Protein engineering as a tool for understanding electron transfer

Hijacking Chemical Reactions of P450 Enzymes for Altered Chemical Reactions and Asymmetric Synthesis

Cytochrome P450s are heme-containing enzymes capable of the oxidative transformation of a wide range of organic substrates. A protein scaffold that coordinates the heme iron, and the catalytic pocket residues, together, determine the reaction selectivity and regio- and stereo-selectivity of the P450 enzymes. Different substrates also affect the properties of P450s by binding to its catalytic pocket. Modulating the redox potential of the heme by substituting iron-coordinating residues changes the chemical reaction, the type of cofactor requirement, and the stereoselectivity of P450s. Around hundreds of P450s are experimentally characterized, therefore, a mechanistic understanding of the factors affecting their catalysis is increasingly vital in the age of synthetic biology and biotechnology. Engineering P450s can enable them to catalyze a variety of chemical reactions viz. oxygenation, peroxygenation, cyclopropanation, epoxidation, nitration, etc., to synthesize high-value chiral organic molecules with exceptionally high stereo- and regioselectivity and catalytic efficiency. This review will focus on recent studies of the mechanistic understandings of the modulation of heme redox potential in the engineered P450 variants, and the effect of small decoy molecules, dual function small molecules, and substrate mimetics on the type of chemical reaction and the catalytic cycle of the P450 enzymes.

A Single Iron Porphyrin Shows pH Dependent Switch between "Push" and "Pull" Effects in Electrochemical Oxygen Reduction

The "push-pull" effects associated with heme enzymes manifest themselves through highly evolved distal amino acid environments and axial ligands to the heme. These conserved residues enhance their reactivities by orders of magnitude relative to small molecules that mimic the primary coordination. An instance of a mononuclear iron porphyrin with covalently attached pendent phenanthroline groups is reported which exhibit reactivity indicating a pH dependent "push" to "pull" transition in the same molecule. The pendant phenanthroline residues provide proton transfer pathways into the iron site, ensuring selective 4e^-/4H⁺ reduction of O₂ to water. The protonation of these residues at lower pH mimics the pull effect of peroxidases, and a coordination of an axial hydroxide ligand at high pH emulates the push effect of P450 monooxygenases. Both effects enhance the rate of O₂ reduction by orders of magnitude over its value at neutral pH while maintaining exclusive selectivity for 4e^-/4H⁺ oxygen reduction reaction.

Structural analysis of diheme cytochrome c by hydrogen-deuterium exchange mass spectrometry and homology modeling

A lack of X-ray or nuclear magnetic resonance structures of proteins inhibits their further study and characterization, motivating the development of new ways of analyzing structural information without crystal structures. The combination of hydrogen–deuterium exchange mass spectrometry (HDX-MS) data in conjunction with homology modeling can provide improved structure and mechanistic predictions. Here a unique diheme cytochrome c (DHCC) protein from Heliobacterium modesticaldum is studied with both HDX and homology modeling to bring some definition of the structure of the protein and its role. Specifically, HDX data were used to guide the homology modeling to yield a more functionally relevant structural model of DHCC.

The role of key residues in structure, function, and stability of cytochrome-c

Cytochrome-c (cyt-c), a multi-functional protein, plays a significant role in the electron transport chain, and thus is indispensable in the energy-production process. Besides being an important component in apoptosis, it detoxifies reactive oxygen species. Two hundred and eighty-five complete amino acid sequences of cyt-c from different species are known. Sequence analysis suggests that the number of amino acid residues in most mitochondrial cyts-c is in the range 104 ± 10, and amino acid residues at only few positions are highly conserved throughout evolution. These highly conserved residues are Cys14, Cys17, His18, Gly29, Pro30, Gly41, Asn52, Trp59, Tyr67, Leu68, Pro71, Pro76, Thr78, Met80, and Phe82. These are also known as "key residues", which contribute significantly to the structure, function, folding, and stability of cyt-c. The three-dimensional structure of cyt-c from ten eukaryotic species have been determined using X-ray diffraction studies. Structure analysis suggests that the tertiary structure of cyt-c is almost preserved along the evolutionary scale. Furthermore, residues of N/C-terminal helices Gly6, Phe10, Leu94, and Tyr97 interact with each other in a specific manner, forming an evolutionary conserved interface. To understand the role of evolutionary conserved residues on structure, stability, and function, numerous studies have been performed in which these residues were substituted with different amino acids. In these studies, structure deals with the effect of mutation on secondary and tertiary structure measured by spectroscopic techniques; stability deals with the effect of mutation on T m (midpoint of heat denaturation), ∆G D (Gibbs free energy change on denaturation) and folding; and function deals with the effect of mutation on electron transport, apoptosis, cell growth, and protein expression. In this review, we have compiled all these studies at one place. This compilation will be useful to biochemists and biophysicists interested in understanding the importance of conservation of certain residues throughout the evolution in preserving the structure, function, and stability in proteins.

