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Hongkonoids A-D (1-4), the first example of ascorbylated terpenoids featuring a unique 5,5,5-fused tricyclic spiroketal butyrolactone moiety and diterpenoid-derived long chain, were isolated from Dysoxylum hongkongense. Their structures were unambiguously assigned by a combination of spectroscopic data, chemical degradation, Xray crystallography, CD analysis, and total synthesis. The total syntheses of compounds 1-4 were effectively accomplished by a convergent strategy with the longest linear sequences of 12-14 steps and overall yields of 5.4- 9.6%. Notably, we exploited a bioinspired one-pot method to construct the key intermediate 14 from an easily made compound 12 by involving the cascade reactions of an elaborate Claisen rearrangement, deprotections, and a 5-exo-trig cyclization. The desired major epimer 14a was then transformed to the main building block 21. Assembly of 21 and the long chain vinyl iodide 7 was made by an NHK coupling reaction to furnish the framework of 1-4. Some of the hongkonoids and/or synthetic analogs showed significant to moderate inhibitory activities against NF-κB, 11β-HSD1, and sterol synthesis. The most active NF-κB inhibitor 34 exhibited distinct inhibition on the LPS-induced inflammatory responses in RAW 246.7 and primary BMDM cells. [ABSTRACT FROM AUTHOR]

The fundamental biogeochemical cycle of nitrogen includes cytochrome c nitrite reductase, which catalyzes the reduction of nitrite ions to ammonium with eight protons and six electrons (NO2- + 8H+ + 6e- → NH4+ + 2H2O). This reaction has motivated researchers to explore the reduction of nitrite. Although a number of electrochemical reductions of NO2- have been reported, the synthetic nitrite reduction reaction remains limited. To the best of our knowledge, formation of ammonia has not been reported. We report a three-step nitrite reduction cycle on a dinuclear ruthenium platform {(TpRu)2(μ-pz)} (Tp = HB(pyrazol-1-yl)3), producing ammonia. The cycle comprises conversion of a nitrito ligand to a NO ligand using 2H+ and e-, subsequent reduction of the NO ligand to a nitrido and a H2O ligand by consumption of 2H+ and 5e-, and recovery of the parent nitrito ligand. Moreover, release of ammonia was detected. [ABSTRACT FROM AUTHOR]

In addition to serving as respiratory electron shuttle, ferricytochrome c (cyt c) acts as a peroxidase; i.e., it catalyzes the oxidation of organic substrates by H2O2. This peroxidase function plays a key role during apoptosis. Typical peroxidases have a five-coordinate heme with a vacant distal coordination site that permits the iron center to interact with H2O2. In contrast, native cyt c is six-coordinate, as the distal coordination site is occupied by Met80. It thus seems counterintuitive that native cyt c would exhibit peroxidase activity. The current work scrutinizes the origin of this structure-function mismatch. Cyt c-catalyzed peroxidase reactions show an initial lag phase that is consistent with the in situ conversion of a precatalyst to an active peroxidase. Using mass spectrometry, we demonstrate the occurrence of cyt c self-oxidation in the presence of H2O2. The newly generated oxidized proteoforms are shown to possess significantly enhanced peroxidase activity. H2O2-induced modifications commence with oxidation of Tyr67, followed by permanent displacement of Met80 from the heme iron. The actual peroxidase activation step corresponds to subsequent side chain carbonylation, likely at Lys72/73. The Tyr67-oxidized/carbonylated protein has a vacant distal ligation site, and it represents the true peroxidase-active structure of cyt c. Subsequent self-oxidation eventually causes deactivation. It appears that this is the first report that identifies H2O2-induced covalent modifications as an essential component for the peroxidase activity of "native" cyt c. [ABSTRACT FROM AUTHOR]

Dicarboxylic acids are commodity chemicals used in the production of plastics, polyesters, nylons, fragrances, and medications. Bio-based routes to dicarboxylic acids are gaining attention due to environmental concerns about petroleum-based production of these compounds. Some industrial applications require dicarboxylic acids with specific carbon chain lengths, including odd-carbon species. Biosynthetic pathways involving cytochrome P450-catalyzed oxidation of fatty acids in yeast and bacteria have been reported, but these systems produce almost exclusively even-carbon species. Here we report a novel pathway to odd-carbon dicarboxylic acids directly from glucose in Escherichia coli by employing an engineered pathway combining enzymes from biotin and fatty acid synthesis. Optimization of the pathway will lead to industrial strains for the production of valuable odd-carbon diacids. [ABSTRACT FROM AUTHOR]

The decaheme cytochrome MtrC from Shewanella oneidensis MR-1 immobilized on an ITO electrode displays unprecedented H2O2 reduction activity. Although MtrC showed lower peroxidase activity in solution compared to horseradish peroxidase, the ten heme cofactors enable excellent electronic communication and a superior activity on the electrode surface. A hierarchical ITO electrode enabled optimal immobilization of MtrC and a high current density of 1 mA cm-2 at 0.4 V vs SHE could be obtained at pH 6.5 (Eonset = 0.72 V). UV-visible and Resonance Raman spectroelectrochemical studies suggest the formation of a high valent iron-oxo species as the catalytic intermediate. Our findings demonstrate the potential of multiheme cytochromes to catalyze technologically relevant reactions and establish MtrC as a new benchmark in biotechnological H2O2 reduction with scope for applications in fuel cells and biosensors. [ABSTRACT FROM AUTHOR]

A major goal in metalloprotein design is to build protein scaffolds from scratch that allow precise control over metal coordination. A particular challenge in this regard is the construction of allosteric systems in which metal coordination equilibria are coupled to other chemical events that take place elsewhere in the protein scaffold. We previously developed a metal-templated self-assembly strategy (MeTIR) to build supramolecular protein complexes with tailorable interfaces from monomeric building blocks. Here, using this strategy, we have incorporated multiple disulfide bonds into the interfaces of a Zn-templated cytochrome cb562 assembly in order to create mechanical strain on the quaternary structural level. Structural and biophysical analyses indicate that this strain leads to an allosteric system in which Zn2+ binding and dissociation are remotely coupled to the formation and breakage of a disulfide bond over a distance of >14 Å. The breakage of this strained bond upon Zn2+ dissociation occurs in the absence of any reductants, apparently through a hydrolytic mechanism that generates a sulfenic acid/thiol pair. [ABSTRACT FROM AUTHOR]

In this study, the effector role of Pdx (putidaredoxin) on cytochrome P450cam conformation is refined by attaching two different spin labels, MTSL or BSL (bifunctional spin-label) onto the F or G helices and using DEER (double electron-electron resonance) to measure the distance between labels. Recent EPR and crystallographic studies have observed that oxidized Pdx induces substrate-bound P450cam to change from the closed to the open state. However, this change was not observed by DEER in the reduced Pdx complex with carbon-monoxide-bound P450cam (Fe2+CO). In addition, recent NMR studies have failed to observe a change in P450cam conformation upon binding Pdx. Hence, resolving these issues is important for a full understanding the effector role of Pdx. Here we show that oxidized Pdx induces camphor-bound P450cam to shift from the closed to the open conformation when labeled on either the F or G helices with MTSL. BSL at these sites can either narrow the distance distribution widths dramatically or alter the extent of the conformational change. In addition, we report DEER spectra on a mixed oxidation state containing oxidized Pdx and ferrous CO-bound P450cam, showing that P450cam remains closed. This indicates that CO binding to the heme prevents P450cam from opening, overriding the influence exerted by Pdx binding. Finally, we report the open form P450cam crystal structure with substrate bound, which suggests that crystal packing effects may prevent conformational conversion. Using multiple labeling approaches, DEER provides a unique perspective to resolve how the conformation of P450cam depends on Pdx and ligand states. [ABSTRACT FROM AUTHOR]

