Kinetic isotope effects implicate the iron-oxene as the sole oxidant in P450-catalyzed N-dealkylation

Multiple oxidants have been implicated as playing a role in cytochrome P450-mediated oxidations. Herein, we report results on N-dealkylation, one of the most facile reactions mediated by P450 enzymes. We have employed the N-oxides of a series of para-substituted 13C2H2-labeled N,N-dimethylanilines to function as both substrates and surrogate oxygen atom donors for P450cam and P4502E1. Kinetic isotope effect profiles obtained using the N-oxide system were found to closely match the profiles produced using the complete NAD(P)H/NAD(P)-P450 reductase/O2 system. The results are consistent with oxidation occurring solely through an iron-oxene species.     

Electron-transfer reactions and functionalization of cytochrome P450cam monooxygenase system in reverse micelles

Enzyme-based electron-transfer reactions involved in the cytochrome P450 monooxygenase system were investigated in nanostructural reverse micelles. A bacterial flavoprotein, putidaredoxin reductase (PdR), was activated and shown to be capable of catalyzing the electron transport from NADH to electron-carrier proteins such as cytochrome b5 (tCyt-b5) and putidaredoxin (Pdx) in reverse micelles. Ferric tCyt-b5 in reverse micelles was effectively converted to its ferrous form by the exogenous addition of separately prepared reverse micellar solution harboring PdR and NADH. The fact that direct interactions of macromolecular proteins should be possible in the reverse micellar system encouraged us to functionalize a multicomponent monooxygenase system composed of the bacterial cytochrome P450cam (P450cam), putidaredoxin (Pdx), and PdR in reverse micelles. The successful camphor hydroxylation reaction catalyzed by P450cam was significantly dependent on the coexistence of Pdx, PdR, and NADH but not H2O2, suggesting that the oxygen-transfer reactions proceeded via a "monooxygenation" mechanism. This is the first report of a multicomponent cytochrome P450 system exhibiting enzymatic activity in organic media.     

Substrate modulation of the properties and reactivity of the oxy-ferrous and hydroperoxo-ferric intermediates of cytochrome P450cam as shown by cryoreduction-EPR/ENDOR spectroscopy

EPR/ENDOR studies have been carried out on oxyferrous cytochrome P450cam one-electron cryoreduced by gamma-irradiation at 77 K in the absence of substrate and in the presence of a variety of substrates including its native hydroxylation substrate, camphor (a), and the alternate substrates, 5-methylenyl-camphor (b), 5,5-difluorocamphor (c), norcamphor (d), and adamantanone (e); the equivalent experiments have been performed on the T252A mutant complexed with a and b. The present study shows that the properties and reactivity of the oxyheme and of both the primary and the annealed intermediates are modulated by a bound substrate. This includes alterations in the properties of the heme center itself (g tensor; (14)N, (1)H, hyperfine couplings). It also includes dramatic changes in reactivity: the presence of any substrate increases the lifetime of hydroperoxoferri-P450cam (2) no less than ca. 20-fold. Among the substrates, b stands out as having an exceptionally strong influence on the properties and reactivity of the P450cam intermediates, especially in the T252A mutant. The intermediate, 2(T252A)-b, does not lose H(2)O(2), as occurs with 2(T252A)-a, but decays with formation of the epoxide of b. Thus, these observations show that substrate can modulate the properties of both the monoxygenase active-oxygen intermediates and the proton-delivery network that encompasses them.     

Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters

Quantum mechanical/molecular mechanical (QM/MM) methods have been used in conjunction with density functional theory (DFT) and correlated ab initio methods to predict the electron paramagnetic resonance (EPR) and Mossbauer (MB) properties of Compound I in P450(cam). For calibration purposes, a small Fe(IV)-oxo complex [Fe(O)(NH(3))(4)(H(2)O)](2+) was studied. The (3)A(2) and (5)A(1) states (in C(4)(v)() symmetry) are found to be within 0.1-0.2 eV. The large zero-field splitting (ZFS) of the (FeO)(2+) unit in the (3)A(2) state arises from spin-orbit coupling with the low-lying quintet and singlet states. The intrinsic g-anisotropy is very small. The spectroscopic properties of the model complex [Fe(O)(TMC)(CH(3)CN)](2+) (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane) are well reproduced by theory. In the model complexes [Fe(O)(TMP)(X)](+) (TMP = tetramesitylporphyrin, X = nothing or H(2)O) the computations again account for the observed spectroscopic properties and predict that the coupling of the (5)A(1) state of the (FeO)(2+) unit to the porphyrin radical leads to a low-lying sextet/quartet manifold approximately 12 kcal/mol above the quartet ground state. The calculations on cytochrome P450(cam), with and without the simulation of the protein environment by point charges, predict a small antiferromagnetic coupling (J approximately -13 to -16 cm(-)(1); H(HDvV) = - 2JS(A)S(B)) and a large ZFS > 15 cm(-)(1) (with E/D approximately 1/3) which will compete with the exchange coupling. This leads to three Kramers doublets of mixed multiplicity which are all populated at room temperature and may therefore contribute to the observed reactivity. The MB and ligand hyperfine couplings ((14)N, (1)H) are fairly sensitive to the protein environment which controls the spin density distribution between the porphyrin ring and the axial cysteinate ligand.     

Proton transfer at helium temperatures during dioxygen activation by heme monooxygenases

In the first measurement of enzymatic proton transfer at liquid helium temperatures, we examine protonation of the peroxo-ferriheme state of heme oxygenase (HO) produced by in situ radiolytic cryoreduction of oxy-HO in H2O and D2O solvents at ca. 4 K and above, and compare these findings with analogous measurements for oxy-P450cam and for oxy-Mb. Proton transfer in HO occurs at helium temperatures in both solvents; it occurs in P450cam at approximately 50 K and higher; in Mb it does not occur until T > 170 K. For Mb, this transfer at 180 K is biphasic, and the majority phase shows a solvent kinetic isotope effect of 3.8. We discuss these results in the context of the picture of environmentally coupled tunneling, which links proton transfer to two classes of protein motions: environmental reorganization (lambda in Marcus-like equations) and protein fluctuations ("active dynamics"; gating) which modulate the distance of proton transfer.     

Evidence for basic ferryls in cytochromes P450

Using a combination of M?ssbauer spectroscopy and density functional calculations, we have determined that the ferryl forms of P450(BM3) and P450cam are protonated at physiological pH. Density functional calculations were performed on large active-site models of these enzymes to determine the theoretical M?ssbauer parameters for the ferryl and protonated ferryl (Fe(IV)OH) 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 P450(BM3) are DeltaE(Q) = 2.17 mm/s and DeltaE(Q) = 1.05 mm/s, respectively. For P450cam, they are DeltaE(Q) = 1.84 mm/s and DeltaE(Q) = 0.66 mm/s, respectively. The experimentally determined quadrupole splittings (P450(BM3), DeltaE(Q) = 2.16 mm/s; P450cam, DeltaE(Q) = 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.     

Can ferric-superoxide act as a potential oxidant in P450(cam)? QM/MM investigation of hydroxylation, epoxidation, and sulfoxidation

In view of recent reports of high reactivity of ferric-superoxide species in heme and nonheme systems (Morokuma et al. J. Am. Chem. Soc. 2010, 132, 11993-12005; Que et al. Inorg. Chem. 2010, 49, 3618-3628; Nam et al. J. Am. Chem. Soc. 2010, 132, 5958-5959; J. Am. Chem. Soc. 2010, 132, 10668-10670), we use herein combined quantum mechanics/molecular mechanics (QM/MM) methods to explore the potential reactivity of P450(cam) ferric-superoxide toward hydroxylation, epoxidation, and sulfoxidation. The calculations demonstrate that P450 ferric-superoxide is a sluggish oxidant compared with the high-valent oxoiron porphyrin cation-radical species. As such, unlike heme enzymes with a histidine axial ligand, the P450 superoxo species does not function as an oxidant in P450(cam). The origin of this different behavior of the superoxo species of P450 vis-a?-vis other heme enzymes like tryptophan 2, 3-dioxygenase (TDO) is traced to the ability of the latter superoxo species to make a stronger FeOO-X (X = H,C) bond and to stabilize the corresponding bond-activation transition states by resonance with charge-transfer configurations. By contrast, the negatively charged thiolate ligand in the P450 superoxo species minimizes the mixing of charge transfer configurations in the transition state and raises the reaction barrier. However, as we demonstrate, an external electric field oriented along the Fe-O axis with a direction pointing from Fe toward O will quench Cpd I formation by slowing the reduction of ferric-superoxide and will simultaneously lower the barriers for oxidation by the latter species, thereby enabling observation of superoxo chemistry in P450. Other options for nascent superoxo reactivity in P450 are discussed.     