A serine-substituted P450 catalyzes highly efficient carbene transfer to olefins in vivo

Whole-cell catalysts for non-natural chemical reactions will open new routes to sustainable production of chemicals. We designed a cytochrome 'P411' with unique serine-heme ligation that catalyzes efficient and selective olefin cyclopropanation in intact Escherichia coli cells. The mutation C400S in cytochrome P450(BM3) gives a signature ferrous CO Soret peak at 411 nm, abolishes monooxygenation activity, raises the resting-state Fe(III)-to-Fe(II) reduction potential and substantially improves NAD(P)H-driven activity.

Redox tuning of cytochrome b562 through facile metal porphyrin substitution

The biologically and nanotechnologically important heme protein cytochrome b(562) was reconstructed with zinc and copper porphyrins, leading to significant changes in the spectral, redox and electron transfer properties. The Cu form shifts the redox potential by +300 mV and exhibits high electron transfer, while the Zn form is redox inert.

Ferric His93Gly myoglobin cavity mutant and its complexes with thioether and selenolate as heme protein models

The composition of ferric exogenous ligand-free His93Gly sperm whale myoglobin (H93G Mb) at neutral pH has been determined by examination of the spectral properties of the protein over the pH range from 3.0 to 10.5. An apparent pKa value of ~6.6 has been observed for the conversion of a postulated six-coordinate bis-water-bound coordination structure at pH 5.0 to a five-coordinate hydroxide-bound form at pH 10.5. Starting from the exogenous ligand-free ferric H93G protein, ferric mono- and bis-thioether (tetrahydrothiophene, THT)-ligated adducts have been prepared and characterized by UV-visible (UV-vis) absorption and magnetic circular dichroism (MCD) spectroscopy. The mon-THT ferric H93G Mb species has hydroxide as the sixth ligand. The bis-THT derivative is a model for the low-spin ferric heme binding site of native bis-Met-ligated bacterioferritin or streptococcal heme-associated protein (Shp). A novel THT-bound ferryl H93G Mb moiety has been partially formed. The high-spin five-coordinate ferric H93G(selenolate) Mb complex has been prepared using benzeneselenol and characterized by UV-vis and MCD spectroscopy as a model for Se-Cys-ligated ferric cytochrome P450. The results described herein further demonstrate the versatility of the H93G cavity mutant for modeling the coordination structures of novel heme iron protein active sites.

Miniaturized hemoproteins

The present paper highlights and reviews current research in the field of hemoprotein models. Hemoproteins have been extensively studied in order to understand structure-function relationships, and to design new molecules with desired functions. A wide number of synthetic analogues have been developed, using quite different approaches. They differ in molecular structures, ranging from simple meso-substituted tetraaryl-metalloporphyrins and peptide-porphyrin conjugates. In this paper we summarize the state of the art on peptide based hemoprotein models. We also report here the approach used by us to develop a new class of molecules, named mimochromes. They can be regarded as miniaturized hemoproteins, because mimochromes are low molecular weight compounds with some structural and functional properties common to those of the parent high molecular weight protein. The basic structure of mimochromes is a deuteroporphyrin ring covalently linked to two helical peptide chains. Two molecules of this series have been fully characterized. All the information derived from their structural analysis has been applied to the design of new analogues with additional functions.

Photosynthetic reaction centers

The reaction center is the key component for the primary events in the photochemical conversion of light into chemical energy. After excitation by light, a charge separation that spans the cell membrane is formed in the reaction center in a few hundred picoseconds with a quantum yield of essentially one. A conserved pattern in the cofactors and core proteins of reaction centers from different organisms can be defined based on comparisons of the three dimensional structure of two types of reaction centers. Different functional aspects of the reaction center are discussed, including the properties of the bacteriochlorophyll or chlorophyll dimer that constitutes the primary electron donor, the pathway of electron transfer, and the different functional roles of the electron acceptors. The implication of these results on the evolution of the reaction center is presented.