Glycopeptide antibiotics (GPAs) are nonribosomal peptides rich in modifications introduced by external enzymes. These enzymes act on the free peptide aglycone or intermediates bound to the nonribosomal peptide synthetase (NRPS) assembly line. In this process the terminal module of the NRPS plays a crucial role as it contains a unique recruitment platform (X-domain) interacting with three to four modifying Cytochrome P450 (P450) enzymes that are responsible for cyclizing bound peptides. However, whether these enzymes share the same binding site on the X-domain and how the order of the cyclization steps is orchestrated has remained elusive. In this study we investigate the first two reactions in teicoplanin aglycone maturation catalyzed by the enzymes OxyBtei and OxyAtei. We demonstrate that both enzymes interact with the X-domain via the identical interaction site with similar affinities, irrespective of the peptide modification stage, while their catalytic activity is restricted to the correctly cross-linked peptide. On the basis of steady state kinetics of the OxyBtei-catalyzed reaction, we propose a model for P450 recruitment and peptide modification that involves continuous association/dissociation of the P450 enzymes with the NRPS, followed by specific recognition of the peptide cyclization state by the P450 (scanning). This leads to an induced conformational change that enhances the affinity of the enzyme/substrate complex and initiates catalysis; product release then occurs, with the product itself becoming the substrate for the second enzyme in the pathway. This model rationalizes our experimental findings for this complex enzyme cascade and provides insights into the orchestration of the sequential peptide tailoring reactions on the terminal NRPS module in GPA biosynthesis. [ABSTRACT FROM AUTHOR]

We have developed an aptameric nanosensor for fluorescence activation imaging of cytochrome c (Cyt c). Fluorescence imaging tools that enable visualization of key molecular players in apoptotic signaling are essential for cell biology and clinical theranostics. Cyt c is a major mediator in cell apoptosis. However, fluorescence imaging tools allowing direct visualization of Cyt c translocation in living cells have currently not been realized. We report for the first time the realization of a nanosensor tool that enables direct fluorescence activation imaging of Cyt c released from mitochondria in cell apoptosis. This strategy relies on spatially selective cytosolic delivery of a nanosensor constructed by assembly of a fluorophore-tagged DNA aptamer on PEGylated graphene nanosheets. The cytosolic release of Cyt c is able to dissociate the aptamer from graphene and trigger an activated fluorescence signal. The nanosensor is shown to exhibit high sensitivity and selectivity, rapid response, large signal-to-background ratio for in vitro, and intracellular detection of Cyt c. It also enables real-time visualization of the Cyt c release kinetics and direct identification of the regulators for apoptosis. The developed nanosensor may provide a very valuable tool for apoptotic studies and catalyze the fundamental interrogations of Cyt c-mediated biology. [ABSTRACT FROM AUTHOR]

We report here that photoinitiated electron flow involving a metal-substituted (M = Mg, Zn) myoglobin (Mb) and its physiological partner protein, cytochrome b5 (cyt b5) can be “symmetrized”: the [Mb:cyt b5] complex stabilized by three D/E → K mutations on Mb (D44K/D60K/E85K, denoted MMb) exhibits both oxidative and reductive ET quenching of both the singlet and triplet photoexcited MMb states, the direction of flow being determined by the oxidation state of the cyt b5 partner. The first-excited singlet state of MMb (1MMb) undergoes ns-time scale reductive ET quenching by Fe2+2+cyt b5 as well as ns-time scale oxidative ET quenching by Fe3+cyt b5, both processes involving an ensemble of structures that do not interconvert on this time scale. Despite a large disparity in driving force favoring photooxidation of 1MMb relative to photoreduction (δ(−ΔG0) ≈ 0.4 eV, M = Mg; ≈ 0.2 eV, M = Zn), for each M the average rate constants for the two reactions are the same within error, 1kf > 108 s–1. This surprising observation is explained by considering the driving-force dependence of the Franck–Condon factor in the Marcus equation. The triplet state of the myoglobin (3MMb) created by intersystem crossing from 1MMb likewise undergoes reductive ET quenching by Fe2+cyt b5 as well as oxidative ET quenching by Fe3+cyt b5. As with singlet ET, the rate constants for oxidative ET quenching and reductive ET quenching on the triplet time scale are the same within error, 3kf ≈ 105 s–1, but here the equivalence is attributable to gating by intracomplex conversion among a conformational ensemble. [ABSTRACT FROM AUTHOR]

Cytochrome aa3 from Paracoccus denitrificans and cytochrome ba3 from Thermus thermophilus, two distinct members of the heme—copper oxidase superfamily, were immobilized on electrodes modified with gold nanoparticles. This procedure allowed us to achieve direct electron transfer between the enzyme and the gold nanoparticles and to obtain evidence for different electrocatalytic properties of the two enzymes. The pH dependence and thermostability reveal that the enzymes are highly adapted to their native environments. These results suggest that evolution resulted in different solutions to the common problem of electron transfer to oxygen. [ABSTRACT FROM AUTHOR]

CYP19A1, or aromatase, a cytochrome P450 responsible for estrogen biosynthesis in humans, is an important therapeutic target for the treatment of breast cancer. There is still controversy surrounding the identity of reaction intermediate that catalyzes carbon–carbon scission in this key enzyme. Probing the oxy-complexes of CYP19A1 poised for hydroxylase and lyase chemistries using resonance Raman spectroscopy and drawing a comparison with CYP17A1, we have found no significant difference in the frequencies or isotopic shifts for these two steps in CYP19A1. Our experiments implicate the involvement of Compound I in the terminal lyase step of CYP19A1 catalysis. [ABSTRACT FROM AUTHOR]

Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two a-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of a-helical segments rather than a general hydrophobic collapse. [ABSTRACT FROM AUTHOR]

Present and emerging biotechnological applications for iron (oxyhydr)oxide nanomaterials depend on their interaction with microorganisms, as do their toxicity, transport, and fate in biological and environmental systems. However, mass or electron transfer along key molecular pathways at microbe—nanomaterial interfaces is extremely difficult to quantify because of system complexity. Inspired by Fe(II)-oxidizing microbes widespread in nature, we isolate and characterize one such pathway by examining the oxidation of Fe3–xTixO4 (magnetite-titanomagnetite) nanoparticles by the bacterial electron transfer enzyme MtoA, a decaheme c-type cytochrome. Oxidation by MtoA was studied as a function of the thermodynamic driving force for electron transfer by controlling the Ti(IV) doping content (x), which tunes the solid-state Fe(II)/Fe(III) ratio built into the nanoparticles. A higher Fe(II)/Fe(III) ratio appears to systematically increase the electron transfer kinetics to the cytochrome. In situ X-ray diffraction indicated that, during oxidation, the spinel ferrite lattice remains intact while structural Fe(II) is progressively depleted. Surface and atomic site specific Fe L2,3-edge X-ray magnetic circular dichroism indicated that MtoA directly accesses magnetically ordered B-sublattice Fe(II) at the interface. This study provides the first quantitative insights into an isolated molecular pathway for biotransformation of iron (oxyhydr)oxide nanomaterials, and more generally, it also illustrates new techniques for probing these pathways in detail, featuring use of tailored nanoparticles, purified metalloenzyme, and synchrotron X-ray absorption spectroscopies. [ABSTRACT FROM AUTHOR]

Protein complex formation is thought to be at least a two-step process, in which the active complex is preceded by the formation of an encounter complex. The interactions in the encounter complex are usually dominated by electrostatic forces, whereas the active complex is also stabilized by noncovalent short-range forces. Here, the complex of cytochrome f and plastocyanin, electron-transfer proteins involved in photosynthesis, was studied using paramagnetic relaxation NMR spectroscopy. Spin labels were attached to cytochrome f, and the relaxation enhancements of plastocyanin nuclei were measured, demonstrating that a large part of the cytochrome f surface area is sampled by plastocyanin. In contrast, plastocyanin is always oriented with its hydrophobic patch toward cytochrome f. The complex was visualized using ensemble docking, showing that the encounter complex is stabilized by hydrophobic as well as electrostatic interactions. The results suggest a model of electrostatic preorientation before the proteins make contact, followed by the formation of an encounter complex that rapidly leads to electron-transfer active conformations by gradual increase of the overlap of nonpolar surface areas on cytochrome f and plastocyanin. In this model the distinction between the encounter and active complexes vanishes, at least in the case of electron-transfer complexes, which do not require a high degree of specificity. [ABSTRACT FROM AUTHOR]