Thermodynamic and kinetic studies on the binding of nitric oxide to a new enzyme mimic of cytochrome p450

A new model for the P450 enzyme carrying a SO(3)(-) ligand coordinated to iron(III) (complex 2) reversibly binds NO to yield the nitrosyl adduct. The rate constant for NO binding to 2 in toluene is of the same order of magnitude as that found for the nitrosylation of the native, substrate-bound form of P450(cam) (E.S-P450(cam)). Large and negative activation entropy and activation volume values for the binding of NO to complex 2 support a mechanism that is dominated by bond formation with concomitant iron spin change from S = (5)/(2) to S = 0, as proposed for the reaction between NO and E.S-P450(cam). In contrast, the dissociation of NO from 2(NO) was found to be several orders of magnitude faster than the corresponding reaction for the E.S-P450(cam)/NO system. In a coordinating solvent such as methanol, the alcohol coordinates to iron(III) of 2 at the distal position, generating a six-coordinate, high-spin species 5. The reaction of NO with 5 in methanol was found to be much slower in comparison to the nitrosylation reaction of 2 in toluene. This behavior can be explained in terms of a mechanism in which methanol must be displaced during Fe-NO bond formation. The thermodynamic and kinetic data for NO binding to the new model complexes of P450 (2 and 5) are discussed in reference to earlier results obtained for closely related nitrosylation reactions of cytochrome P450(cam) (in the presence and in the absence of the substrate) and a thiolate-ligated iron(III) model complex.     

Roles of the proximal heme thiolate ligand in cytochrome p450(cam).

To examine the roles of the proximal thiolate iron ligand, the C357H mutant of P450(cam) (CYP101) was characterized by resonance Raman, UV, circular dichroism, and activity measurements. The C357H mutant must be reconstituted with hemin for activity to be observed. The reconstituted enzyme is a mixture of high and low spin species. Low temperature (10 degrees C), low enzyme concentration (1 microM), high camphor concentration (1 mM), and 5--50 mM buffer concentrations increase the high to low spin ratio, but under no conditions examined was the protein more than 60% high spin. The C357H mutant has a poorer K(m) for camphor (23 vs 2 microM) and a poorer K(d) for putidaredoxin (50 vs 20 microM) than wild-type P450(cam). The mutant also exhibits a greatly decreased camphor oxidation rate, elevated uncoupling rate, and much greater peroxidase activity. Electron transfer from putidaredoxin to the mutant is much slower than to the wild-type even though redox potential measurements show that the electron transfer remains thermodynamically favored. These experiments confirm that the thiolate ligand facilitates the O--O bond cleavage by P450 enzymes and also demonstrate that this ligand satisfies important roles in protein folding, substrate binding, and electron transfer.     

