Spectroscopic evidence for a heme-superoxide/Cu(I) intermediate in a functional model of cytochrome c oxidase

A superstructured tetraphenylporphyrin with a covalently attached proximal imidazole axial base and three distal imidazole pickets has been developed as a model for the active site of terminal oxidases such as cytochrome c oxidase. The oxygen adduct of the Fe-only heme (at low temperature) has a diamagnetic NMR and is EPR silent, which taken together with a resonance Raman oxygen isotope sensitive band (nuFe-O) at 575/554 cm-1 (16O2/18O2) indicates formation of a six-coordinate heme-superoxide complex. Unexpectedly, the Fe/Cu complex, where the copper is in a trisimidazole environment approximately 5 A above the heme plane, displays similar characteristics: a diamagnetic NMR, EPR silence, and nuFe-O at 570/544 cm-1. This indicates the dioxygen adduct of this Fe/Cu system is also a superoxide. This contrasts with previously characterized partially reduced dioxygen intermediates of binuclear heme/copper complexes that form Fe/Cu mu-peroxo complexes.     

Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA

Phosphorothioates were substituted into double-stranded DNA to study protonated Class I A+.C basepairs by 31P NMR. The method was effective in reporting the A+.C pKa. pKa values near 7.0 were found with optimal nearest-neighbor partners. Such pKa values could expand the catalytic repertoire of nucleic acids.     

The indirect coulometric titration of cytochrome c oxidase with cytochrome c

The indirect coulometric titration of cytochrome c oxidase and dioxygen using cytochrome c as a mediator is described. Results of both the indirect coulometric titrations and the cyclic voltammetric experiments reported herein verify that the reaction mechanism involves the catalytic regeneration of the electroactive species, the cytochrome c mediator, with the selective reduction of cytochrome c oxidase alone. During the indirect coulometric titrations dioxygen is reduced to water only by cytochrome c oxidase and not by either direct reduction at the electrode surface or reaction with cytochrome c. This system utilizes the electron transfer selectivity of cytochrome c for cytochrome c oxidase over dioxygen and offers a means by which the reaction of cytochrome c oxidase and dioxygen can be examined.     

Determination of pK(a) values of N-heterocyclic bases by fluorescence spectrophotometry

Fluorimetry is a relatively fast and accurate means of determining the dissociation constants of sparingly soluble heterocyclic bases. Complications can arise, however, from the dependence of fluorescence on excited-state as well as ground-state acid-base chemistry. Several approaches to circumventing or compensating for this difficulty are discussed. To demonstrate the utility of the methods, the pK(a), values of the conjugate acids of two bases are evaluated by the methods described.     

Proton pumping mechanism in cytochrome c oxidase

Two different issues, important for the pumping mechanism of cyctochrome c oxidase, have been addressed in the present study. One of them concerns the nature of two key proton transfer transition states. A simple electrostatic model is used to suggest that the transition state (TS) for transfer to the pump-site should be positively charged, while the one for transfer to the binuclear center should be charge-neutral. The character of the former TS will guarantee that the protons will be pumped to the outside and not return to the inside, while the neutral character of the latter one will allow transfer with a sufficiently low barrier. In the simple electrostatic analysis, leading to this qualitative picture of the pumping process, the results from the kinetic experiments are strictly followed, but it is at least as important to follow the fundamental requirements for pumping. In this perspective, the uncertainties in the quantitative analysis should be rather unimportant for the emerging qualitative picture of the pumping mechanism. The second problem addressed concerns the purpose of the K-channel. It is argued that the reason for the presence of the K-channel could be that protons cannot pass through the binuclear center at some stage of pumping. Barriers and water binding energies were computed using hybrid density functional theory (DFT) to investigate this question.     

Determination of pK(a) values of diastereomers of phosphinic pseudopeptides by CZE