Electron-transporting multi-heme cytochromes are essential to the metabolism of microbes that inhabit soils and carry out important biogeochemical processes. Recently the first crystal structure of a prototype bacterial deca-heme cytochrome (MtrF) has been resolved and its electrochemistry characterized. However, the molecular details of electron transport along heme chains in the cytochrome are difficult to access via experiment due to the nearly identical chemical nature of the heme cofactors. Here we employ large-scale molecular dynamics simulations to compute the redox potentials of the 10 hemes of MtrF in aqueous solution. We find that as a whole they fall within a range of ~0.3 V, in agreement with experiment. Individual redox potentials give rise to a free energy profile for electron transport that is approximately symmetric with respect to the center of the protein. Our calculations indicate that there is no significant potential bias along the orthogonal octa- and tetra-heme chains, suggesting that under aqueous conditions MtrF is a nearly reversible two-dimensional conductor. [ABSTRACT FROM AUTHOR]

CYP125 from Mycobacterium tuberculosis catalyzes sequential oxidation of the cholesterol side-chain terminal methyl group to the alcohol, aldehyde, and finally acid. Here, we demonstrate that CYP125 simultaneously catalyzes the formation of five other products, all of which result from deformylation of the sterol side chain. The aldehyde intermediate is shown to be the precursor of both the conventional acid metabolite and the five deformylation products. The acid arises by protonation of the ferric-peroxo anion species and formation of the ferryl-oxene species, also known as Compound I, followed by hydrogen abstraction and oxygen transfer. The deformylation products arise by addition of the same ferric-peroxo anion to the aldehyde intermediate to give a peroxyhemiacetal that leads to C-C bond cleavage. This bifurcation of the catalytic sequence has allowed us to examine the effect of electron donation by the proximal ligand on the properties of the ferric-peroxo anion. Replacement of the cysteine thiolate iron ligand by a selenocysteine results in UV-vis, EPR, and resonance Raman spectral changes indicative of an increased electron donation from the proximal selenolate ligand to the iron. Analysis of the product distribution in the reaction of the selenocysteine substituted enzyme reveals a gain in the formation of the acid (Compound I pathway) at the expense of deformylation products. These observations are consistent with an increase in the pKa of the ferric-peroxo anion, which favors its protonation and, therefore, Compound I formation. [ABSTRACT FROM AUTHOR]

Cytochrome c oxidase (CcO), known as complex IV of the electron transport chain, plays several important roles in aerobic cellular respiration. Electrons transferred from cytochrome c to CcO's catalytic site reduce molecular oxygen and produce a water molecule. These electron transfers also drive active proton pumping from the matrix (N-side) to intermembrane region (P-side) in mitochondria; the resultant proton gradient activates ATP synthase to produce ATP from ADP. Although the existence of the coupling between the electron transfer and the proton transport (PT) is established experimentally, its mechanism is not yet fully understood at the molecular level. In this work, it is shown why the reduction of heme a is essential for proton pumping. This is demonstrated via novel reactive molecular dynamics (MD) simulations that can describe the Grotthuss shuttling associated with the PT as well as the dynamic delocalization of the excess proton electronic charge defect. Moreover, the "valve" role of the Glu242 residue (bovine CcO notation) and the gate role of d-propionate of heme a3 (PRDa3) in the explicit PT are explicitly demonstrated for the first time. These results provide conclusive evidence for the CcO proton transporting mechanism inferred from experiments, while deepening the molecular level understanding of the CcO proton switch. [ABSTRACT FROM AUTHOR]

In many biochemical processes, proteins need to bind partners amidst a sea of other molecules. Generally, partner selection is achieved by formation of a single-orientation complex with well-defined, short-range interactions. We describe a protein network that functions effectively in a metabolic electron transfer process but lacks such specific interactions. The soil bacterium Paracoccus denitrificans oxidizes a variety of compounds by channeling electrons into the main respiratory pathway. Upon conversion of methylamine by methylamine dehydrogenase, electrons are transported to the terminal oxidase to reduce molecular oxygen. Steady-state kinetic measurements and NMR experiments demonstrate a remarkable number of possibilities for the electron transfer, involving the cupredoxin amicyanin as well as four c-type cytochromes. The observed interactions appear to be governed exclusively by the electrostatic nature of each of the proteins. It is concluded that Paracoccus provides a pool of cytochromes for efficient electron transfer via weak, ill-defined interactions, in contrast with the view that functional biochemical interactions require well-defined molecular interactions. It is proposed that the lack of requirement for specificity in these interactions might facilitate the integration of new metabolic pathways. [ABSTRACT FROM AUTHOR]

Cytochrome (cyt) P450s comprise the enzyme superfamily responsible for human oxidative metabolism of a majority of drugs and xenobiotics. Electronic delivery of electrons to cyt P4SOs could be used to drive the natural catalytic cycle for fundamental investigations, stereo- and regioselective synthesis, and biosensors. We describe herein 30 nm nanometer-thick films on electrodes featuring excess human cyt P450s and cyt P450 reductase (CPR) microsomes that efliciently mimic the natural catalytic pathway for the first time. Redox potentials, electron-transfer rates, CO-binding, and substrate conversion rates confirmed that electrons are delivered from the electrode to CPR, which transfers them to cyt P450. The film system enabled electrochemical probing of the interaction between cyt P450 and CPR for the first time. Agreement of film voltammetry data with theoretical simulations supports a pathway featuring a key equilibrium redox reaction in the natural catalytic pathway between reduced CPR and cyt P450 occurring within a CPR-cyt P450 complex uniquely poised for substrate conversion. [ABSTRACT FROM AUTHOR]

Resonance Raman (RR) spectroscopy is used to help define active site structural responses of nanodisc-incorporated CYP3A4 to the binding of three substrates: bromocriptine (BC), erythromycin (ERY), and testosterone (TST). We demonstrate that nanodisc-incorporated assemblies reveal much more well-defined active site RR spectroscopic responses as compared to those normally obtained with the conventional, detergent-stabilized, sampling strategies. While ERY and BC are known to bind to CYP3A4 with a 1:1 stoichiometry, only the BC induces a substantial conversion from low- to high-spin state, as clearly manifested in the RR spectra acquired herein. The third substrate, TST, displays significant homotropic interactions within CYP3A4, the active site binding up to 3 molecules of this substrate, with the functional properties varying in response to binding of individual substrate molecules. While such behavior seemingly suggests the possibility that each substrate binding event induces functionally important heme structural changes, up to this time spectroscopic evidence for such structural changes has not been available. The current RRspectroscopic studies show clearly that accommodation of different size substrates, and different loading of TST, do not significantly affect the structure of the substrate-bound ferric heme. However, it is here demonstrated that the nature and number of bound substrates do have an extraordinary influence on the conformation of bound exogenous ligands, such as CO or dioxygen and its reduced forms, implying an effective mechanism whereby substrate structure can impact reactivity of intermediates so as to influence function, as reflected in the diverse reactivity of this drug metabolizing cytochrome. [ABSTRACT FROM AUTHOR]

The acceleration of electron transfer (ET) rates in redox proteins relative to aqueous solutes can be attributed to the protein's ability to reduce the nuclear response or reorganization upon ET, while maintaining sufficiently high electronic coupling. Quantitative predictions of reorganization free energy remain a challenge, both experimentally and computationally. Using density functional calculations and molecular dynamics simulation with an electronically polarizable force field, we report reorganization free energies for intraprotein ET in four heme-containing ET proteins that differ in their protein fold, hydrophilicity, and solvent accessibility of the electron-accepting group. The reorganization free energies for ET from the heme cofactors of cytochrome c and b5 to solvent exposed Ru-complexes docked to histidine residues at the surface of these proteins fall within a narrow range of 1.2-1.3 eV. Reorganization free energy is significantly lowered in a designed 4-helix bundle protein where both redox active cofactors are protected from the solvent. For all ET reactions investigated, the major components of reorganization are the solvent and the protein, with the solvent contributing close to or more than 50% of the total. In three out of four proteins, the protein reorganization free energy can be viewed as a collective effect including many residues, each of which contributing a small fraction. These results have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by single point mutations, but to a large extent by the degree of solvent exposure of the ionizable cofactors. [ABSTRACT FROM AUTHOR]

