Arylhydrazines as probes of hemoprotein structure and function

Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations

Bioorganometallic Fe-C bonds are biologically relevant species that may result from the metabolism of natural or synthetic hydrazines. The molecular structures of four new sperm whale mutant myoglobin derivatives with Fe-aryl moieties, namely H64A-tolyl-m, H64A-chlorophenyl-p, H64Q-tolyl-m, and H64Q-chlorophenyl-p, have been determined at 1.7-1.9Å resolution. The structures reveal conformational preferences for the substituted aryls resulting from attachment of the aryl ligands to Fe at the site of net -NHNH2 release from the precursor hydrazines, and show distal pocket changes that readily accommodate these bulky ligands.

A joint experimental and theoretical investigation of kinetics and mechanistic study in a synthesis reaction between triphenylphosphine and dialkyl acetylenedicarboxylates in the presence of benzhydrazide

Stable crystalline phosphorus ylides were obtained in excellent yields from the 1:1:1 addition reaction between triphenylphosphine (TPP) and dialkyl acetylenedicarboxylates, in the presence of NH-acids, such as benzhydrazide. To determine the kinetic parameters of the reactions, they were monitored by UV spectrophotometery. The second order fits were automatically drawn and the values of the second order rate constant (k(2)) were calculated using standard equations within the program. At the temperature range studied the dependence of the second order rate constant (Ln k(2)) on reciprocal temperature was compatible with Arrhenius equation. This provided the relevant plots to calculate the activation energy of all reactions. Furthermore, useful information were obtained from studies of the effect of solvent, structure of reactants (different alkyl groups within the dialkyl acetylenedicarboxylates) and also concentration of reactants on the rate of reactions. On the basis of experimental data the proposed mechanism was confirmed according to the obtained results and a steady state approximation and the first step (k(2)) and third (k(3)) steps of the reactions were recognized as the rate determining steps, respectively. In addition, three speculative proposed mechanisms were theoretically investigated using quantum mechanical calculation. The results, arising from the second and third speculative mechanisms, were far from the experimental data. Nevertheless, there was a good agreement between the theoretical kinetic data, emerge from the first speculative mechanism, and experimental kinetic data of proposed mechanism.

In vivo effects of zearalenone on the expression of proteins involved in the detoxification of rat xenobiotics

Zearalenone (ZEN) is a lactone derivative of the resorcylic acid produced by various Fusarium species that are widely found in foods and animal feeds. ZEN exerts species-specific estrogenic effects, possibly because of the metabolism differences arising from reduction, hydroxylation, or glucuro-conjugation. The main objective of this study was to determine the levels of expression of rat proteins that are involved in the ZEN detoxification pathway upon acute ZEN treatment. This was achieved by monitoring the mRNA associated with 25 genes using RT-PCR upon ZEN uptake. These genes code for a variety of proteins that are involved in cellular detoxifying pathways, transporters, cytochromes P450 (CYPs), hydroxysteroid dehydrogenases, and transferases, and receptors that are involved in CYP expression or steroid metabolism. Liver samples from rats treated with ZEN were compared to untreated rats or animals treated with classical CYP inducers (phenobarbital, dexamethasone, β-naphtoflavone, and clofibrate). Significant changes of mRNA expression were observed for the efflux transporter, P-glycoprotein, monooxygenases (CYP2C7, CYP2E1, CYP3A1, CYP3A2, and aromatase), steroid dehydrogenases, and Uridine diphospho-glucuronyl transferases (UGTs). Following a single ZEN treatment, the initial modifications in mRNA levels indicate a close association with microsomal enzyme activity of the CYP2B, CYP2C, and CYP3A protein families.

Catalase-like activity of bovine met-hemoglobin: interaction with the pseudo-catalytic peroxidation of anthracene traces in aqueous medium

Hemoglobin is a member of the hemoprotein superfamily whose main role is to transport O(2) in vertebrate organisms. It has two known promiscuous enzymatic activities, peroxidase and oxygenase. Here we show for the first time that bovine hemoglobin also presents a catalase-like activity characterized by a V(max )of 344 microM/min, a K(M )of 24 mM and a k(cat) equal to 115/min. For high anthracene and hemoglobin concentrations and low hydrogen peroxide concentrations, this activity inhibits the expected oxidation of anthracene, which occurs through a peroxidase-like mechanism. Anthracene belongs to the polycyclic aromatic hydrocarbon (PAH) family whose members are carcinogenic and persistent pollutants found in industrial waste waters. Our results show that anthracene oxidation by hemoglobin and hydrogen peroxide follows a typical bi-bi ping-pong mechanism with a V(max) equal to 0.250 microM/min, K(M(H2O2) )of 80 microM, K(M(ANT)) of 1.1 microM and k(cat) of 0.17/min. The oxidation of anthracene is shown to be pseudo-catalytic because an excess of hemoglobin and hydrogen peroxide is required to make PAH completely disappear. Thus, bovine hemoglobin presents, in different degrees, all the catalytic activities of the hemoprotein group, which makes it a very interesting protein for biotechnological processes and one with which structure-activity relationships can be studied.

