Correspondence of the pK values of oxyHb-titration states detected by resonance Raman scattering to kinetic data of ligand dissociation and association

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.

Hemoglobin-ligand binding: understanding Hb function and allostery on atomic level

The major physiological function of hemoglobin (Hb) is to bind oxygen in the lungs and deliver it to the tissues. This function is regulated and/or made efficient by endogenous heterotropic effectors. A number of synthetic molecules also bind to Hb to alter its allosteric activity. Our purpose is to review the current state of Hb structure and function that involves ensemble of tense and relaxed hemoglobin states and the dynamic equilibrium of the multistate due to the binding of endogenous heterotropic or synthetic allosteric effectors. The review also discusses the atomic interactions of synthetic ligands with the function or altered allosteric function of Hb that could be potentially harnessed for the treatment of diseases. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

Raman dispersion spectroscopy probes heme distortions in deoxyHb-trout IV involved in its T-state Bohr effect

The depolarization ratios of heme protein Raman lines arising from vibrations of the heme group exhibit significant dependence on the excitation wavelength. From the analysis of this depolarization ratio dispersion, one obtains information about symmetry-lowering distortions deltaQ(Gamma) of the heme group that can be classified in terms of the symmetry races Gamma = A(1g), B(1g), B(2g), and A(2g) in D(4h) symmetry. The heme-protein interaction can be changed by the protonation of distinct amino acid side chains (i.e., for instance the Bohr groups in hemoglobin derivates), which gives rise to specific static heme distortions for each protonation state. From the Raman dispersion data, it is possible to obtain parameters by fitting to a theoretical expression of the Raman tensor, which provide information on these static distortions and also about the pK values of the involved titrable side chains. We have applied this method to the nu(4) (1,355 cm(-1)) and nu(10) (1,620 cm(-1)) lines of deoxygenated hemoglobin of the fourth component of trout and have measured their depolarization ratio dispersion as a function of pH between 6 and 9. From the pH dependence of the thus derived parameters, we obtain pK values identical to those of the Bohr groups, which were earlier derived from the corresponding O(2)-binding isotherms. These are pK(alpha1) = pK(alpha2) = 8.5 for the alpha and pK(beta1) = 7.5, pK(beta2) = 7.4 for the beta chains. We also obtain the specific distortion parameters for each protonation state. As shown in earlier studies, the nu(4) mode mainly probes distortions from interactions between the proximal histidine and atoms of the heme core (i.e., the nitrogens and the C(alpha) atoms of the pyrroles). Group theoretical argumentation allows us to relate specific changes of the imidazole geometry as determined by its tilt and azimuthal angle and the iron-out-of-plane displacement to distinct variations of the normal distortions deltaQ(Gamma) derived from the Raman dispersion data. Thus, we found that the pH dependence of the heme distortions deltaQ(A1g) (totally symmetric) and deltaQ(B1g) (asymmetric) is caused by variations of the azimuthal rather than the tilt angle of the Fe-His (F8) bond. In contrast to this, the nu(10) line mainly monitors changes resulting from the interaction between peripheral substituents of the porphyrin macrocycle (vinyl). From the pH dependence of the parameters, it is possible to separately identify distortions deltaQ(Gamma) affecting the hemes in the alpha and beta chains, respectively. From this, we find that in the alpha subunit structural changes induced on protonation of the corresponding Bohr groups are mainly transferred via the Fe-N(epsilon) bond and give rise to changes in the azimuthal angle. In the beta subunit, however, in addition, structural changes of the heme pocket arise, which most probably result from protonation of the imidazole of the COOH-terminal His (HC3 beta). This rearranges the net of H bonds between His HC3 beta, Ser (F9 beta), and Glu (F7 beta).

pH-induced conformational changes of the Fe(2+)-N epsilon (His F8) linkage in deoxyhemoglobin trout IV detected by the Raman active Fe(2+)-N epsilon (His F8) stretching mode