A water-soluble octacarboxyhemicarcerand was used as a shuttle to transport redox-active substrates across the aqueous medium and deliver them to the target protein. The results show that weak multivalent interactions and conformational flexibility can be exploited to reversibly bind complex supramolecular assemblies to biological molecules. Hydrophobic electron donors and acceptors were encapsulated within the hemicarcerand, and photoinduced electron transfer (ET) between the Zn-substituted cytochrome c (MW = 12.3 kD) and the host-guest complexes (MW = 2.2 kO) was used to probe the association between the negatively charged hemicarceplex and the positively charged protein. The behavior of the resulting ternary protein-hemicarcerand-guest assembly was investigated in two binding limits: (1) when Kencaps ⪢ Kassoc, the hemicarcerand transports the ligand to the protein while protecting it from the aqueous medium; and (2) when Kassoc > Kencaps, the hemicarcerand-protein complex is formed first, and the hemicarcerand acts as an artificial receptor site that intercepts ligands from solution and positions them close to the active site of the metalloenzyme. In both cases, ET mediated by the protein-bound hemicarcerand is much faster than that due to diffusional encounters with the respective free donor or acceptor in solution. The measured ET rates suggest that the dominant binding region of the host-guest complex on the surface of the protein is consistent with the docking area of the native redox partner of cytochrome c. The strong association with the protein is attributed to the flexible conformation and adaptable charge distribution of the hemicarcerand, which allow for surface-matching with the cytochrome. [ABSTRACT FROM AUTHOR]

Out-of-plane (OOP) deformations of the heme cofactor are found in numerous heme-containing proteins and the type of deformation tends to be conserved within functionally related classes of heme proteins. We demonstrate correlations between the heme ruffling OOP deformation and the 13C and ¹H nuclear magnetic resonance (NMR) hyperfine shifts of heme aided by density functional theory (DFT) calculations. The degree of ruffling in the heme cofactor of Hydrogenobacter thermophilus cytochrome c552 has been modified by a single amino acid mutation in the second coordination sphere of the cofactor. The 13C and ¹H resonances of the cofactor have been assigned using one- and two-dimensional NMR spectroscopy aided by selective 13C-enrichment of the heme. DFT has been used to predict the NMR hyperfine shifts and electron paramagnetic resonance (EPR) g-tensor at several points along the ruffling deformation coordinate. The DFT-predicted NMR and EPR parameters agree with the experimental observations, confirming that an accurate theoretical model of the electronic structure and its response to ruffling has been established. As the degree of ruffling increases, the heme methyl ¹H resonances move upfield while the heme methyl and meso 13C resonances move downfield. These changes are a consequence of altered overlap of the Fe 3d and porphyrin π orbitals, which destabilizes all three occupied Fe 3d-based molecular orbitals and decreases the positive and negative spin density on the β-pyrrole and meso carbons, respectively. Consequently, the heme ruffling deformation decreases the electronic coupling of the cofactor with external redox partners and lowers the reduction potential of heme. [ABSTRACT FROM AUTHOR]

The Rieske protein component of the cytochrome bccomplex contains a [2Fe-2S] cluster ligated by two cysteines and two histidines. We report here the PKa values of each of the imidazole rings of the two ligating histidines (His134 and His154) in the oxidized and reduced states of the Rieske protein from Therm us thermophilus (TtRp) as determined by NMR spectroscopy. Knowledge of these PKa values is of critical interest because of their pertinence to the mechanism of electron and proton transfer in the bifurcated O-cycle. Although we earlier had observed the pH dependence of a 15N NMR signal from each of the two ligand histidines in oxidized TtRp (Lin, I. J.; Chen, Y.; Fee, J. A.; Song, J.; Westler, W. M.; Markley, J. L. J. Am. Chem. Soc. 2006, 128, 10672-10673), the strong paramagnetism of the [2Fe-2S] cluster prevented the assignment of these signals by conventional methods. Our approach here was to take advantage of the unique histidine-leucine (Hisi 34-Leul 35) sequence and to use residue-selective labeling to establish a key sequence-specific assignment, which was then extended. Analysis of the pH dependence of assigned 13C, 13Cα, and 15Nϵ2 signals from the two histidine cluster ligands led to unambiguous assignment of the PKa values of oxidized and reduced TtRp. The results showed that the pKa of His134 changes from 9.1 in oxidized to ∼12.3 in reduced TtRp, whereas the pKa of His154 changes from 7.4 in oxidized to ∼12.6 in reduced TtRp. This establishes His154, which is close to the quinone when the Rieske protein is in the cytochrome b site, as the residue experiencing the remarkable redox-dependent pKa shift. Secondary structural analysis of oxidized and reduced TtRp based upon our extensive chemical shift assignments rules out a large conformational change between the oxidized and reduced states. Therefore, TtAp likely translocates between the cytochrome b and cytochrome c sites by passive diffusion. Our results are most consistent with a mechanism involving the coupled transfer of an electron and transfer of the proton across the hydrogen bond between the hydroquinone and His154 at the cytochrome b site. [ABSTRACT FROM AUTHOR]

Direct electron transfer (ET) of redox proteins immobilized on biomimetic or biocompatible electrodes represents an active field of fundamental and applied research. In this context, several groups have reported for a variety of proteins unexpected distance dependencies of the El rate, whose origin remains largely speculative and controversial, but appears to be a quite general phenomenon. Here we have employed molecular dynamics (MD) simulations and electron pathway analyses to study the El properties of cytochrome c (Cyt) electrostatically immobilized on Au coated by carboxyl–terminated alkylthiols. The MD simulations and concomitant binding energy calculations allow identification of preferred binding configurations of the oxidized and reduced Cyt which are established via different lysine residues and, thus, correspond to different orientations and dipole moments. Calculations of the electronic coupling matrices for the various Cyt/self–assembled monolayer (SAM) complexes indicate that the thermodynamically preferred protein orientations do not coincide with the orientations of optimum coupling. These findings demonstrate that the El of the immobilized Cyt is controlled by an interplay between protein dynamics and tunneling probabilities. Protein dynamics exerts two level of tuning on the electronic coupling via reorientation (coarse) and low amplitude thermal fluctuations (fine). Upon operating the Au support as an electrode, electric–field–dependent alignment of the protein dipole moment becomes an additional determinant for the protein dynamics and thus for the overall ET rate. The present results provide a consistent molecular description of previous (spectro)electrochemical data and allow conclusions concerning the coupling of protein dynamics and ET of Cyt in physiological complexes. [ABSTRACT FROM AUTHOR]

Cytochrome bc1 complex (EC 1.10.2.2, bc1), an essential component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria, has been identified as a promising target for new drugs and agricultural fungicides. X-ray diffraction structures of the free bc1 complex and its complexes with various inhibitors revealed that the phenyl group of Phe274 in the binding pocket exhibited significant conformational flexibility upon different inhibitors binding to optimize respective π-π interactions, whereas the side chains of other hydrophobic residues showed conformational stability. Therefore, in the present study, a strategy of optimizing the π-π interaction with conformationally flexible residues was proposed to design and discover new bc1 inhibitors with a higher potency. Eight new compounds were designed and synthesized, among which compound 5c, with Ki value of 570 pM, was identified as the most promising drug or fungicide candidate, significantly more potent than the commercially available bc1 inhibitors, including azoxystrobin (AZ), kresoxim-methyl (KM), and pyraclostrobin (PY). To our knowledge, this is the first bc1 inhibitor discovered from structure-based design with a potency of subnanomolar Ki value. For all of the compounds synthesized and assayed, the calculated binding free energies correlated reasonably well with the binding free energies denved from the experimental Ki values, with a correlation coefficient of r² = 0.89. The further inhibitory kinetics studies revealed that 5c is a noncompetitive inhibitor with respect to substrate cytochrome c, but it is a competitive inhibitor with respect to substrate ubiquinol. Due to its subnanomolar Ki potency and slow dissociation rate constant (k-0 = 0.00358 s-1), 5c could be used as a specific probe for further elucidation of the mechanism of bc1 function and as a new lead compound for future drug discovery. [ABSTRACT FROM AUTHOR]