Investigation of the mechanisms underlying the differential effects of the K262R mutation of P450 2B6 on catalytic activity

Human P450 2B6 is a polymorphic enzyme involved in the oxidative metabolism of a number of clinically relevant substrates. The lysine 262-to-arginine mutant of cytochrome P450 2B6 (P450 2B6.4) has been shown to have differential effects on P450 2B6 catalytic activity. We reported previously that the mutant enzyme was unable to metabolize 17-alpha-ethynylestradiol (17EE) or become inactivated by 17EE or efavirenz, which are inactivators of the wild-type enzyme. Studies were performed to elucidate the mechanism by which this mutation affects P450 2B6 catalytic activity. Studies using phenyldiazene to investigate differences between the active site topologies of the wild-type and mutant enzymes revealed only minor differences. Likewise, Ks values for the binding of both benzphetamine and efavirenz were comparable between the two enzymes. Using the alternate oxidant tert-butyl hydroperoxide, the mutant enzyme was inactivated by both 17EE and efavirenz. The stoichiometry of 17EE and efavirenz metabolism by P450s 2B6 and 2B6.4 revealed that the mutant enzyme was more uncoupled, producing hydrogen peroxide as the primary product. Interestingly, the addition of cytochrome b5 improved the coupling of the mutant, resulting in increased catalytic activity. In the presence of cytochrome b5 the variant readily metabolized 17EE and was inactivated by both 17EE and efavirenz. It is therefore proposed that the oxyferrous or iron-peroxo intermediate formed by the mutant enzyme in the presence of 17EE and efavirenz may be less stable than the same intermediates formed by the wild-type enzyme.

Radical energies and the regiochemistry of addition to heme groups. Methylperoxy and nitrite radical additions to the heme of horseradish peroxidase

The heme of hemoproteins, as exemplified by horseradish peroxidase (HRP), can undergo additions at the meso carbons and/or vinyl groups of the electrophilic or radical species generated in the catalytic oxidation of halides, pseudohalides, carboxylic acids, aryl and alkyl hydrazines, and other substrates. The determinants of the regiospecificity of these reactions, however, are unclear. We report here modification of the heme of HRP by autocatalytically generated, low-energy NO2* and CH3OO* radicals. The NO2* radical adds regioselectively to the 4- over the 2-vinyl group but does not add to the meso positions. Reaction of HRP with tert-BuOOH does not lead to heme modification; however, reaction with the F152M mutant, in which the heme vinyls are more sterically accessible, results in conversion of the heme 2-vinyl into a 1-hydroxy-2-(methylperoxy)ethyl group [-CH(OH)CH2OOCH3]. [18O]-labeling studies indicate that the hydroxyl group in this adduct derives from water and the methylperoxide oxygens from O2. Under anaerobic conditions, methyl radicals formed by fragmentation of the autocatalytically generated tert-BuO* radical add to both the delta-meso carbon and the 2-vinyl group. The regiochemistry of these and the other known additions to the heme indicate that only high-energy radicals (e.g., CH3*) add to the meso carbon. Less energetic radicals, including NO2* and CH3OO*, add to heme vinyl groups if they are small enough but do not add to the meso carbons. Electrophilic species such as HOBr, HOCl, and HOSCN add to vinyl groups but do not react with the meso carbons. This meso- versus vinyl-reactivity paradigm, which appears to be general for autocatalytic additions to heme prosthetic groups, suggests that meso hydroxylation of the heme by heme oxygenase occurs by a controlled radical reaction rather than by electrophilic addition.