Solid state coordination chemistry of metal oxides: structural consequences of fluoride incorporation into the oxovanadium-copper-bisterpy-{O3P(CH2)nPO3}4- system, n= 1-5 (bisterpy = 2,2':4',4":2",2"'-quaterpyridyl-6', 6"-di-2-pyridine)

Hydrothermal reactions of a vanadate source, an appropriate Cu(II) source, bisterpy and an organodiphosphonate, H2O3P(CH2)nPO3H2(n= 1-5), in the presence of HF, yielded a family of materials of the type oxyfluorovanadium/copper-bisterpy/organodiphosphonate. Under similar reaction conditions, variations in diphosphonate tether length n provided the one-dimensional [{Cu2(bisterpy)}V2F2O2{HO3PCH2PO3}{O3PCH2PO3}](1) and [{Cu2(bisterpy)}V2F4O4{HO3P(CH2)2PO3H}](3), the two-dimensional [{Cu2(bisterpy)}V2F2O2(H2O)2{HO3P(CH2)2PO3}2] x 2H2O (2 x 2H2O), [{Cu2(bisterpy)(H2O2}V2F2O2{O3P(CH2)3PO3}{HO3P(CH2)3PO3H}(4) and [{Cu2(bisterpy)}V4F4O4(OH)(H2O){HO3P(CH2)5PO3}{O3P(CH2)5PO3}] x H2O (9 x H2O) and the three-dimensional [{Cu2(bisterpy)}3V8F6O17{HO3P(CH2)3PO3}4]0.8H2O (5 x 0.8H2O), [{Cu2(bisterpy)}V4F2O6{O3P(CH2)4PO3}2](8) and [{Cu2(bisterpy)(H2O)}2V8F4O8(OH)4{HO3P(CH2)5PO3H}2{O3P(CH2)5PO)}3] x 4.8H2O (10 x 4.8H2O). In addition, two members of the oxovanadium/Cu2(bisterpy)/organodiphosphonate family [{Cu2(bisterpy)}V2O4{HO3P(CH2)3PO3}2](6) and [{Cu2(bisterpy)}3V4O8(OH)2{O3P(CH2)3PO3}2{HO3P(CH2)3PO3}2] x 5H2O (7 x 5H2O) cocrystallized from the reaction mixture which provided 5. The overall architectures reveal embedded substructures based on V/P/O(F) clusters, chains, networks, and frameworks. In contrast to the oxovanadium/Cu2(bisterpy)/ organodiphosphonate family, several of the materials of this study also exhibit the direct condensation of vanadium polyhedra to produce binuclear and/or tetranuclear building units.     

Biotransformation of the sesquiterpene (+)-valencene by cytochrome P450cam and P450BM-3

The sesquiterpenoids are a large class of naturally occurring compounds with biological functions and desirable properties. Oxidation of the sesquiterpene (+)-valencene by wild type and mutants of P450cam from Pseudomonas putida, and of P450BM-3 from Bacillus megaterium, have been investigated as a potential route to (+)-nootkatone, a fine fragrance. Wild type P450cam did not oxidise (+)-valencene but the mutants showed activities up to 9.8 nmol (nmol P450)(-1) min(-1), with (+)-trans-nootkatol and (+)-nootkatone constituting >85% of the products. Wild type P450BM-3 and mutants had higher activities (up to 43 min(-1)) than P450cam but were much less selective. Of the many products, cis- and trans-(+)-nootkatol, (+)-nootkatone, cis-(+)-valencene-1,10-epoxide, trans-(+)-nootkaton-9-ol, and (+)-nootkatone-13S,14-epoxide were isolated from whole-cell reactions and characterised. The selectivity patterns suggest that (+)-valencene has one binding orientation in P450cam but multiple orientations in P450BM-3.     

Hydroxylation of camphor by reduced oxy-cytochrome P450cam: mechanistic implications of EPR and ENDOR studies of catalytic intermediates in native and mutant enzymes.