Here we present a new implementation and extension of the stochastic titration method which makes it possible to perform MD simulations at constant pH and reduction potential. The method was applied to the redox titration of cytochrome c3 from Desulfovibrio vulgaris Hildenborough, and a major finding of this study was that the method showed a better performance when the protein region is assigned a high dielectric constant. This dependence on the value of the protein dielectric constant was not found in previous constant-pH MD simulations and is attributed to excessively high heme-heme interactions at low dielectric constants. The simulations revealed strong coupling between hemes in close proximity, and we also showed how these couplings can be used to estimate the sensibility of the heme reductions to small pH changes. [ABSTRACT FROM AUTHOR]

The factors that determine the extent to which diffusion and thermal activation processes govern electron transfer (ET) between proteins are debated. The process of ET between plastocyanin (PC) and cytochrome f(CytF) from the cyanobacterium Phormidium laminosum was initially thought to be diffusion-controlled but later was found to be under activation control (Schlarb-Ridley, B. G.; et al. Biochemistry 2005, 44, 6232). Here we describe Brownian dynamics simulations of the diffusional association of PC and CyIF, from which El rates were computed using a detailed model of ET events that was applied to all of the generated protein configurations. The proteins were modeled as rigid bodies represented in atomic detail. In addition to electrostatic forces, which were modeled as in our previous simulations of protein-protein association, the proteins interacted by a nonpolar desolvation (hydrophobic) force whose derivation is described here. The simulations yielded close to realistic residence times of transient protein-protein encounter complexes of up to tens of microseconds. The activation barrier for individual ET events derived from the simulations was positive. Whereas the electrostatic interactions between P. laminosum PC and CytF are weak, simulations for a second cyanobacterial PC-CytF pair, that from Nostoc sp. PCC 7119, revealed El rates influenced by stronger electrostatic interactions. In both cases, the simulations imply significant contributions to ET from both diffusion and thermal activation processes. [ABSTRACT FROM AUTHOR]

The Met80Ala variant of yeast iso-1-cytochrome c, immobilized on a gold electrode, is found to exchange electrons efficiently with it in nondenaturing conditions and to provide robust and persistent catalytic currents for O[sub2] and nitrite ion reduction from pH 3 to 11. Direct covalent protein linkage to gold yields the best electrochemical and electrocatalytic performances without drastically affecting the structural properties of the bound protein compared to the freely diffusing species. Therefore, this biocatalytic interface can be of use for the amperometric detection of the above species, which are of great environmental, industrial, and clinical interest, with particular reference to the exploitation in nanostructured biosensing devices. This work shows that the use of a small engineered electron transfer (ET) protein, featuring an axial heme iron coordination position available for the binding of exogenous ligands, in place of a large heme enzyme is a viable strategy for the improvement of the heterogeneous ET rate and the stability and efficiency of sensing gold-protein interfaces over a wide range of T and pH. [ABSTRACT FROM AUTHOR]

The nature of transient protein complexes can range from a highly dynamic ensemble of orientations to a single well-defined state. This represents variation in the equilibrium between the encounter and final, functional state. The transient complex between plastocyanin (Pc) and cytochrome f(cytf) of the cyanobacterium Prochlorothrix hollandica was characterized by NM R spectroscopy. Intermolecular pseudocontact shifts and chemical shift perturbations were used as restraints in docking calculations to determine the structure of the wild-type Pc-cytf complex. The orientation of Pc is similar to orientations found in Pc-cytf complexes from other sources. Electrostatics seems to play a modest role in complex formation. A large variability in the ensemble of lowest energy structures indicates a dynamic nature of the complex. Two unusual hydrophobic patch residues in Pc have been mutated to the residues found in other plastocyanins (Y12G/P14L). The binding constants are similar for the complexes of cytf with wild-type Pc and mutant Pc, but the chemical shift perturbations are smaller for the complex with mutant Pc. Docking calculations for the Y12G/P14L Pc-cytf complex did not produce a converged ensemble of structures. Simulations of the dynamics were performed using the observed averaged NMR parameters as input. The results indicate a surprisingly large amplitude of mobility of Y12G/P14L Pc within the complex. It is concluded that the double mutation shifts the complex further from the well-defined toward the encounter state. [ABSTRACT FROM AUTHOR]

Electrode potentials for every intermediate in the cytochrome P450 cycle were estimated and evaluated by means of an oxidation state diagram. By this approach, and within the uncertainties of the approximations, the superoxide complex of cytochrome P450 at pH 7 is oxidizing: E°′ (P450FeO22+, H+/P450FeOOH2+) = +0.93 V, and the Gibbs energy for the reaction of the hydroperoxo complex of cytochrome P450 to form compound I and water, P450FeOOH2+ + H+ = P450FeO2+ por•+ + H2O, is 0 kJ/mol. Although cytochrome P450FeOOH2+ and cytochrome P450FeO2+por•+ are approximately isoenergetic, they are likely to react at different rates with substrates and may yield different products. Homolysis of the hydroperoxo complex of cytochrome P450 to compound II and the hydroxyl radical, P450FeOOH2+ = P450FeO2+ + HO•, is unfavorable (ΔG°′ = +92 kJ/mol), as is the dissociation into HOO- and cytochrome P450Fe3+ (+73 kJ/mol). It is shown that the sum of the Gibbs energy of association for cytochrome P450Fe3+ with the hydroperoxo anion and the Gibbs energy for the one-electron reduction of cytochrome P450FeOOH2+, relative to NHE, is constant (–203 kJ/mol). While the estimated E°+ (P450FeO22+, H+/P450FeOOH2+) = +0.93 V at pH 7 is larger than necessary to effect reduction of cytochrome P450FeO22+, the magnitude of this electrode potential implies that the binding constant for cytochrome P450Fe3+ with hydrogen peroxide is ca. 3 × 106 M-1 at pH 7. An association constant of this magnitude ensures that a fraction of cytochrome P450FeOOH2+ is available to form compound I or to react with substrates directly, while a larger one would imply that compound I is too weak an oxidant. In general, the energetics of the reduction of dioxygen to water determines the energetics of catalysis of hydroxylations by cytochrome P450. These results enable calibration of energy levels obtained for intermediates in the cytochome P450 reaction cycle obtained by ab initio calculations and provide insights into the catalytic efficiency of cytochrome P450 and guidelines for the development of competent hydroxylation catalysts. [ABSTRACT FROM AUTHOR]

The peptide group connecting Tyr440 and Ser441 of the bovine cytochrome c oxidase is involved in a recently proposed proton-transfer path (H-path) where, at variance with other pathways (D- and K-paths), a usual hydrogen-bond network is interrupted, thus making this proton propagation rather unconventional. Our density-functional based molecular dynamics simulations show that, despite this anomaly and provided that a proton can reach a nearby water, a multistep proton-transfer pathway can become a viable pathway for such a reaction: A proton is initially transferred to the carbonyl oxygen of a keto form of the Tyr440- Ser441 peptide group [—CO—NH—], producing an imidic acid [—C(OH)—NH—] as a metastable state; the amide proton of the imidic acid is then transferred, spontaneously to the deprotonated carboxyl group of the Asp51 side chain, leading to the formation of an enol form [—C(OH)=N—] of the Tyr440-Ser441 peptide group. Then a subsequent enol-to-keto tautomerization occurs via a double proton-transfer path realized in the two adjacent Tyr440-Ser441 and Ser441 -Asp442 peptide groups. An analysis of this multistep proton-transfer pathway shows that each elementary process occurs through the shortest distance, no permanent conformational changes are induced, thus preserving the X-ray crystal structure, and the reaction path is characterized by a reasonable activation barrier. [ABSTRACT FROM AUTHOR]

