme. The effect of complete or distal calcium removal on the heme also results in increased A(1g) ip distortions, but in significantly decreased E(u) distortions. The overall effect is to decrease the nonplanarity of the heme: the total ip distortion of the native HRPC heme is 0.200 and 0.134 A for the Ca(2+)-depleted species. Our NSD results corroborate the role proposed for the protein matrix, namely to fine-tune the active site by inducing subtle changes in heme planarity and spin state of the iron.

Heme structural perturbation of PEG-modified horseradish peroxidase C in aromatic organic solvents probed by optical absorption and resonance Raman dispersion spectroscopy

The heme structure perturbation of poly(ethylene glycol)-modified horseradish peroxidase (HRP-PEG) dissolved in benzene and toluene has been probed by resonance Raman dispersion spectroscopy. Analysis of the depolarization ratio dispersion of several Raman bands revealed an increase of rhombic B(1g) distortion with respect to native HRP in water. This finding strongly supports the notion that a solvent molecule has moved into the heme pocket where it stays in close proximity to one of the heme's pyrrole rings. The interactions between the solvent molecule, the heme, and the heme cavity slightly stabilize the hexacoordinate high spin state without eliminating the pentacoordinate quantum mixed spin state that is dominant in the resting enzyme. On the contrary, the model substrate benzohydroxamic acid strongly favors the hexacoordinate quantum mixed spin state and induces a B(2g)-type distortion owing to its position close to one of the heme methine bridges. These results strongly suggest that substrate binding must have an influence on the heme geometry of HRP and that the heme structure of the enzyme-substrate complex (as opposed to the resting state) must be the key to understanding the chemical reactivity of HRP.