A CE method was used for the determination of acidity constants (pK(a)) of a series of ten phosphinic pseudopeptides, which varied in number and type of ionogenic groups. Effective electrophoretic mobilities were measured in the 1.8-12.0 pH range in the BGEs of constant ionic strength of 25 mM. Effective electrophoretic mobilities, corrected to standard temperature of 25 degrees C, were subjected to non-linear regression analysis and the obtained apparent pK(a) values were recalculated to thermodynamic pK(a)'s by extrapolation to zero ionic strength according to the extended Debye-Hückel model. The pK(a) values of the phosphinic acid group fell typically in the 1.5-2.25 interval, C-terminal carboxylic groups in the 2.94-3.50 interval, carboxylic groups of the lateral chain of glutamate and aspartate in the 4.68-4.97 interval, imidazolyl moiety of histidine in the 6.55-8.32 interval, N-terminal amino groups in the 7.65-8.28 interval and epsilon-amino group of the lateral chain of lysine in the 10.46-10.61 interval. Further, separation of diastereomers of the phosphinic pseudopeptides was investigated in achiral BGEs. Evaluation of the resolution of the diastereomers as a function of pH of the BGE revealed that most suitable pH region for separation of the diastereomers is around the pK(a) values of the central phosphinic acid group of the pseudopeptides. Successful separation of some diastereomers was, however, achieved in the neutral and alkaline BGEs as well.     

Calculated reaction cycle of cytochrome c oxidase

The catalytic cycle of cytochrome c oxidase has been simulated by means of quantum mechanical calculations. The experimental energetics of the catalytic cycle is nearly reproduced. The atomic structures of the intermediates are suggested. In particular, the structures of nonactive "resting" intermediates are proposed.     

Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy

Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange between folded and unfolded forms of the protein gives rise to separate NMR resonances for both folded and unfolded states at equilibrium. As a result, kinetic data can be derived from magnetization transfer between these two states without the need for denaturants. Using the fact that ionization of Asp8 dominates the electrostatic behavior of the protein between pH 2 and 3, along with pKa values for titrating groups in both folded and unfolded states that have been determined in a previous study, values of 2.9 +/- 0.1 and 3.3 +/- 0.2 are obtained for the pKa of Asp8 in the transition state for the wild-type protein and for a His7Ala mutant, respectively. The data are consistent with the partial formation in the transition state ensemble of an Asp8 side chain carboxylate-a Lys21 backbone amide interaction that represents a highly conserved contact in folded SH3 domains.     

Proton exit channels in bovine cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal transmembrane enzyme of the respiratory electron transport chain in aerobic cells. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping, a process which results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping and proton exit pathways remain unknown. In our previous work, the continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine cytochrome c oxidase for different redox states of the enzyme. A possible mechanism of oxygen reduction and proton pumping via His291 was proposed. In this paper, using electrostatic calculations, we examine the proton exit pathways in the enzyme. By monitoring the changes of the protonation states, proton affinities, and energies of electrostatic interactions between the titratable groups in different redox states of CcO, we identified the clusters of strongly interacting residues. Using these data, we detected four possible proton exit points on the periplasmic side of the membrane (Lys171B/Asp173B, His24B/Asp25B, Asp51, and Asp300). We then were able to trace the proton exit pathways and to evaluate the energy profiles along the paths. On the basis of energetic considerations and the conservation of the residues in a protein sequence, the most likely exit pathway is one via the Lys171B/Asp173B site. The obtained results are fully consistent with our His291 model of proton pumping, and provide a rationale for the absence of proton leaking in CcO between the pumping strokes.     

Iron porphyrins as models of cytochrome c oxidase

A series of iron porphyrins has been synthesized as models of cytochrome c oxidase; their activity as 4e catalysts in the reduction of dioxygen has been studied at pH 7. These compounds have been obtained by grafting very different residues onto the same iron complex, namely tripodal tetraamines, pickets, and straps, in order to change the environment of the metal center. In the case of porphyrins bearing a tripodal cap, the secondary amines have been alkylated with different substituents so as to modify the electronic environment of the distal pocket. Surprisingly, when the iron porphyrin is functionalized with four identical acrylamido pickets, the resulting complex exhibits biomimetic activity in that it catalyzes oxygen reduction with almost no production of hydrogen peroxide. The crystal structure of the redox-inactive zinc(II) analogue is reported; this shows how the metal influences the spatial arrangement of the four pickets through axial coordination and hydrogen bonding. Even a bis-strapped iron porphyrin, for which no dimerization or self-aggregation can occur at the electrode surface, acts as a 4e catalyst for O2 reduction. It is thus demonstrated that at pH close to physiological values, the iron porphyrin is an intrinsically efficient catalyst for the reduction of oxygen to water.     

Synthesis of cytochrome c oxidase models bearing a Tyr244 mimic

A close structural analogue of the metal-free cytochrome c oxidase active site has been synthesized. This model has a proximal imidazole tail and three distal imidazole pickets attached to a porphyrin. One distal imidazole is cross-linked to a phenol, mimicking Tyr(244). The strategy behind the successful synthesis of this regioisomerically pure model involved discovering the best sequence to introduce the phenol-substituted imidazole and employing a fluorinated substituent.     