We have employed gamma-irradiation at cryogenic temperatures (77 K and also approximately 6 K) of the ternary complexes of camphor, dioxygen, and ferro-cytochrome P450cam to inject the "second" electron of the catalytic process. We have used EPR and ENDOR spectroscopies to characterize the primary product of reduction as well as subsequent states created by annealing reduced oxyP450, both the WT enzyme and the D251N and T252A mutants, at progressively higher temperatures. (i) The primary product upon reduction of oxyP450 4 is the end-on, "H-bonded peroxo" intermediate 5A. (ii) This converts even at cryogenic temperatures to the hydroperoxo-ferriheme species, 5B, in a step that is sensitive to these mutations.Yields of 5B are as high as 40%. (iii) In WT and D251N P450s, brief annealing in a narrow temperature range around 200 K causes 5B to convert to a product state, 7A, in which the product 5-exo-hydroxycamphor is coordinated to the ferriheme in a nonequilibrium configuration. Chemical and EPR quantitations indicate the reaction pathway involving 5B yields 5-exo-hydroxycamphor quantitatively. Analogous (but less extensive) results are seen for the alternate substrate, adamantane. (iv) Although the T252A mutation does not interfere with the formation of 5B, the cryoreduced oxyT252A does not yield product, which suggests that 5B is a key intermediate at or near the branch-point that leads either to product formation or to nonproductive "uncoupling" and H(2)O(2) production. The D251N mutation appears to perturb multiple stages in the catalytic cycle. (v) There is no spectroscopic evidence for the buildup of a high-valence oxyferryl/porphyrin pi-cation radical intermediate, 6. However, ENDOR spectroscopy of 7A in H(2)O and D(2)O buffers shows that 7A contains hydroxycamphor, rather than water, bound to Fe(3+), and that the proton removed from the C(5) carbon of substrate during hydroxylation is trapped as the hydroxyl proton. This demonstrates that hydroxylation of substrates by P450cam in fact occurs by the formation and reaction of 6. (vi) Annealing at > or = 220 K converts the initial product state 7A to the equilibrium product state 7, with the transition occurring via a second nonequilibrium product state, 7B, in the D251N mutant; in states 7B and 7 the hydroxycamphor hydroxyl proton no longer is trapped. (vii) The present results are discussed in the context of other efforts to detect intermediates in the P450 catalytic cycle.     

Revisiting the mechanism of P450 enzymes with the radical clocks norcarane and spiro[2,5]octane

Norcarane (1) and spiro[2.5]octane (2) yield different product distributions depending on whether they are oxidized via concerted, radical, or cationic mechanisms. For this reason, these two probes were used to investigate the mechanisms of hydrocarbon hydroxylation by two mammalian and two bacterial cytochrome P450 enzymes. Products indicative of a radical intermediate with a lifetime ranging from 16 to 52 ps were detected during the oxidation of norcarane by P450(cam) (CYP101), P450(BM3) (CYP102), CYP2B1, and CYP2E1. Trace amounts of the cation rearrangement product were observed with norcarane for all but CYP2E1, while no cation or radical rearrangement products were observed for spiro[2.5]octane. The results for the oxidation of norcarane with a radical rearrangement rate of 2 x 10(8) s(-1) are consistent with the involvement of a two-state radical rebound mechanism, while for the slower (5 x 10(7) s(-1)) spiro[2,5]oct-4-yl radical rearrangement products were beyond detection. Taken together with earlier data for the hydroxylation of bicyclo[2.1.0]pentane, which also suggested a 50 ps radical lifetime, these three structurally similar and functionally simple substrates show a consistent pattern of rearrangement that supports a radical rebound mechanism for this set of cytochrome P450 enzymes.     

Substrate binding favors enhanced NO binding to P450cam

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

Structural diversity of the oxovanadium organodiphosphonate system: a platform for the design of void channels