Metabolism of aminoguanidine, diaminoguanidine, and NG-amino-L-arginine by neuronal NO-synthase and covalent alteration of the heme prosthetic group

It is established that aminoguanidine (AG), diaminoguanidine (DAG), and NG-amino-l-arginine (NAA) are metabolism-based inactivators of the three major isoforms of nitric oxide synthase (NOS). In the case of neuronal NOS (nNOS), heme alteration is known to be a major cause of inactivation, although the exact mechanism by which this occurs is not well-understood. We show here by the use of LC/MS/MS techniques that AG, DAG, and NAA are metabolized by nNOS to products with corresponding mass ions at m/z of 45.2, 60.2, and 160.0, respectively. These results are consistent with the loss of a hydrazine moiety from each inactivator. These findings are confirmed by exact mass measurements and comparison to authentic standards in the case of the products for NAA and AG, respectively. Moreover, the major dissociable heme product that was formed during inactivation of nNOS by AG, DAG, and NAA had molecular ions at m/z 660.2, 675.2, and 775.3, respectively. These results are consistent with an adduct of heme and inactivator minus a hydrazine moiety. In support of this, MS/MS studies reveal a fragment ion of heme in each case. With the use of 14C-labeled heme, we also show that in the case of AG, the dissociable heme adduct accounts for approximately one-half of the heme that is altered. In addition, we employ a software-based differential metabolic profiling method by subtracting LC/MS data sets derived from samples that contained nNOS from those that did not contain the enzyme to search for products and substrates in complex reaction mixtures. The metabolic profiling method established in this study can be used as a general tool to search for substrates and products of enzyme systems, including the drug-metabolizing liver microsomal P450 cytochromes. We propose that the metabolism-based inactivation of nNOS by AG, DAG, and NAA occurs through oxidative removal of the hydrazine group and the formation of a radical intermediate that forms stable products after H-atom abstraction or reacts with the heme prosthetic moiety and inactivates nNOS.

Topological role of cytochrome P450 2D6 active site residues

Recent reports have identified Phe120, Asp301, Thr309, and Glu216 as important residues in cytochrome P450 2D6 (CYP2D6) substrate binding and catalysis. Complementary homology models have located these amino acids within the binding pocket of CYP2D6 and in the present study we have used aryldiazenes to test these models and gain further insight in the role these amino acids have in maintaining the integrity of the active site cavity. When Phe120 was replaced to alanine, there was a significant increase in probe migration to pyrrole nitrogens C and D, in agreement with homology models which have located the phenyl side-chain of Phe120 above these two pyrrole rings. No changes in topology were observed with the D301Q mutant, supporting claims that in this mutant the electrostatic interactions with the B/C-loop are largely maintained and the loop retains its native orientation. The T309V mutation resulted in significant topological alteration suggesting that, in addition to its potential role in dioxygen activation, Thr309 plays an important structural role within the active site crevice. Replacement of Ile106 with Glu, engineered to cause electrostatic repulsion with Glu216, had a profound topological effect in the higher region within the active site cavity and impaired the catalytic activity towards CYP2D6 probe substrates.

Transient species involved in catalytic dioxygen/peroxide activation by hemoproteins: possible involvement of protonated Compound I species

Interaction of hemoproteins with peroxide leads in several cases to transient formation of ferric peroxo, ferric hydroperoxo, and "high-valent", formally Fev, oxo or hydroxo Compound species. Here, density functional calculations on ferric peroxo, ferric hydroperoxo, Compound and protonated Compound heme active site models are reported. The theoretical results, including calculated isotropic Fermi contact couplings and anisotropic spin dipole couplings, are found to generally correlate well with experimental EPR/ENDOR data. Hydrogen bonding and solvation affect the ferric-peroxo/ferrous-superoxo electromerism. The transition between the two electromers appears smooth, but neither hydrogen bonding to up to two water molecules, nor solvation appear able to dramatically alter the redox state of the superoxo ligand or of the iron. The presence of almost one full unpaired electron on the iron and of one full unpaired electron on the dioxygenic ligand in the "ferric-peroxo" state suggests a possible description of non-protonated "ferric-peroxo" as {ferric-superoxo+porphyrin radical}. Emerging from the DFT data is the possibility that a protonated Compound has already been detected in ENDOR experiments on cytochrome P450. The general feasibility of a protonated Compound in P450 monooxygenases is probed in light of these findings. To encompass the multiple mechanisms available in P450 for substrate oxidation, we define "mechanistic promiscuity" as the feature allowing an enzyme to perform the same reaction, with the same product, using more than one mechanism.

Thermophilic cytochrome P450 enzymes

Thermophilic cytochrome P450 enzymes are of potential interest from structural, mechanistic, and biotechnological points of view. The structures and properties of two such enzymes, CYP119 and CYP175A1, have been investigated and provide the foundation for future work on thermophilic P450 enzymes.