The pK(a) values of N,N,N',N'-tetrakis-(2-hydroxypropyl)ethylenediamine

Aqueous solutions of the industrially important chelating agent N,N,N',N'-tetrakis(2-hydroxypropyl)ethylenediamine exhibit basic properties. The proton dissociation constants were determined to be 8.99 +/- 0.04 (pK(1)) and 4.30 +/- 0.04 (pK(2)) by potentiometric titration at 25 degrees in 0.15M sodium chloride.     

Accurate determination of low pK values by (1)H NMR titration

The NMR titration methodology to determine acid dissociation constants in aqueous solutions is extended for pK(a) values between 0 and 2, where potentiometric titrations are no longer applicable. (1)H NMR spectra are acquired for single samples of constant acid concentration (e.g. 0.02M), controlled ionic strength (I=1M with HNO(3)/NaNO(3)) and varying pH. To avoid biased pH readings due to the acid error of the glass electrode, true, concentration-based pH values are deduced by combination of the charge balance equation with information from (1)H NMR chemical shifts of the investigated acid. The method has been tested on histidine (pK(1)=1.83+/-0.02) and yielded the dissociation constant of dichloroacetic acid (pK=1.06+/-0.01) for the first time with good accuracy and precision. Dichloroacetic acid is recommended as an NMR spectroscopical "indicator molecule" for in situ monitoring the pH in strong acidic solutions of other equilibrium systems.     

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models

Ionizable residues play important roles in protein structure and activity, and proton binding is a valuable reporter of electrostatic interactions in these systems. We use molecular dynamics free energy simulations (MDFE) to compute proton pKa shifts, relative to a model compound in solution, for three aspartate side chains in two proteins. Simulations with explicit solvent and with an implicit, dielectric continuum solvent are reported. The implicit solvent simulations use the generalized Born (GB) model, which provides an approximate, analytical solution to Poisson's equation. With explicit solvent, the direction of the pKa shifts is correct in all three cases with one force field (AMBER) and in two out of three cases with another (CHARMM). For two aspartates, the dielectric response to ionization is found to be linear, even though the separate protein and solvent responses can be nonlinear. For thioredoxin Asp26, nonlinearity arises from the presence of two substates that correspond to the two possible orientations of the protonated carboxylate. For this side chain, which is partly buried and has a large pKa upshift, very long simulations are needed to correctly sample several slow degrees of freedom that reorganize in response to the ionization. Thus, nearby Lys57 rotates to form a salt bridge and becomes buried, while three waters intercalate along the opposite edge of Asp26. Such strong and anisotropic reorganization is very difficult to predict with Poisson-Boltzmann methods that only consider electrostatic interactions and employ a single protein structure. In contrast, MDFE with a GB dielectric continuum solvent, used for the first time for pKa calculations, can describe protein reorganization accurately and gives encouraging agreement with experiment and with the explicit solvent simulations.     

Single-turnover intermolecular reaction between a Fe(III)-superoxide-Cu(I) cytochrome c oxidase model and exogeneous Tyr244 mimics

An Fe(III)-superoxide-Cu(I) cytochrome c oxidase model reacts intermolecularly with hindered phenols leading to phenoxyl radicals, as was observed in the enzyme and evidence for the formation of an Fe(IV)-oxo is presented.     

Conformational transitions in the regulation of cytochrome c oxidase activity

Oxidation of cytochrome c, catalyzed by cytochrome oxidase embedded in artificial liposomes of high respiratory control ratio (between 5 and 9.5), has been studied by rapid mixing techniques, under which conditions the enzyme undergoes a limited number of turnovers (from 1 to 5). The time course of the reaction could be satisfactorily simulated by a procedure derived from the concerted two-state model of Monod-Wyman-Changeux.The bulk of data and the novel analytical approach confirm the proposal that cytochrome oxidase undergoes a transition from a fast-reacting to a slow-reacting form as a consequence of the electrochemical gradient built up across the phospholipidic bilayer, and substantiate the idea that the conformational change:

• •occurs as an all-or-none process after about one turnover irrespective of the molar ratio between substrate and enzyme, and
• •is not immediately correlated to the other well known transition from the resting to the pulsed form of the enzyme.