Peroxynitrite has come into the spotlight in recent years. Its effects on proteins have been implicated in several diseases such as acute lung injury, rheumatoid arthritis, implant rejection, artherosclerosis, Parkinson's disease, and Alzheimer's disease. Peroxynitrite is thought to inactivate a variety of proteins including thiolate-ligated heme proteins such as cytochrome P450 2B1 and PGI2 synthase, through the nitration of tyrosine residues. In previous studies it was reported that thiolate-ligated heme enzymes react with peroxynitrite to form a ferryl intermediate. In an effort to spectroscopically characterize this species in P450BM3, we discovered that the peroxynitrite-generated intermediate is not an FeIVoxo, but rather an iron-nitrosyl {FeNO}6 complex. We present density functional calculations as well as Mössbauer and stopped-flow spectroscopic characterizations of the peroxynitrite-generated intermediate in P450BM3. [ABSTRACT FROM AUTHOR]

Conformational flexibility and cooperativity in ligand recognition are two key aspects of the catalytic diversity of cytochrome P450 enzymes. In this study, we dissect the ligand binding stoichiometry and energetics of the soluble bacterial P450eryF by isothermal titration calorimetry (ITC) using three allosteric and two non-allosteric ligands of diverse chemistry. Complementary spectral binding studies and sequential, two-ligand docking simulations were performed to help assign the binding sites. Binding of 4-phenylpyridine (4-PP) or 4-(4-chlorophenyl)imidazole (4-CPI) showed 1:1 stoichiometry in ITC, consistent with the lack of cooperativity observed in spectral binding studies. The larger ligands 9-aminophenanthrene (9-AP), 1-pyrenebutanol (1-PB), and a-naphthoflavone (ANF) show cooperative spectral binding and yielded 2:1 stoichiometry. The associated thermodynamic parameters for the sites were calculated using a sequential binding mechanism. The binding constant (KD) for the first site was almost two times lower than that of the second site for all three compounds. Ligand binding at site 1 was entropically favored, whereas binding at site 2 was weak and entropically unfavorable. Simulations showed that two molecules of 9-AP, ANF or 1-PB can be adequately docked to two individual sub-sites within a large binding pocket. The absence of hydrophobic tethering and ligand stacking are consistent with the single low affinity binding site observed for 4-CPI and 4-PP. Competitive binding studies with P450eryF preloaded with either 1-PB or ANF showed a decrease in the affinities for 9-AP at both the sites, with large entropy-enthalpy compensation, indicating the ability of the binding pocket to accommodate two ligands of diverse chemistry and enable cooperativity. [ABSTRACT FROM AUTHOR]

Cytochrome P450 3A4 (CYP3A4) is a key enzyme responsible for the metabolism of 50% of all orally administered drugs which exhibit an intriguing kinetic behavior typified by a sigmoidal dependence of the reaction velocity on the substrate concentration. There is evidence for the binding of two substrates in the active site of the enzyme, but the mechanism of this cooperative binding is unclear. Diazepam is such a drug that undergoes metabolism by CYP3A4 with sigmoidal dependence. Metabolism is initiated by hydrogen atom abstraction from the drug. To understand the factors that determine the cooperative binding and the juxtaposition of the CH bond undergoing abstraction, we carried out molecular dynamics simulations for two enzymatic conformers and examined the differences between the substrate-free and the bound enzymes, with one and two diazepam molecules. Our results indicate that the effector substrate interacts both with the active substrate and with the enzyme, and that this interaction results in side chain reorientation with relatively minor long-range effects. In accord with experiment, we find that F304, in the interface between the active and effector binding sites, is a key residue in the mechanism of cooperative binding. The addition of the effector substrate stabilizes F304 and its environment, especially F213, and induces a favorable orientation of the active substrate, leading to a short distance between the targeted hydrogen for abstraction and the active species of the enzyme. In addition, in one conformer of the enzyme, residue R212 may strongly interact with F304 and counteract the effector's impact on the enzyme. [ABSTRACT FROM AUTHOR]

Bleomycins (BLMs) can utilize H2O2 to cleave DNA in the presence of ferric ions. DFT calculations were used to study the mechanism of O-O bond cleavage in the low-spin FeIII-hydroperoxo complex of BLM. The following alternative hypotheses were investigated using realistic structural models: (a) heterolytic cleavage of the O-O bond, generating a Compound I (Cpd I) like intermediate, formally BLM-FeV=O; (b) homolytic O-O cleavage, leading to a BLM-FeIV=O species and an OH· radical; and (c) a direct O-O cleavage/H-abstraction mechanism by ABLM. The calculations showed that (a) is a facile and viable mechanism; it involves acid-base proton reshuffle mediated by the side-chain linkers of BLM, causing thereby heterolytic cleavage of the O-O bond and generation of Cpd I. Formation of Cpd I is found to involve a barrier of 13.3 kcal/mol, which is lower than the barriers in the alternative mechanisms (b and c) that possess respective barriers of 31 and 17 kcal/mol. The so-formed Cpd I species with a radical on the side-chain linker, methylvalerate (V), adjacent to the BLM-FeIV=O complex, resembles the formation of the active species of cytochrome c peroxidase in the Poulos—Kraut proton-shuffle mechanism in heme peroxidases (Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199–8205). Experimental data are discussed and shown to be in accord with this proposal. It suggests that the high-valence Cpd I species of BLM participates in the DNA cleavage. This is an alternative mechanistic hypothesis to the exclusive reactivity scenario based on ABLM (FeIII-OOH). [ABSTRACT FROM AUTHOR]

Using a combination of Mössbauer spectroscopy and density functional calculations, we have determined that the ferryl forms of P450BM3 and P450cam are protonated at physiological pH. Density functional calculations were performed on large active-site models of these enzymes to determine the theoretical Mössbauer parameters for the ferryl and protonated ferryl (FeIVOH) species. These calculations revealed a significant enlargement of the quadrupole splitting parameter upon protonation of the ferryl unit. The calculated quadrupole splittings for the protonated and unprotonated ferryl forms of P450BM3 are ΔEQ = 2.17 mm/s and ΔEQ = 1.05 mm/s, respectively. For P450cam, they are ΔEQ = 1.84 mm/s and ΔEQ = 0.66 mm/s, respectively. The experimentally determined quadrupole splittings (P450BM3, ΔEQ = 2.16 mm/s; P450cam, ΔEQ = 2.06 mm/s) are in good agreement with the values calculated for the protonated forms of the enzymes. Our results suggest that basic ferryls are a natural consequence of thiolate-ligated hemes. [ABSTRACT FROM AUTHOR]

Cytochrome c functions as an electron carrier in the mitochondrial electron-transport chain using the Fe(II)-Fe(III) redox couple of a covalently attached heme prosthetic group, and it has served as a paradigm for both biological redox activity and protein folding. On the basis of a wide variety of biophysical techniques, it has been suggested that the protein is more flexible in the oxidized state than in the reduced state, which has led to speculation that it is the dynamics of the protein that has been evolved to control the cofactor's redox properties. To test this hypothesis, we incorporated carbon-deuterium bonds throughout cytochrome c and characterized their absorption frequencies and line widths using IR spectroscopy. The absorption frequencies of several residues on the proximal side of the heme show redox-dependent changes, but none show changes in line width, implying that the flexibility of the oxidized and reduced proteins is not different. However, the spectra demonstrate that folded protein is in equilibrium with a surprisingly large amount of locally unfolded protein, which increases with oxidation for residues localized to the proximal side of the heme. The data suggest that while the oxidized protein is not more flexible than the reduced protein, it is more locally unfolded. Local unfolding of cytochrome c might be one mechanism whereby the protein evolved to control electron transfer. [ABSTRACT FROM AUTHOR]