TOPOLOGICAL CHANGES IN THE CYP3A4 ACTIVE SITE PROBED WITH PHENYLDIAZENE: EFFECT OF INTERACTION WITH NADPH-CYTOCHROME P450 REDUCTASE AND CYTOCHROMEB5AND OF SITE-DIRECTED MUTAGENESIS

The active site topology of heterologously expressed CYP3A4 purified from an Escherichia coli expression system was examined using phenyldiazene. Incubation of CYP3A4 with phenyldiazene and subsequent oxidation yielded all four potential N-phenylprotoporphyrin IX regioisomers derived from attack on an available nitrogen atom in pyrrole rings B, A, C, or D (N(B):N(A):N(C):N(D) = 6:73:7: 13). Further study using 28 active site mutants showed that substitution of residues closer to the heme, Ala-305, Thr-309, or Ala-370, with a larger residue caused the most drastic changes in regioisomer formation, which reflected the location of each amino acid residue replaced in a CYP3A4 homology model. Previous studies have suggested a conformational change in CYP3A4 upon binding of NADPH-cytochrome P450 reductase (CPR) or cytochrome b(5) (b(5)). Therefore, regioisomer formation was also compared in the absence of redox partners and in the presence of CPR, b(5), or both. Formation of all four regioisomers in CYP3A4 wild type, particularly the minor ones, was reduced in the presence of b(5). CPR also greatly decreased the three minor isomers but increased the major isomer significantly. The presence of b(5) and CPR restored minor isomer formation and suppressed the enhancement of N(A) formation caused by CPR alone. Interestingly, the effects of the redox partners differed among representative active site mutants. In particular, the increase in N(C) upon substitution of Ala-370 with Phe was significantly reversed in the presence of redox partners, strongly suggesting that a conformational change occurs around pyrrole ring C due to protein-protein interactions between CYP3A4 and CPR or b(5).

Mechanism of horseradish peroxidase inactivation by benzhydrazide: a critical evaluation of arylhydrazides as peroxidase inhibitors

Many compounds are oxidized by haem enzymes, such as peroxidases and cytochromes P450, to highly reactive intermediates that function as enzyme inactivators. To evaluate the potential of arylhydrazides as selective metabolically activated peroxidase inhibitors, the mechanism of HRPC (horseradish peroxidase isoenzyme C) inhibition by BZH (benzhydrazide) was investigated in detail. No oxygen consumption was detected in BZH solutions at pH 7.0-12.0, but addition of HRPC resulted in significant O2 uptake above pH 8.0, indicating that the enzyme catalyses BZH oxidation. Addition of H2O2 to HRPC plus BZH activates the latter as an inhibitor. This involves the three-electron oxidation of BZH in one-electron steps by the peroxidase catalytic intermediates, Compounds I and II, to produce a benzoyl radical that covalently alters the active site and inhibits peroxidase activity. Alternatively, the benzoyl radical could be produced by di-imide (NH=NH) elimination from the BZH radical. Production of Compound III (oxyperoxidase) followed by p-670 (m/z =583, biliverdin-like derivative) was observed for HRPC incubated with excess H2O2, and the addition of BZH resulted in an increase in the rate of p-670 production. BZH is an inefficient inhibitor of HRPC with a K(I) of 80 muM, an apparent inactivation rate constant (k(inact)) of 0.035 min(-1), and an IC50 of 1.0 mM. This prompted the investigation of HRPC inactivation by a series of related arylhydrazides with known binding affinities for HRPC. The hydrazide with the highest affinity (2-naphthoichydrazide; K(d)=5.2 muM) was also found to be the most effective inhibitor with K(I), k(inact) and IC50 values of 14 muM, 0.14 min(-1) and 35 muM, respectively.

Dioxygen-dependent metabolism of nitric oxide in mammalian cells

Steady-state gradients of NO within tissues and cells are controlled by rates of NO synthesis, diffusion, and decomposition. Mammalian cells and tissues actively decompose NO. Of several cell lines examined, the human colon CaCo-2 cell produces the most robust NO consumption activity. Cellular NO metabolism is mostly O2-dependent, produces near stoichiometric NO3-, and is inhibited by the heme poisons CN-, CO (K(I) approximately 3 microM), phenylhydrazine, and NO and the flavoenzyme inhibitor diphenylene iodonium. NO consumption is saturable by O2 and NO and shows apparent K(M) values for O2 and NO of 17 and 0.2 microM, respectively. Mitochondrial respiration, O2*-, and H2O2 are neither sufficient nor necessary for O2-dependent NO metabolism by cells. The existence of an efficient mammalian heme and flavin-dependent NO dioxygenase is suggested. NO dioxygenation protects the NO-sensitive aconitases, cytochrome c oxidase, and cellular respiration from inhibition, and may serve a dual function in cells by limiting NO toxicity and by spatially coupling NO and O2 gradients.

