Thermodynamic aspects of the CO-binding reaction to cytochrome P-450cam. Relevance with their biological significance and structure

Substrate binding favors enhanced NO binding to P450cam

Ferric cytochrome P450cam from Pseudomonas putida (P450cam) in buffer solution at physiological pH 7.4 reversibly binds NO to yield the nitrosyl complex P450cam(NO). The presence of 1R-camphor affects the dynamics of NO binding to P450cam and enhances the association and dissociation rate constants significantly. In the case of the substrate-free form of P450cam, subconformers are evident and the NO binding kinetics are much slower than in the presence of the substrate. The association and dissociation processes were investigated by both laser flash photolysis and stopped-flow techniques at ambient and high pressure. Large and positive values of S and V observed for NO binding to and release from the substrate-free P450cam complex are consistent with the operation of a limiting dissociative ligand substitution mechanism, where the lability of coordinated water dominates the reactivity of the iron(III)-heme center with NO. In contrast, NO binding to P450cam in the presence of camphor displays negative activation entropy and activation volume values that support a mechanism dominated by a bond formation process. Volume profiles for the binding of NO appear to be a valuable approach to explain the differences observed for P450cam in the absence and presence of the substrate and enable the clarification of the underlying reaction mechanisms at a molecular level. Changes in spin state of the iron center during the binding/release of NO contribute significantly to the observed volume effects. The results are discussed in terms of relevance for the biological function of cytochrome P450 and in context to other investigations of the related reactions between NO and imidazole- and thiolate-ligated iron(III) hemoproteins.

Substrates modulate the rate-determining step for CO binding in cytochrome P450cam (CYP101). A high-pressure stopped-flow study

The high-pressure stopped-flow technique is applied to study the CO binding in cytochrome P450cam (P450cam) bound with homologous substrates (1R-camphor, camphane, norcamphor and norbornane) and in the substrate-free protein. The activation volume DeltaV # of the CO on-rate is positive for P450cam bound with substrates that do not contain methyl groups. The kon rate constant for these substrate complexes is in the order of 3 x 10(6) M(-1) x s(-1). In contrast, P450cam complexed with substrates carrying methyl groups show a negative activation volume and a low kon rate constant of approximately 3 x 10(4) M(-1) x s(-1). By relating kon and DeltaV # with values for the compressibility and the influx rate of water for the heme pocket of the substrate complexes it is concluded that the positive activation volume is indicative for a loosely bound substrate that guarantees a high solvent accessibility for the heme pocket and a very compressible active site. In addition, subconformers have been found for the substrate-free and camphane-bound protein which show different CO binding kinetics.

Cytochrome P-450-CO and substrates: lessons from ligand binding under high pressure

An overview of the application of high-pressure studies on the carbon monoxide complex of cytochrome P-450 is given. Different approaches to characterize ligand binding steps, the conformational states and substates and the compressibility of the ligand-bound complex are reviewed. A particular focus is the effect of substrates on these properties. It is shown that substrate mobility, compressibility and water accessibility are interrelated and may have functional meaning.

Clay-bridged electron transfer between cytochrome p450(cam) and electrode

We demonstrate a very fast heterogeneous redox reaction of substrate-free cytochrome P450(cam) on a glassy carbon electrode modified with sodium montmorillonite. The linear relationship of the peak current in the cyclic voltammogram with the scan rate indicates a reversible one-electron transfer surface process. The electron transfer rate is in the range from 5 to 152 s(-1) with scan rates from 0.4 to 12 V/s, respectively. These values are comparable to rates reported for the natural electron transfer from putidaredoxin to P450(cam). The formal potential of adsorbed P450(cam) is -139 mV (vs NHE) and therefore positively shifted by 164 mV compared to the potential of substrate-free P450(cam) in solution. UV-VIS and FTIR spectra do not indicate an influence of the clay colloidal particles on the heme and the secondary structure of P450(cam) in solution. However, P450(cam) adsorbed on the surface of the clay-modified electrode may undergo partial dehydration resulting in the shift of the formal potential.

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Step-scan time-resolved FTIR spectroscopy of cytochrome P-450cam carbon monoxide complex: a salt link involved in the ligand-rebinding process

Step-scan time-resolved Fourier transform infrared spectroscopy with a time resolution of 5 micros was applied to the carbon monoxide complex of cytochrome P-450cam (CYP101) to study the bimolecular ligand-rebinding process after flash photolysis. Spectral changes in the CO ligand stretch vibration band and in the protein amide I' band were monitored simultaneously. In substrate complexes having the camphor C-8, C-9, and C-10 methyl groups, rebinding of the ligand and the relaxation of the protein proceed at the same rate within experimental errors. For substrate complexes missing the methyl groups, the relaxation fo the protein tends to relax slightly faster than the CO ligand rebinding to the heme iron. compared to the (1R)-camphor and the camphane complex, the bimolecular rebinding rate constant for P-450 bound with substrates lacking the methyl groups are increased by a factor of 10-40. An unusual signal at about 1719 cm-1 was found in the difference spectrum of the photolyzed minus nonphotolyzed CO complex which has not ben reported for other heme proteins so far. This signal is strongly pronounced in wild-type P-450cam bound with (1R)-camphor or camphane and in the D251N mutant bound with (1R)-camphor. In contrast, substrate-free P-450 and the norbornane and norcamphor complexes reveal only a very weak signal or a changed band shape. On the basis of the crystal structure data, we suggest that this signal originates from the rearrangement of the hydrogen-bonding pattern or the protonation state of the salt link between Asp297, Arg299, and the heme propionate group.