To investigate heme-protein coupling via the Fe(2+)-N epsilon (His F8) linkage we have measured the profile of the Raman band due to the Fe(2+)-N epsilon (His F8) stretching mode (nu Fe-His) of deoxyHb-trout IV and deoxyHbA at various pH between 6.0 and 9.0. Our data establish that the band of this mode is composed of five different sublines. In deoxyHb-trout IV, three of these sublines were assigned to distinct conformations of the alpha-subunit (omega alpha 1 = 202 cm-1, omega alpha 2 = 211 cm-1, omega alpha 3 = 217 cm-1) and the other two to distinct conformations of the beta-subunit (omega beta 1 = 223 cm-1 and omega beta 2 = 228 cm-1). Human deoxyHbA exhibits two alpha-chain sublines at omega alpha 1 = 203 cm-1, omega alpha 2 = 212 cm-1 and two beta-chain sublines at omega beta 1 = 217 cm-1 and omega beta 2 = 225 cm-1. These results reveal that each subunit exists in different conformations. The intensities of the nu Fe-His sublines in deoxyHb-trout IV exhibit a significant pH dependence, whereas the intensities of the corresponding sublines in the deoxyHbA spectrum are independent on pH. This finding suggests that the structural basis of the Bohr effect is different in deoxyHbA and deoxyHb-trout IV. To analyse the pH dependence of the deoxyHb-trout IV sublines we have applied a titration model describing the intensity of each nu Fe-His subline as an incoherent superposition of the intensities from sub-sublines with the same frequency but differing intrinsic intensities due to the different protonation states of the respective subunit. The molar fractions of these protonation states are determined by the corresponding Bohr groups (i.e., pK alpha 1 = pK alpha 2 = 8.5, pK beta 1 = 7.5, pK beta 2 = 7.4) and pH. Hence, the intensities of these sublines reflect the pH dependence of the molar fractions of the involved protonation states. Fitting this model to the pH-dependent line intensities yields a good reproduction of the experimental data. To elucidate the structural basis of the observed results we have employed models proposed by Bangchoroenpaurpong, O., K. T. Schomaker, and P. M. Champion. (1984. J. Am. Chem. Soc. 106:5688-5698) and Friedman, J. M., B. F. Campbell, and R. W. Noble. (1990. Biophys. Chem. 37:43-59) which describe the coupling between the sigma *orbitals of the Fe2+-NJ(His F8) bond and the phi * orbitals of the pyrrole nitrogens in terms of the tilt angle theta between its Fe2+-N,(HisF8)-bond and the heme normal and the azimuthal angle phi between the Fe2+-N.(His F8) projection on the heme and the N1-N3 axis.Our results indicate that each subconformation reflected by different frequencies of the VFe His-subline is related to different tilt angles theta, whereas the pH-induced intensity variations of each VFe His subline of the deoxy Hb trout IV spectrum are caused by changes of the azimuthal angle phi.

Allosteric linkage-induced distortions of the prosthetic group in haem proteins as derived by the theoretical interpretation of the depolarization ratio in resonance Raman scattering

The relationship between functional properties of haem proteins, particularly ligand binding and Bohr effect, and associated variations of the tertiary and quaternary structures is one of the main objectives of haem protein research. In this context one aims to get detailed knowledge of the coupling mechanisms which are involved in the transduction of structural changes from the protein to the functional haem group along distinct pathways.

The influence of structural variations in the F- and FG-helix of the beta-subunit modified oxyHb-NES on the heme structure detected by resonance Raman spectroscopy

The dispersion of the depolarization ratio of two prominent Raman lines (1,375 cm-1 and 1,638 cm-1) of oxyhemoglobin-N-ethyl succinimide have been examined for pH values between pH = 6.0 and 8.5. Both exhibit a significant pH dependence. Calculation of the Raman tensor in terms of a fifth-order time dependent theory provides information about the pH-dependence of parameters reflecting symmetry classified distortions of the prosthetic heme group. To correlate these distortions with the functional properties of the molecule the following protocol was used: 1) An allosteric model suggested by Herzfeld and Stanley (1974) has been applied to O2-binding curves measured at different pH values between 6.5 and 9.0. From this calculation one obtains both, the energy differences between different molecular conformations and the equilibrium constants of oxygen and proton binding. 2) A titration model was formulated relating each conformation of a molecule to a distinct set of distortion parameters of the heme group. 3) The distortion parameters resulting from the analysis of our Raman data were assigned as an effective value due to incoherent superposition of the distortion parameters related to the different titration states. The application of this procedure yields an excellent reproduction of the pH-dependent effective distortion parameters of both Raman lines investigated. It is shown that the protonation of two tertiary effector groups located in the beta-subunits affect the symmetry of the heme in a contrary manner: the protonation of a His-residue (pK = 8.2, probably His(FG4) beta) causes a symmetric position of the proximal imidazole thus lowering the perturbations of the heme core. Further it influences the interaction between amino acid residues of the heme cavity and pyrrole side chains (probably Val(FG5) beta-vinyl (pyrrole 3) thus causing a decrease of the distortions related to the peripheral part of the heme. In contrast, the protonation of Lys (EF6) beta causes a tilt position of the proximal imidazole and an increase of asymmetric perturbations of the heme core, whereas the interaction between the pyrrole side chains and the heme cavity is weakened. Our results are consistent with stereochemical predictions of Moffat (1971) concerning the existence of a H-bond between His(FG4) beta and Cys(F9) beta.