Reversible pressure deformation of a thermophilic cytochrome P450 enzyme (CYP119) and its active-site mutants

The pressure stability of the thermophilic CYP119 from Sulfolobus solfataricus and its active-site Thr213 and Thr214 mutants was investigated. At 20 degrees C and pH 6.5, the protein undergoes a reversible P450-to-P420 inactivation with a midpoint at 380 MPa and a reaction volume change of -28 mL/mol. The volume of activation of the process was -9.5 mL/mol. The inactivation transition was retarded, and the absolute reaction volume was decreased by increasing temperature or by mutations that decrease the size of the active-site cavity. High pressure affected the tryptophan fluorescence yield, which decreased by about 37% at 480 MPa. The effect was reversible and suggested considerable contraction of the protein. Aerobic decomposition of iron-aryl complexes of the CYP119 T213A mutant under increasing hydrostatic pressure resulted in variation of the N-arylprotoporphyrin-IX regioisomer (N(B):N(A):N(C):N(D)) adduct pattern from 39:47:07:07 at 0.1 MPa to 23:36:14:27 at 400 MPa. Preincubation of the protein at 400 MPa followed by complex formation and decomposition gave the same regioisomer distribution as untreated protein. The results indicate that the protein is reversibly inactivated by pressure, in contrast to the irreversible inactivation of P450(cam) and other P450 enzymes, and that this inactivation process is modulated by changes in the active-site cavity dimensions.

The active site of the thermophilic CYP119 from Sulfolobus solfataricus

CYP119 from Sulfolobus solfataricus, the first thermophilic cytochrome P450, is stable at up to 85 degrees C. UV-visible and resonance Raman show the enzyme is in the low spin state and only modestly shifts to the high spin state at higher temperatures. Styrene only causes a small spin state shift, but T(1) NMR studies confirm that styrene is bound in the active site. CYP119 catalyzes the H(2)O(2)-dependent epoxidation of styrene, cis-beta-methylstyrene, and cis-stilbene with retention of stereochemistry. This catalytic activity is stable to preincubation at 80 degrees C for 90 min. Site-specific mutagenesis shows that Thr-213 is catalytically important and Thr-214 helps to control the iron spin state. Topological analysis by reaction with aryldiazenes shows that Thr-213 lies above pyrrole rings A and B and is close to the iron atom, whereas Thr-214 is some distance away. CYP119 is very slowly reduced by putidaredoxin and putidaredoxin reductase, but these proteins support catalytic turnover of the Thr-214 mutants. Protein melting curves indicate that the thermal stability of CYP119 does not depend on the iron spin state or the active site architecture defined by the threonine residues. Independence of thermal stability from active site structural factors should facilitate the engineering of novel thermostable catalysts.

The catalytic site of cytochrome P4504A11 (CYP4A11) and its L131F mutant

CYP4A11, the principal known human fatty acid omega-hydroxylase, has been expressed as a polyhistidine-tagged protein and purified to homogeneity. Based on an alignment with P450BM-3, the CYP4A11 L131F mutant has been constructed and similarly expressed. The two proteins are spectroscopically indistinguishable, but wild-type CYP4A11 primarily catalyzes omega-hydroxylation, and the L131F mutant only omega-1 hydroxylation, of lauric acid. The L131F mutant is highly uncoupled in that it slowly (omega-1)-hydroxylates lauric acid yet consumes NADPH at approximately the same rate as the wild-type enzyme. Wild-type CYP4A11 is inactivated by 1-aminobenzotriazole under turnover conditions but the L131F mutant is not. This observation, in conjunction with the binding affinities of substituted imidazoles for the two proteins, indicates that the L131F mutation decreases access of exogenous substrates to the heme site. Leu-131 thus plays a key role in controlling the regioselectivity of substrate hydroxylation and the extent of coupled versus uncoupled enzyme turnover. A further important finding is that the substituted imidazoles bind more weakly to CYP4A11 and its L131F mutant when these proteins are reduced by NADPH-cytochrome P450 reductase than by dithionite. This finding suggests that the ferric enzyme undergoes a conformational change that depends on both reduction of the iron and the presence of cytochrome P450 reductase and NADPH.