Relationship between the oxidation potential and electron spin density of the primary electron donor in reaction centers from Rhodobacter sphaeroides

The primary electron donor in bacterial reaction centers is a dimer of bacteriochlorophyll a molecules, labeled L or M based on their proximity to the symmetry-related protein subunits. The electronic structure of the bacteriochlorophyll dimer was probed by introducing small systematic variations in the bacteriochlorophyll-protein interactions by a series of site-directed mutations that replaced residue Leu M160 with histidine, tyrosine, glutamic acid, glutamine, aspartic acid, asparagine, lysine, and serine. The midpoint potentials for oxidation of the dimer in the mutants showed an almost continuous increase up to approximately 60 mV compared with wild type. The spin density distribution of the unpaired electron in the cation radical state of the dimer was determined by electron-nuclear-nuclear triple resonance spectroscopy in solution. The ratio of the spin density on the L side of the dimer to the M side varied from approximately 2:1 to approximately 5:1 in the mutants compared with approximately 2:1 for wild type. The correlation between the midpoint potential and spin density distribution was described using a simple molecular orbital model, in which the major effect of the mutations is assumed to be a change in the energy of the M half of the dimer, providing estimates for the coupling and energy levels of the orbitals in the dimer. These results demonstrate that the midpoint potential can be fine-tuned by electrostatic interactions with amino acids near the dimer and show that the properties of the electronic structure of a donor or acceptor in a protein complex can be directly related to functional properties such as the oxidation-reduction midpoint potential.

Effects of folding on metalloprotein active sites

Experimental data for the unfolding of cytochrome c and azurin by guanidinium chloride (GuHCl) are used to construct free-energy diagrams for the folding of the oxidized and reduced proteins. With cytochrome c, the driving force for folding the reduced protein is larger than that for the oxidized form. Both the oxidized and the reduced folded forms of yeast cytochrome c are less stable than the corresponding states of the horse protein. Due to the covalent attachment of the heme and its fixed tetragonal coordination geometry, cytochrome c folding can be described by a two-state model. A thermodynamic cycle leads to an expression for the difference in self-exchange reorganization energies for the folded and unfolded proteins. The reorganization energy for electron exchange in the folded protein is approximately 0.5 eV smaller than that for a heme in aqueous solution. The finding that reduced azurin unfolds at lower GuHCl concentrations than the oxidized protein suggests that the coordination structure of copper is different in oxidized and reduced unfolded states: it is likely that the geometry of CuI in the unfolded protein is linear or trigonal, whereas CuII prefers to be tetragonal. The evidence indicates that protein folding lowers the azurin reorganization energy by roughly 1.7 eV relative to an aqueous Cu(1, 10-phenanthroline)22+/+ reference system.

A missing link in cupredoxins: crystal structure of cucumber stellacyanin at 1.6 A resolution

Stellacyanins are blue (type I) copper glycoproteins that differ from other members of the cupredoxin family in their spectroscopic and electron transfer properties. Until now, stellacyanins have eluded structure determination. Here we report the three-dimensional crystal structure of the 109 amino acid, non-glycosylated copper binding domain of recombinant cucumber stellacyanin refined to 1.6 A resolution. The crystallographic R-value for all 18,488 reflections (sigma > 0) between 50-1.6 A is 0.195. The overall fold is organized in two beta-sheets, both with four beta-stands. Two alpha-helices are found in loop regions between beta-strands. The beta-sheets form a beta-sandwich similar to those found in other cupredoxins, but some features differ from proteins such as plastocyanin and azurin in that the beta-barrel is more flattened, there is an extra N-terminal alpha-helix, and the copper binding site is much more solvent accessible. The presence of a disulfide bond at the copper binding end of the protein confirms that cucumber stellacyanin has a phytocyanin-like fold. The ligands to copper are two histidines, one cysteine, and one glutamine, the latter replacing the methionine typically found in mononuclear blue copper proteins. The Cu-Gln bond is one of the shortest axial ligand bond distances observed to date in structurally characterized type I copper proteins. The characteristic spectroscopic properties and electron transfer reactivity of stellacyanin, which differ significantly from those of other well-characterized cupredoxins, can be explained by its more exposed copper site, its distinctive amino acid ligand composition, and its nearly tetrahedral ligand geometry. Surface features on the cucumber stellacyanin molecule that could be involved in interactions with putative redox partners are discussed.

Cloning, expression, and spectroscopic characterization of Cucumis sativus stellacyanin in its nonglycosylated form

The cDNA encoding the 182 amino acid long precursor stellacyanin from Cucumis sativus was isolated and characterized. The protein precursor consists of four sequence domains: I, a 23 amino acid hydrophobic N-terminal signal peptide with features characteristic of secretory proteins; II, a 109 amino acid copper-binding domain; III, a 26 amino acid hydroxyproline- and serine-rich peptide characteristic of motifs found in the extension family, extracellular structural glycoproteins found in plant cell walls; and IV, a 22 amino acid hydrophobic extension. Maturation of the protein involves posttranslational processing of domains I and IV. The copper-binding domain (domain II), which shares high sequence identity with other stellacyanins, has been expressed without its carbohydrate attachment sites, refolded from the Escherichia coli inclusion bodies, purified, and characterized by electronic absorption, EPR, ESEEM, and RR spectroscopy. Its spectroscopic properties are nearly identical to those of stellacyanin from the Japanese lacquer tree Rhus vernicifera, the most extensively studied and best characterized stellacyanin, indicating that this domain folds correctly, even in the absence of its carbohydrate moiety. The presence of a hydroxyproline- and serine-rich domain III suggests that stellacyanin may have a function other than that of a diffusible electron transfer protein, conceivably participating in redox reactions localized at the plant cell wall, which are known to occur in response to wounding or infection of the plant.