Detection of the heme perturbations caused by the quaternary R----T transition in oxyhemoglobin trout IV by resonance Raman scattering

The depolarization ratio dispersion and the respective excitation profiles of two structural sensitive Raman lines of oxyhemoglobin-trout IV (1,375 and 1,638 cm-1) have been measured at pH-values between 6.5 and 8.5. They were analyzed by employing a fifth order time dependent perturbation theory to calculate the polarizability tensor. This provides information about the pH-dependence of parameters reflecting symmetry classified distortions of the prosthetic heme groups. In order to correlate these distortions with functional properties of the molecule the following protocol has been employed: (a) a titration model was formulated relating each conformation of the molecule to a distinct set of distortion parameters the incoherent superposition of which provides the respective distortion parameter obtained from our Raman data. (b) The thermodynamic constants determining the equilibrium between these molecular conformations (i.e., the quaternary T and R-states, the low affinity t and the high affinity r-states of the distinct subunits, the pK-values of the Root- and Bohr groups) were obtained from a set of O2-binding curves that were analyzed in terms of an allosteric model suggested by Herzfeld and Stanley 1974. J. Mol. Biol. 82:231. The application of this procedure yields excellent reproduction of the pH-dependent effective distortion parameters of both Raman lines investigated. Thus established correlation between hemoglobin function (O2-binding) and structure (asymmetric perturbation of the hemegroup) provides some interesting insights into the molecular basis of the allosteric Root effect.

Oxygen-organophosphate linkage in hemoglobin A. The double hump effect

At low concentrations of chloride ions, and in the presence of nonsaturating concentrations of organophosphates, the oxygen equilibrium curves (OEC) for solutions of human adult hemoglobin exhibit a biphasic shape conveniently revealed by graphical analysis of the first derivative of the Hill equation with a characteristic form that we call "the double hump effect." This shape, observed for sub-saturating concentrations of organophosphates, stands in marked contrast to the simple lateral shifts of the OEC represented largely by scaling factors when pH or chloride are varied. In the case of protons or chloride, there is a self-buffering effect due to the presence of a large reservoir of proton or chloride binding sites not necessarily linked to oxygen, whereas such sites do not exist in the case of organophosphates. In addition, in the former case, we are dealing with curves measured at constant activity of the effector, while in the latter, at constant concentration. In the presence of saturating concentrations of inositol hexaphosphate (IHP), at low chloride concentration, the entire OEC is shifted to the right, including both its upper and lower asymptotes, indicating a decrease in the intrinsic oxygen affinities of both the T and R states. Theoretical considerations leading to a successful modeling of OEC obtained under nonsaturating and saturating concentrations of IHP required an expanded two-state allosteric model in which IHP-dependent variations in oxygen association constants for both the T and R conformations are taken into account.

pH-dependent absorption in the B and Q bands of oxyhemoglobin and chemically modified oxyhemoglobin (BME) at low Cl- concentrations

We have measured the optical absorbance in the maxima of the Q and B bands for oxyhemoglobin and oxyhemoglobin (BME) in dependence on the pH value of the solution in the region between pH 4.4 and pH 10. From the absorbance data optical titration curves are derived for both bands. These yield for oxyhemoglobin pK values 4.3, 5.3, 6.8, 7.8, and 9.0, whereas for oxyhemoglobin (BME) only one pK value at 4.3 is observed. These data are in good agreement to those derived recently from resonance Raman spectroscopy. The changes of the oscillator strengths in the Q bands are interpreted in terms of Gouterman's four-orbital model to arise from A1g-distortions of the heme group, resulting from changes of the heme-apoprotein interactions due to protonation processes of amino acid-side groups in the beta-chains. The difference between the sets of pK values in oxyhemoglobin and oxyhemoglobin BME is explained from the fact that the bifunctional reagent BME blocks important pathways of heme-apoprotein interactions. The fact that in any case increase of the Q band absorbance is accompanied by a corresponding increase in the B band absorbance leads us to the conclusion that the electronic structure of the B bands has to be described in terms of a six-orbital model, taking into account configurational interaction with the L and N bands.