The hydrothermal reactions of a vanadium source, an appropriate diphosphonate ligand, and water in the presence of HF provide a series of compounds with neutral V-P-O networks as the recurring structural motif. When the {O3P(CH2)(n)PO3}4- diphosphonate tether length n is 2-5, metal-oxide hybrids of type 1, [V2O2(H2O){O3P(CH2)(n)PO3}] x xH2O, are isolated. The type 1 oxides exhibit the prototypical three-dimensional (3-D) "pillared" layer architecture. When n is increased to 6-8, the two-dimensional (2-D) "pillared" slab structure of the type 2 oxides [V2O2(H2O)4{O3P(CH2)6PO3}] is encountered. Further lengthening of the spacer to n = 9 provides another 3-D structure, type 3, constructed from the condensation of pillared slabs to give V-P-O double layers as the network substructure. When organic cations are introduced to provide charge balance for anionic V-P-O networks, oxides of types 4-7 are observed. For spacer length n = 3, a range of organodiammonium cations are accommodated by the same 3-D "pillared" layer oxovanadium diphosphonate framework in the type 4 materials [H3N(CH2)(n)NH3][V4O4(OH)2 {O3P(CH)3PO3}2] x xH2O [n = 2, x = 6 (4a); n = 3, x = 3 (4b); n = 4, x = 2 (4c); n = 5, x = 1 (4d); n = 6, x = 0.5 (4e); n = 7, x = 0 (4f)] and [H3NR]y[V4O4(OH)2 {O3P(CH)3PO3}2] x xH2O [R = -CH2(NH3)CH2CH3, y = 1, x = 0 (4g); R = -CH3, n = 2, x = 3 (4h); R = -CH2CH3, y = 2, x = 1 (4i); R = -CH2CH2CH3, y = 2, x = 0 (4j); cation = [H2N(CH2CH3)2], y = 2, x = 0 (4k)]. These oxides exhibit two distinct interlamellar domains, one occupied by the cations and the second by water of crystallization. Furthermore, as the length of the cation increases, the organodiammonium component spills over into the hydrophilic domain to displace the water of crystallization. When the diphosphonate tether length is increased to n = 5, structure type 5, [H3N(CH2)2NH3][V4O4(OH)2(H2O){O3P(CH2)5PO3}2] x H2O, is obtained. This oxide possesses a 2-D "pillared" network or slab structure, similar in gross profile to that of type 2 oxides and with the cations occupying the interlamellar domain. In contrast, shortening the diphosphonate tether length to n = 2 results in the 3-D oxovanadium organophosphonate structure of the type 7 oxide [H3N(CH2)5NH3][V3O3{O3P(CH2)2PO3}2]. The ethylenediphosphonate ligand does not pillar V-P-O networks in this instance but rather chelates to a vanadium center in the construction of complex polyhedral connectivity of 7. Substitution of piperazinium cations for the simple alkyl chains of types 4, 5, and 7 provides the 2-D pillared layer structure of the type 6 oxides, [H2N(CH2CH2)NH2][V2O2{O3P(CH)(n)PO3H}2] [n = 2 (6a); n = 4 (6b); n = 6 (6c)]. The structural diversity of the system is reflected in the magnetic properties and thermal behavior of the oxides, which are also discussed.     

Solid-state coordination chemistry of the oxomolybdate-organodiphosphonate/nickel-organoimine system: structural influences of the secondary metal coordination cation and diphosphonate tether lengths