Relationship between the oxidation potential of the bacteriochlorophyll dimer and electron transfer in photosynthetic reaction centers

The primary electron donor in the photosynthetic reaction center from purple bacteria is a bacteriochlorophyll dimer containing four conjugated carbonyl groups that may form hydrogen bonds with amino acid residues. Spectroscopic analyses of a set of mutant reaction centers confirm that hydrogen bonds can be formed between each of these carbonyl groups and histidine residues in the reaction center subunits. The addition of each hydrogen bond is correlated with an increase in the oxidation potential of the dimer, resulting in a 355-mV range in the midpoint potential. The resulting changes in the free-energy differences for several reactions involving the dimer are related to the electron transfer rates using the Marcus theory. These reactions include electron transfer from cytochrome c2 to the oxidized dimer, charge recombination from the primary electron acceptor quinone, and the initial forward electron transfer.

Biological electron transfer: structural and mechanistic studies

The developments in the field of biological electron transfer over the past 2 years are reviewed. Attention is given to theoretical developments, especially with respect to the concept of 'electronic pathways' inside proteins, and the association process of redox proteins in solution and the idea of 'conformational gating'.

Rack-induced bonding in blue-copper proteins

The unique spectroscopic properties of blue-copper centers, i.e. the strong charge-transfer band at approximately 600 nm and the narrow hyperfine coupling in the EPR spectrum, are reviewed. The concept of rack-induced bonding is summarized. The tertiary structure of the protein creates a performed chelating site with very little flexibility, the geometry of which is in conflict with that preferred by Cu2+. The structure of the metal site in azurin is discussed. It is shown that the three strong ligands, one thiolate S and two imidazole N, are in a configuration intermediate between those preferred by Cu2+ and Cu+. It is emphasized that cysteine is an obligatory component of a blue site, whereas the weak interaction with a methionine S is not necessary. The minimum rack energy is estimated to be 70 kJ.mol-1. It is pointed out that the high reduction potentials of blue-copper centers are a result of the protein-forced ligand-field-destabilized site structure. It is suggested that the potentials are tuned by variations in pi back bonding, and this is supported by a linear increase in delta LF (ligand field) with decreasing electron-transfer enthalpy. Site-directed mutagenesis has shown that large hydrophobic residues in the site increase the potential, whereas negative groups or water decrease it. It is also shown that the fine-tuning of the properties of the metal site by rack-induced bonding can alter the electron-transfer reorganization energy. Kinetic results with azurin mutants support a through-bond tunneling mechanism for intramolecular electron transfer in proteins. Finally, it is pointed out that the concept of rack-induced bonding is a universal principle of macromolecular structure/function relationships, which should be applied also to other systems.

Electron transfer in cytochrome c depends upon the structure of the intervening medium

BACKGROUND

Long-distance electron-transfer (ET) reactions through proteins are involved in a great many biochemical processes; however, the way in which the protein structure influences the rates of these reactions is not well understood. We have therefore measured the rates of intramolecular ET from the ferroheme to a bis(2,2'-bipyridine)imidazoleruthenium(III) acceptor at histidine 39 or 54 in derivatives of yeast iso-1-cytochrome c, and studied the effect of an asparagine to isoleucine mutation at position 52, a residue situated between the heme and the electron acceptor.

RESULTS

The Fe2+-->Ru3+ rate constants demonstrate that residue 52 affects ET from the heme to His54 (Ile52 > Asn52), but not to His39 (Ile52 = Asn52). The enhanced Fe(2+)-Ru3+(His54) electronic coupling for the N52I/K54H protein is in good agreement with sigma-tunneling calculations, which predict the length of the ET pathways between the heme and His54.

CONCLUSION

The structure of the intervening medium between the heme and electron acceptors at the protein surface influences the donor-acceptor couplings in cytochrome c.

Structural dynamics in an electron-transfer complex

The dynamic behaviour of the complex of horse cytochrome c with cytochrome c peroxidase, an electron-transfer complex, was studied in solution by a hydrogen exchange labelling method together with two-dimensional NMR analysis. Although cytochrome c hydrogens in the expected binding region exhibit slowed exchange, the measured slowing factors are very small, indicating that hydrogen-exchange occurs with little hindrance from within the binding interface. The complex in solution must therefore be highly mobile rather than rigidly defined, as implied by the crystalline complex. This result is in conflict with the concept that biological electron transfer occurs by way of predetermined covalent pathways.