The contact domain utilized by horse cytochrome c when adsorptively bound to a C10COOH self-assembled monolayer (SAM) was delineated using a chemical method based on differential modification of surface amino acids. Horse cytochrome c was adsorbed at low ionic strength (pH 7.0, 4.4 mM potassium phosphate) onto 10 μm diameter gold particles coated with HS(CH2)10COOH SAMs. After in situ modification of lysyl groups by reductive Schiff-base methylation, the protein was desorbed, digested using trypsin, and the peptide mapped using LC/MS. Relative lysyl reactivities were ascertained by comparing the resulting peptide frequencies to control samples of solution cytochrome c modified to the same average extent. The least reactive lysines in adsorbed cytochrome c were found to be 13, 72, 73, 79, and 86–88, consistent with a contact region located up and to the left (Met-80 side) of the solvent-exposed heme edge (conventional front face view). The most reactive lysines were 39, 53, 55, and 60, located on the lower backside. The proposed orientation features a heme tilt angle of approximately 35–40° with respect to the substrate surface normal. Factors that can complicate or distort data interpretation are discussed, and the generality of differential modification relative to existing in situ methods for protein orientation determination is also addressed. [ABSTRACT FROM AUTHOR]

Cyclic voltammetry experiments were carried out on native Saccharomyces cerevisiae iso-1-cytochrome c and its C102T/N62C variant immobilized on bare polycrystalline gold electrode through the S-Au bond formed by a surface cysteine. Experiments were carried out at different temperatures (5-65 °C) and pH values (1.5-7). The E°' value at pH 7 (+370 mV vs SHE) is approximately 100 mV higher than that for the protein in solution. This difference is enthalpic in origin and is proposed to be the result of the electrostatic repulsion among the densely packed molecules onto the electrode surface. Two additional electrochemical waves are observed upon lowering the pH below 5 (E°' = +182 my) and 3 (E°' = +71 mV), which are attributed to two conformers (referred to as "intermediate" and "acidic", respectively) featuring an altered heme axial ligation. This is the first determination of the reduction potential for low-pH conformers of cytochrome c in the absence of denaturants. Since the native form of cytochrome c can be restored, bringing back the pH to neutrality, the possibility offered by this transition to reversibly modulate the redox potential of cytochrome c is appealing for bioelectronic applications. The immobilized C102T/N62C variant, which differs from the native protein in the orientation of the heme group with respect to the electrode, shows very similar reduction thermodynamics. For both species, the rate constant for electron transfer between the heme and the electrode increases for the acidic conformer, which is also found to act as a biocatalytic interface for dioxygen reduction. [ABSTRACT FROM AUTHOR]

The tetraheme cytochrome c554 (cyt c554) from Nitrosomonas europaea is believed to function as an electron-transfer protein from hydroxylamine oxidoreductase (HAO). We show here that cyt c554 also has significant NO reductase activity. The protein contains one high-spin and three low-spin c-type hemes. HAO catalyzed reduction of the cyt c554, ligand binding, intermolecular electron transfer, and kinetics of NO reduction by cyt c554 have been investigated. We detect the formation of a NO-bound ferrous heme species in cyt c554 by EPR and Mössbauer spectroscopies during the HAO catalyzed oxidation of hydroxylamine, indicating that N-oxide intermediates produced from HAO readily bind to cyt c554. In the half-reduced state of cyt c554, we detect a spin interaction between the [FeNO]7 state of heme 2 and the low-spin ferric state of heme 4. We find that ferrous cyt c554 will reduce NO at a rate greater than 16 s-1, which is comparable to rates of other known NO reductases. Carbon monoxide or nitrite are shown not to bind to the reduced protein, and previous results indicate the reactions with O2 are slow and that a variety of ligands will not bind in the oxidized state. Thus, the enzymatic site is highly selective for NO. The NO reductase activity of cyt c554 may be important during ammonia oxidation in N. europaea at low oxygen concentrations to detoxify NO produced by reduction of nitrite or incomplete oxidation of hydroxylamine. [ABSTRACT FROM AUTHOR]

The suicide substrate activity of N-benzyl-N-cyclopropylamine (1) and N-benzyl-N-(1′-methyl-cyclopropyl)amine (2) toward cytochrome P450 and other enzymes has been explained by a mechanism involving single electron transfer (SET) oxidation, followed by ring-opening of the aminium radical cation (protonated aminyl radical) and reaction with the P450 active site. Although the SET oxidation of N-cyclopropyI-N-methylaniline (3) by horseradish peroxidase leads exclusively to ring-opened (noncyclopropyl) products, P450 oxidation of 3 leads to formation of cyclopropanone hydrate and no ring-opened products, and 3 does not inactivate P450. To help reconcile these discrepant behaviors we have determined the complete metabolic fate of 1 with P450 in vitro. 3-Hydroxypropionaldehyde (3HP), the presumptive ‘signature metabolite’ for SET oxidation of a cyclopropylamine, was observed for the first time in 57% yield, along with cyclopropanone hydrate (34%), cyclopropylamine (9%), benzaldehyde (6%), benzyl alcohol (12%), and benzaldoxime (19%). Unexpectedly, N-benzyI-N-cyclopropyI-N-methylamine (4) was found not to inactivate P450 and not to give rise to 3HP as a metabolite without first undergoing oxidative N-demethylation to 1. These and other observations argue against a role for SET mechanisms in the P450 oxidation of cyclopropylamines. We suggest that a conventional hydrogen abstraction/hydroxyl recombination mechanism (or its equivalent as a one-step ‘insertion’ mechanism) at C-H bonds in 1–4 leads to nonrearranged carbinolamine intermediates and thereby to ‘ordinary’ N-dealkylation products including cyclopropanone hydrate. Alternatively, hydrogen abstraction at the N-H bond of secondary cyclopropylamines 1 gives a neutral aminyl radical which could undergo rapid ring-opening leading either to enzyme inactivation or 3HP formation. [ABSTRACT FROM AUTHOR]

An electrode surface is presented that enables the characterization of redox-active membrane enzymes in a native-like environment. An ubiquinol oxidase from Escherichia coli, cytochrome bo3 (cbo3), has been co-immobilized into tethered bilayer lipid membranes (tBLMs). The tBLM is formed on gold surfaces functionalized with cholesterol tethers which insert into the lower leaflet of the membrane. The planar membrane architecture is formed by self-assembly of proteoliposomes, and its structure is characterized by surface plasmon resonance (SPR), electrochemical impedance spectroscopy (EIS), and tapping-mode atomic force microscopy (TM-AFM). The functionality of cbo3 is investigated by cyclic voltammetry (CV) and is confirmed by the catalytic reduction of oxygen. Interfacial electron transfer to cbo3 is mediated by the membrane-localized ubiquinol-8, the physiological electron donor of cbo3. Enzyme coverages observed with TM-AFM and CV coincide (2-8.5 fmol·cm-2), indicating that most-if not all-cbo3 on the surface is catalytically active and thus retains its integrity during immobilization. [ABSTRACT FROM AUTHOR]

Crystalline samples of four low-spin Fe(III) octaalkyltetraphenylporphyrinate and two low-spin Fe(III) tetramesitylporphyrinate complexes, all of which are models of the bis-histidine-coordinated cytochrorres of mitochondrial complexes II, III, and IV and chloroplast complex b6 f, and whose molecular structures and EPR spectra have been reported previously, have been investigated in detail by Mössbauer spectroscopy. The six complexes and the dihedral angles between axial ligand planes of each are [(TMP)-Fe(1-Melm)2]CIO4 (0°), paral-[(OMTPP)Fe(1-Melm)2]Cl (19.5°), paral-((TMP)Fe(5-MeHlm)2]ClO4 (26°, 30° for two molecules in the unit cell whose EPR spectra overlap), [(OETPP)Fe(4-Me2NPy)2]Cl (70°), perp-[(OETPP)Fe(1-Melm)2]Cl (73°), and perp-[(OMTPP)Fe(1-Melm)2]Cl (90°). Of these, the first three have been shown to exhibit normal rhombic EPR spectra, each with three clearly resolved g-values, while the last three have been shown to exhibit "large gmax" EPR spectra at 4.2 K. It is found that the hyperfine coupling constants of the complexes are consistent with those reported previously for low-spin ferriheme systems, with the largest-magnitude hyperfine coupling constant, Azz, being considerably smaller for the "parallel" complexes (400-540 kG) than for the strictly perpendicular complex (902 kG), Axx being negative for all six complexes, and Azz and Axx being of similar magnitude for the "parallel" complexes (for example, for [(TMP)Fe(1-Melm)2]Cl, Azz = 400 kG, Axx = -400 kG). In all cases, Ayy is small but difficult to estimate with accuracy. With results for six structurally characterized model systems, we find for the first time qualitative correlations of gzz, Azz and ΔEQ with axial ligand plane dihedral angle Δ. [ABSTRACT FROM AUTHOR]

