Changes in secondary structure and salt links of cytochrome P-450cam induced by photoreduction: a Fourier transform infrared spectroscopic study

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds

Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.

Application of high pressure laser flash photolysis in studies on selected hemoprotein reactions

This article focuses on the application of high pressure laser flash photolysis for studies on selected hemoprotein reactions with the objective to establish details of the underlying reaction mechanisms. In this context, particular attention is given to the reactions of small molecules such as dioxygen, carbon monoxide, and nitric oxide with selected hemoproteins (hemoglobin, myoglobin, neuroglobin and cytochrome P450(cam)), as well as to photo-induced electron transfer reactions occurring in hemoproteins (particularly in various types of cytochromes). Mechanistic conclusions based on the interpretation of the obtained activation volumes are discussed in this account.

Protein electrodes with direct electrochemical communication

Electrochemistry using direct electron transfer between an electrode and a protein or an enzyme has developed into a means for studying biological redox reactions and for bioanalytics, biosynthesis and bioenergetics. This review summarizes recent work on direct protein electrochemistry with special emphasis on our results in bioelectrocatalysis using isolated enzymes and enzyme-protein couples.

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.

The role of the heme propionates in heme biochemistry

There are numerous studies, relying on both experimental and theoretical observations, illustrating the active role of the heme propionates in regulating electron delivery to the iron center as well as biochemical properties of the heme. Evidences for this come from a wide variety of heme containing systems: cytochromes, heme peroxidases, globins, etc. Here, we shortly summarize these studies and revisit previous theoretical calculations (V. Guallar, M.H. Baik, S.J. Lippard, R.A. Friesner, Proc. Natl. Acad. Sci. USA 100 (2003) 6998-7002) where the propionate groups induced the delocalization of the spin density in the cytochrome P450cam putative active species, Compound I. We introduce novel data, obtained by means of mixed quantum mechanics and molecular mechanics methods, indicating a larger electron delocalization into the protein. We also present novel results based on the recent migration of spin density observed by Barrows et al. (T.P. Barrows, T.L. Poulos, Biochemistry 44 (2005) 14062-68) on an ascorbate peroxidase mutant. All this data strongly supports the importance of the propionate groups in tuning the heme electronic properties.

Identification of residues crucially involved in the binding of the heme moiety of soluble guanylate cyclase

Soluble guanylate cyclase (sGC), a heterodimeric hemeprotein, is the only receptor for the biological messenger nitric oxide (NO) identified to date and is intimately involved in various signal transduction pathways. By using the recently discovered NO- and heme-independent sGC activator BAY 58-2667 and a novel cGMP reporter cell, we could distinguish between heme-containing and heme-free sGC in an intact cellular system. Using these novel tools, we identified the invariant amino acids tyrosine 135 and arginine 139 of the beta(1)-subunit as crucially important for both the binding of the heme moiety and the activation of sGC by BAY 58-2667. The heme is displaced by BAY 58-2667 due to a competition between the carboxylic groups of this compound and the heme propionic acids for the identified residues tyrosine 135 and arginine 139. This displacement results in the release of the axial heme ligand histidine 105 and to the observed activation of sGC. Based on these findings we postulate a signal transmission triad composed of histidine 105, tyrosine 135, and arginine 139 responsible for the enzyme activation by this compound and probably also for transducing changes in heme status and porphyrin geometry upon NO binding into alterations of sGC catalytic activity.

Structural alterations of the heme environment of cytochrome P450cam and the Y96F mutant as deduced by resonance Raman spectroscopy

Resonance Raman spectroscopy at 2.5cm(-1) resolution was used to probe differences in wild-type and Y96F mutant P450cam (CYP101), both with and without bound camphor or styrene substrates. In the substrate-free state, the spin state equilibrium is shifted from 6-coordinate low spin (6CLS) toward more 5-coordinate high spin (5CHS) when tyrosine-96 in the substrate pocket is replaced by phenylalanine. About 25% of substrate-free Y96F mutant is 5CHS as opposed to 8% for substrate-free wild-type P450cam. Spin equilibrium constants calculated from Raman intensities indicate that the driving force for electron transfer from putidaredoxin, the natural redox partner of P450cam, is significantly smaller on styrene binding than for camphor binding. Spectral differences suggest that there is a tilt in camphor toward the pyrrole III ring on Y96F mutation. This finding is consistent with the altered product distribution found for camphor hydroxylation by the Y96F mutant relative to the single enantiomer produced by the wild-type enzyme.

Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin

Substrate binding to cytochrome P450cam is generally considered to be a two-step process. The first step corresponds to the entrance of the substrate, camphor, into the heme pocket. The second step corresponds to a spin transition (low spin-->high spin) of the iron in the protein-substrate complex. This spin transition is related to the mobility of the substrate inside the active site [Biochim Biophys Acta 1338 (1997) 77]. Potassium cations (K(+)) have a specific effect on the spin equilibrium. This is generally attributed to the K(+) ion-induced conformational change of tyrosine 96, the hydroxyl group of which is hydrogen bonded to the keto group of camphor and results in optimum substrate orientation and reduced mobility of this substrate in the active site. In the present paper, we show that K(+) not only affects the substrate-Tyr 96 couple, but acts more globally since K(+) effects are also observed in the Tyr96Phe mutant as well as in complexes with camphor-analogues. Large compounds, that fit well in the heme pocket and bind with higher affinity than camphor, display high spin contents that are less dependent on the presence of K(+). In contrast, K(+) has a significant effect on the high spin content of substrate-cytochrome P450cam complexes with looser interactions. We conclude that large compounds with higher affinities than camphor have more van der Waals contacts with the active site residues. Their mobilities are then reduced and less dependent on the presence of K(+). In this study, we also explored, for comparison, the K(+) effect on the spin transition state of another member of the P450 superfamily, cytochrome P450lin. This effect is not as strong as those observed for cytochrome P450cam. Even though the spin equilibrium does not change dramatically in the presence of K(+) or Na(+), the value of the dissociation constant (K(d)) for linalool binding is significantly affected by ionic strength. Analysis of the thermodynamic parameters for the linalool binding strongly suggests that, similarly to our previous finding for cytochrome P450cam, electrostatic gates participate in the control of substrate access.

Intermolecular electron transfer in cytochrome P450cam covalently bound with Tris(2,2'-bipyridyl)ruthenium(II): structural changes detected by FTIR spectroscopy

Using Fourier transform infrared spectroscopy (FTIR) we have monitored the changes in the protein structure following photoinduced electron transfer from Ru(bpy)(3)(2+) covalently attached to cysteine 334 on the surface of cytochrome P450cam (CYP101). The FTIR difference spectra between the oxidized and reduced form indicate changes in a salt link and the secondary structure (alpha-helix and turn regions). Photoreduction was carried out in the presence of carbon monoxide in order to prove the reduction of the heme iron by means of the appearance of the characteristic CO stretch vibration infrared band at 1940 cm(-1) for the camphor-bound protein. This infrared band has also been used to estimate electron transfer rates. The observed rates depend on the protein concentration, indicating that intermolecular electron transfer occurs between the labeled molecules.

Photochemical properties of a riboflavins/cytochrome P450 2B4 complex

The present study demonstrates the possible use of a non-covalent complex of riboflavins with cytochrome P450 2B4 (artificial flavocytochrome P450 2B4) for photo-induced intermolecular electron transfer between the isoalloxazine cycle of flavins and the ferric heme group of cytochrome P450 2B4. Riboflavin was used as a light-induced electron donor for the transfer of electrons to cytochrome P450. The quantitative measurement of the photocurrent, generated by photoreduction of non-covalent flavocytochrome P450 2B4, was carried out. In the presence of typical substrates for cytochrome P450 2B4 the decrease of cathodic photocurrent occurred, generated not only by riboflavin itself but also by a riboflavin/cytochrome P450 complex. It was demonstrated that flavocytochromes might serve as molecular amplifiers of a photocurrent, generated upon flavins' reduction. Introduction of flavin residues into the cytochrome P450 molecule transformed this haemoprotein into a photoreceptor and a photodiode and, in addition, into a photosensitive and photo-activated enzyme.

Insight into protein structure and protein-ligand recognition by Fourier transform infrared spectroscopy

An overview of the application of Fourier transform infrared spectroscopy for the analysis of the structure of proteins and protein-ligand recognition is given. The principle of the technique and of the spectra analysis is demonstrated. Spectral signal assignments to vibrational modes of the peptide chromophore, amino acid side chains, cofactors and metal ligands are summarized. Several examples for protein-ligand recognition are discussed. A particular focus is heme proteins and, as an example, studies of cytochrome P450 are reviewed. Fourier transform infrared spectroscopy in combination with the various techniques such as time-resolved and low-temperature methods, site-directed mutagenesis and isotope labeling is a helpful approach to studying protein-ligand recognition.

The catalytic pathway of cytochrome p450cam at atomic resolution

Members of the cytochrome P450 superfamily catalyze the addition of molecular oxygen to nonactivated hydrocarbons at physiological temperature-a reaction that requires high temperature to proceed in the absence of a catalyst. Structures were obtained for three intermediates in the hydroxylation reaction of camphor by P450cam with trapping techniques and cryocrystallography. The structure of the ferrous dioxygen adduct of P450cam was determined with 0.91 angstrom wavelength x-rays; irradiation with 1.5 angstrom x-rays results in breakdown of the dioxygen molecule to an intermediate that would be consistent with an oxyferryl species. The structures show conformational changes in several important residues and reveal a network of bound water molecules that may provide the protons needed for the reaction.

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.