Origin of the photoacoustic signal in cytochrome P-450cam: role of the Arg186-Asp251-Lys178 bifurcated salt bridge

The origin of the photoacoustic signal in ferrous CO-camphor-cytochrome P-450cam was investigated. Recently, the Arg186-Asp251-Lys178 bifurcated salt bridge, located above the heme pocket, has been shown to play a key role in the control of the diffusion step of camphor binding [Deprez, E., Gerber, N. C., Di Primo, C., Douzou, P., Sligar, S. G., & Hui Bon Hoa, G. (1994) Biochemistry 33, 14464-14468]. We considered the hypothesis that electrostriction resulting from the transient exposure of these charged residues to the solvent could be responsible for part of the photoacoustic signal. We thus examined the effects of a site-directed mutation of these linkages and ionic strength increases. Upon replacement of the Asp251 residue by an asparagine residue, the overall enthalpy and volume change of the CO dissociation reaction decrease from -5 to -24 kcal/mol and from 11 to 5.4 mL/mol, respectively. The mutation has the same effect on the thermodynamic parameters as increasing the ionic strength of the medium over a range of potassium or sodium concentrations from 0 to 500 mM. For the D251N mutant, the overall enthalpy of the reaction does not change with the ionic strength whereas a small effect is observed on the volume change. The results indicate that electrostriction around the bifurcated salt bridge contributes to the photoacoustic signal and suggest a scheme in which, following photodissociation of CO and diffusion of the molecule through the protein matrix, the structure relaxes and the bifurcated salt bridge desolvates.

Time-resolved Fourier-transform infrared studies of the cytochrome P-450cam carbonmonoxide complex bound with (1R)-camphor and (1S)-camphor substrate

The CO-binding reaction of cytochrome P-450cam bound with (1R)-camphor and (1S)-camphor are compared in the temperature region of 210-260 K using time-resolved Fourier-transform infrared spectroscopy with the CO stretch vibration as spectroscopic probe. For (1S)-camphor as substrate the association of CO is slowed down by a factor of 2, while the dissociation is accelerated by a factor of 3. The CO complex for the (1S)-camphor-bound P-450 is less stabilized (deltaG=-22 kJ/mol) compared to the natural substrate (1R)-camphor (deltaG=-30 kJ/mol). The data are interpreted by a smaller change of the mobility of the (1S)-camphor due to CO binding as compared to (1R)-camphor, which would indicate a higher mobility of (1S)-camphor already in the CO free reduced form of P-450cam. The higher mobility of (1S)-camphor in the heme pocket might explain the increased uncoupling rate (hydrogen peroxide formation) of 11% [Maryniak et al. (1993) Tetrahedron 49, 9373-9384] during the P-450cam catalyzed hydroxylation compared to 3% for the conversion of (1R)-camphor.

Carbon monoxide binding to cytochrome P450BM-3: evidence for a substrate-dependent conformational change

The kinetics of carbon monoxide binding to cytochrome P450BM-3 in the presence and absence of substrate has been investigated using flash photolysis. The second order kinetics for CO association with the substrate-free form of the protein appear biphasic. Deconvolution into two exponentials yields fast and slow rate constants of 11.1 +/- 0.6 x 10(6) M-1 s-1 and 3.5 +/- 0.2 x 10(6) M-1 s-1, respectively with 52% of the signal being attributed to the fast phase. Interestingly, upon binding of a substrate such as laurate, the second order kinetics become monophasic, with a value of 3.5 x 10(6) M-1 s-1, which are similar to the slow rate found in the substrate-free form of the protein. We have also examined the geminate CO rebinding kinetics in the presence and absence of various substrates. In the substrate-free form of the overall geminate yield is 30%, and addition of a substrate increases the geminate yield to roughly 50%. Both the substrate-free and substrate-bound forms exhibit complex geminate kinetics which cannot be described by a simple three-state kinetic model. Extension of this model to include four states is required. The addition of substrate causes an increase in the geminate rate constants resulting in a larger geminate amplitude when compared to the substrate-free form. There is also evidence for a correlation between the volume occupied by the substrate and the geminate rate constants. These results are discussed in terms of substrate-dependent conformational changes in cytochrome P450BM-3 and the overall energy landscape of the hemoprotein which couples to conformer equilibria.

Cytochrome P450 conformation and substrate interactions as probed by CO binding kinetics

The kinetics of CO binding to cytochrome P450, as measured by the flash photolysis technique, is a powerful probe of P450 structure-function relationships. The kinetics are sensitive to P450 conformation and dynamics and are modulated by P450 interactions with substrates and other components of the microsomal membrane. Application of a difference method to kinetic data analysis distinguishes the kinetic behavior of individual P450 forms in the microsomal membrane. This approach shows that substrates differentially modulate the kinetics via: 1) changes in P450 conformation/dynamics that either accelerate or reduce the binding rate; and/or 2) steric effects that reduce the rate. Both mechanisms are observed, the relative contributions of each varying in a substrate- and P450-dependent manner. In addition to microsomes, substrate interactions with individual P450s can be similarly probed using expressed P450s. Experiments with baculovirus-expressed human P450 3A4 show that this P450 consists of multiple conformers with distinct substrate specificities, an observation which provides a basis for its recognition of a wide array of structurally diverse substrates. These studies thus demonstrate the utility of CO binding kinetics in elucidating fundamental P450-substrate interactions in a biological membrane environment.