The electronic structure of the 5-coordinate quantum-mechanically mixed-spin (sextet-quartet) heme center in cytochrome c' was investigated by electron nuclear double resonance (ENDOR), a technique not previously applied to this mixed-spin system. Cytochrome c' was obtained from overexpressing variants of Rhodobacter sphaeroides 2.4.3. ENDOR for this study was done at the g∥ = 2.00 extremum where single-crystal-like, well-resolved spectra prevail. The heme meso protons of cytochrome c' showed a contact interaction that implied spin delocalization arising from the heme (dz²) orbital enhanced by iron out-of- planarity. An exchangeable proton ENDOR feature appeared from the proximal His 123 Nδ hydrogen. This Nδ hydrogen, which crystallographically has no hydrogen-bonding partner and thus belongs to a neutral imidazole, showed a larger hyperline coupling than the corresponding hydrogen-bonded Nδ proton from metmyoglobin. The unique residue Phe14 occludes binding of a sixth ligand in cytochrome c', and ENDOR from a proton of the functionally important Phel4 ring, ∼3.3 Å away from the heme iron, was detected. ENDOR of the nitrogen ligand hyperfine structure is a direct probe into the σ-antibonding (dz²) and (dx²-y²) orbitals whose energies alter the relative stability and admixture of sextet and quartet states and whose electronic details were thus elucidated. ENDOR frequencies showed for cytochrome c' larger hyperfine couplings to the histidine nitrogen and smaller hyperfine couplings to the heme nitrogens than for high- spin ferric hemes. Both of these findings followed from the mixed-spin ground state, which has less (dx²-y²) character than have fully high-spin ferric heme systems. [ABSTRACT FROM AUTHOR]

The present investigation reports the first experimental measurements of the reorganization energy of unfolded metalloprotein in urea solution. Horse heart cytochrome c (cyt c) has been found to undergo reversible one-electron transfer reactions at pH 2 in the presence of 9 M urea. In contrast, the protein is electrochemically inactive at pH 2 under low-ionic strength conditions in the absence of urea. Urea is shown to induce ligation changes at the heme iron and lead to practically complete loss of the a-helical content of the protein. Despite being unfolded, the electron-transfer (El) kinetics of cyt c on a 2-mercaptoethanol- modified Ag(111) electrode remain unusually fast and diffusion controlled. Acid titration of ferric cyt c in 9 M urea down to pH 2 is accompanied by protonation of one of the axial ligands, water binding to the heme iron (pka = 5.2), and a sudden protein collapse (pH < 4). The formal redox potential of the urea-unfolded six-coordinate His18-Fe(II)-H2O/five-coordinate His18-Fe(ll) couple at pH 2 is estimated to be -0.083 V vs NHE, about 130 mV more positive than seen for bis-His-ligated urea-denatured cyt c at pH 7. The unusually fast ET kinetics are assigned to low reorganization energy of acid/urea-unfolded cyt c at pH 2 (0.41 ± 0.01 eV), which is actually lower than that of the native cyt c at pH 7 (0.6 ± 0.02 eV), but closer to that of native bis-His-ligated cyt b5 (0.44 ± 0.02 eV). The roles of electronic coupling and heme-flattening on the rate of heterogeneous ET reactions are discussed. [ABSTRACT FROM AUTHOR]

The synthetic heme-thiolate complex (SR) in methanol binds nitric oxide (kon = (2.7 ± 0.2) × 106 M-1 s-1 at 25 °C) to form SR(NO). The binding of NO to the SR complex in a noncoordinating solvent, such as toluene, was found to be almost 3 orders of magnitude faster than that in methanol. The activation parameters ΔHt†, ΔS†, and ΔV† for the formation of SR(NO) in methanol are consistent with the operation of a limiting dissociative mechanism, dominated by dissociation of methanol in SR(MeOH). In the presence of an excess of NO, the formation of SR(NO) is followed by subsequent slower reactions. The substantially negative activation entropy and activation volume values found for the second observed reaction step support an associative mechanism which involves attack of a second NO molecule on the thiolate ligand in the initially formed SR(NO) complex. The following slower reactions are strongly accelerated by a large excess of NO or by the presence of NO-2 in the SR/NO reaction mixture. They can be accounted for in terms of dynamic equilibria between higher nitrogen oxides (NOx) and reactive SR species, which lead to the formation of a nitrosyl-nitrite complex of SR(FeII) as the final product. This finding is clearly supported by laser flash photolysis studies on the SR/NO reaction mixture, which do not reveal simple NO photolabilization from SR(FeIII)(NO), but rather involve the generation of at least three photoinduced intermediates decaying with different rate constants to the starting material. The species formed along the proposed reaction pathways were characterized by FTIR and EPR spectroscopy. The results are discussed in terms of their relevance for the biological function of cytochrome P450 enzymes and in context of results for the reaction of NO with imidazole- and thiolate-ligated iron(lll) hemoproteins. [ABSTRACT FROM AUTHOR]

B3LYP density functional theory calculations are used to unravel the mysterious third step of aromatase catalysis. The feasibility of mechanisms in which the reduced ferrous dioxygen intermediate mediates androgen aromatization is explored and determined to be unlikely. However, proton-assisted homolysis of the peroxo hemiacetal intermediate to produce P450 compound I and the C19 gem-diol likely proceeds with a low energetic barrier. Mechanisms for the aromatization and deformylation sequence which are initiated by 1β-hydrogen atom abstraction by P450 compound I are considered. 1β-Hydrogen atom abstraction from substrates in the presence of the 2,3-enol encounters strikingly low barriers (5.3-7.8 kcal/mol), whereas barriers for this same process rise to 17.0-27.1 kcal/mol in the keto tautomer. Transition states for 1β-hydrogen atom abstraction from enolized substrates in the presence of the 1 9-gem-diol decayed directly to the experimentally observed products. If the C19 aldehyde remains unhydrated, aromatization occurs with concomitant decarbonylation and therefore does not support dehydration of the C19 aldehyde prior to the final catalytic step. On the doublet surface, the transition state connects to a potentially labile 1(10) dehydrogenated product, which may undergo rapid aromatization, as well as formic acid. Ab initio molecular dynamics confirmed that the 1β-hydrogen atom abstraction and deformylation or decarbonylation occur in a nonsynchronous, coordinated manner. These calculations support a dehydrogenase behavior of aromatase in the final catalytic step, which can be summarized by 1β-hydrogen atom abstraction followed by gem-diol deprotonation. [ABSTRACT FROM AUTHOR]

The effect of a constant magnetic field on bioelectrocatalytic transformations of three different enzyme assemblies linked to electrodes is examined and correlated with a theoretical magnetohydrodynamic model. The systems consist of surface-reconstituted glucose oxidase (GOx), an integrated lactate dehydrogenase/nicotinamide/pyrroloquinoline quinone assembly (LDH/NAD+-PQQ), and a cytochrome c/cytochrome oxidase system (Cyt c/COx) linked to the electrodes. Pronounced effects of a constant magnetic field applied parallel to the electrode surface are observed for the bioelectrocatalyzed oxidation of glucose and lactate by the GOx-electrode and LDH/NAD+-PQQ-electrode, respectively. The enhancement of the bioelectrocatalytic processes correlates nicely with the magnetohydrodynamic model, and the limiting current densities (iL) relate to B⅓ (B magnetic flux density) and to C&frac43; (C = bulk concentration of the substrate). A small magnetic field effect is observed for the Cyt c/COx-electrode, and its origin is still questionable. The effect of the constant magnetic field on the performance of biofuel cells with different configurations is examined. For the biofuel cell consisting of LDH/NAD+-PQQ anode and Cyt c/COx cathode, a 3-fold increase in the power output was observed at an applied magnetic field of B = 0.92 T and external load of 1.2 kφ. [ABSTRACT FROM AUTHOR]