Evidence for a novel heme adduct generated by the in vitro reaction of 2,4,6-trinitrotoluene with human hemoglobin using electrospray ionization mass spectrometry

The bioactivation of nitroaromatic compounds to highly reactive intermediates is responsible for the genotoxic and cytotoxic effects by reaction with DNA and proteins. Due to its continued use as a secondary explosive and its prevalence at contaminated sites, the mechanism of covalent binding of 2,4,6-trinitrotoluene (TNT), or its metabolites, to critical cellular proteins has been of interest. Herein, we report the in vitro reaction of TNT with human hemoglobin under anaerobic and reductive (using sodium hydrosulfite) conditions, yielding a novel adduct between a putative nitrosodinitrotoluene (MW = 211 Da) and the prosthetic heme group (iron protoporphyrin-IX or heme b). While the covalent modification of hemoglobin polypeptide chains by TNT has been established, to our knowledge, this is the first example of a heme-TNT related adduct. This finding could be of relevance in investigation of biotransformation of TNT in subjects exposed to TNT via skin exposure or inhalation.

Nitric oxide prevents oxidative damage produced by tert-butyl hydroperoxide in erythroleukemia cells via nitrosylation of heme and non-heme iron. Electron paramagnetic resonance evidence

We studied protective effects of NO against tert-butylhydroperoxide (t-BuOOH)-induced oxidations in a subline of human erythroleukemia K562 cells with different intracellular hemoglobin (Hb) concentrations. t-BuOOH-induced formation of oxoferryl-Hb-derived free radical species in cells was demonstrated by low temperature EPR spectroscopy. Intensity of the signals was proportional to Hb concentrations and was correlated with cell viability. Peroxidation of phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, and cardiolipin metabolically labeled with oxidation-sensitive cis-parinaric acid was induced by t-BuOOH. An NO donor, (Z)-1-[N-(3-ammoniopropyl)-N-(n-propyl)amino]-diazen-1-iu m-1, 2-diolate], produced non-heme iron dinitrosyl complexes and hexa- and pentacoordinated Hb-nitrosyl complexes in the cells. Nitrosylation of non-heme iron centers and Hb-heme protected against t-BuOOH-induced: (a) formation of oxoferryl-Hb-derived free radical species, (b) peroxidation of cis-parinaric acid-labeled phospholipids, and (c) cytotoxicity. Since NO did not inhibit peroxidation induced by an azo-initiator of peroxyl radicals, 2, 2'-azobis(2,4-dimethylvaleronitrile), protective effects of NO were due to formation of iron-nitrosyl complexes whose redox interactions with t-BuOOH prevented generation of oxoferryl-Hb-derived free radical species.

Active site topologies and cofactor-mediated conformational changes of nitric-oxide synthases

The active site topologies of neuronal (nNOS), endothelial (eNOS), and inducible (iNOS) nitric-oxide synthases heterologously expressed in Escherichia coli have been examined using three aryldiazene (Ar-N=NH) probes. The topological information derives from (a) the rate and extent of aryl-iron complex formation in the presence and absence of tetrahydrobiopterin (H4B), Ca2+-dependent calmodulin (CaM), and L-arginine, and (b) the N-phenylprotoporphyrin IX regioisomer ratios obtained upon migration of the phenyl of the phenyl-iron complex to the heme nitrogen atoms. The N-phenylprotoporphyrin ratios indicate that the three NOS isoforms have related active site topologies with unencumbered space above all four pyrrole rings but particularly above pyrrole ring D. H4B binds directly above the heme pyrrole ring D or causes a conformational change that constricts that region, because H4B markedly decreases phenyl migration to pyrrole ring D. Small CaM-dependent changes in the nNOS N-phenylporphyrin isomer pattern are consistent with a conformational link between the CaM and heme sites in this protein. The ceiling height directly above the heme iron atom differs among the isoforms and is lower than in the P450 enzymes because only nNOS and iNOS react with 2-naphthyldiazene, and none of the isoforms reacts with p-biphenyldiazene. L-Arg blocks access to the heme iron atom in all three NOS isoforms and nearly suppresses the phenyldiazene reaction. The data indicate that topological differences, including differences in the size of the active site, are superimposed on the structural similarities among the NOS active sites.