The hydrothermal reactions of a molybdate source, a nickel(II) salt, tetra-2-pyridylpyrazine (tpyprz), and organodiphosphonic acids H(2)O(3)P(CH(2))(n)()PO(3)H(2) (n = 1-5) of varying tether lengths yielded a series of organic-inorganic hybrid materials of the nickel-molybdophosphonate family. A persistent characteristic of the structural chemistry is the presence of the [Mo(5)O(15)(O(3)PR)(2)](4)(-) cluster as a molecular building block, as noted for the one-dimensional materials [[Ni(2)(tpyprz)(2)]Mo(5)O(15)[O(3)P(CH(2))(4)PO(3)]]x6.65H(2)O (6x6.65H(2)O) and [[Ni(2)(tpyprz)(2)]Mo(5)O(15)[O(3)P(CH(2))(5)PO(3)]]x3.75H(2)O (8x3.75H(2)O), the two-dimensional phases [[Ni(4)(tpyprz)(3)][Mo(5)O(15)(O(3)PCH(2)CH(2)PO(3))](2)]x23H(2)O (3x23H(2)O) and [[Ni(3)(tpyprz)(2)(H(2)O)(2)](Mo(5)O(15))(Mo(2)O(4)F(2))[O(3)P(CH(2))(3)PO(3)](2)]x8H(2)O (5x8H(2)O), and the three-dimensional structures [[Ni(2)(tpyprz)(H(2)O)(3)]Mo(5)O(15)[O(3)P(CH(2))(3)PO(3))]]xH(2)O (4xH(2)O) and [[Ni(2)(tpyprz)(H(2)O)(2)]Mo(5)O(15) [O(3)P(CH(2))(4)PO(3)]]x2.25H(2)O (7x2.25H(2)O). In the case of methylenediphosphonic acid, the inability of this ligand to tether adjacent pentanuclear clusters precludes the formation of the common molybdophosphonate building block, manifesting in contrast a second structural motif, the trinuclear [(Mo(3)O(8))(x)(O(3)PCH(2)PO(3))(y)] subunit of [[Ni(tpyprz)(H(2)O)(2)](Mo(3)O(8))(2) (O(3)PCH(2)PO(3))(2)] (1) which had been previously observed in the corresponding methylenediphosphonate phases of the copper-molybdophosphonate family. Methylenediphosphonic acid also provides a second phase, [Ni(2)(tpyprz)(2)][Mo(7)O(21)(O(3)PCH(2)PO(3))]x3.5H(2)O (9x5H(2)O), which contains a new heptamolybdate cluster [Mo(7)O(21)(O(3)PCH(2)PO(3))](4)(-) and a cationic linear chain [Ni(tpyprz)](n)(4n+) substructure. The structural chemistry of the nickel-molybdophosphonate series contrasts with that of the corresponding copper-molybdophosphonate materials, reflecting in general the different coordination preferences of Ni(II) and Cu(II). Consequently, while the Cu(II)-organic complex building block of the copper family is invariably the binuclear [Cu(2)(tpyprz)](4+) subunit, the Ni(II) chemistry with tpyprz exhibits a distinct tendency toward catenation to provide [Ni(3)(tpyprz)(2)](6+), [Ni(4)(tpyprz)(3)](8+), and [Ni(tpyprz)](n)(4n+) building blocks as well as the common [Ni(2)(tpyprz)](4+) moiety. This results in a distinct structural chemistry for the nickel(II)-molybdophosphonate series with the exception of the methylenediphosphonate derivative 1 which is isostructural with the corresponding copper compound [[Cu(2)(tpyprz)(H(2)O)(2)](Mo(3)O(8))(2)(O(3)PCH(2)PO(3))] (2). The structural chemistry of the nickel(II) series also reflects variability in the number of attachment sites at the molybdophosphonate clusters, in the extent of aqua ligation to the Ni(II) tpyprz subunit, and in the participation of phosphate oxygen atoms as well as molybdate oxo groups in linking to the nickel sites.     

The elusive oxidant species of cytochrome P450 enzymes: characterization by combined quantum mechanical/molecular mechanical (QM/MM) calculations

The primary oxidant of cytochrome P450 enzymes, Compound I, is hard to detect experimentally; in the case of cytochrome P450(cam), this intermediate does not accumulate in solution during the catalytic cycle even at temperatures as low as 200 K (ref 4). Theory can play an important role in characterizing such elusive species. We present here combined quantum mechanical/molecular mechanical (QM/MM) calculations of Compound I of cytochrome P450(cam) in the full enzyme environment as well as density functional studies of the isolated QM region. The calculations assign the ground state of the species, quantify the effect of polarization and hydrogen bonding on its properties, and show that the protein environment and its specific hydrogen bonding to the cysteinate ligand are crucial for sustaining the Fe-S bond and for preventing the full oxidation of the sulfur.     

Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam

An extended accelerated molecular dynamics (AMD) methodology called adaptive AMD is presented. Adaptive AMD (Ad-AMD) is an efficient and robust conformational space sampling algorithm that is particularly-well suited to proteins with highly structured potential energy surfaces exhibiting complex, large-scale collective conformational transitions. Ad-AMD simulations of substrate-free P450cam reveal that this system exists in equilibrium between a fully and partially open conformational state. The mechanism for substrate binding depends on the size of the ligand. Larger ligands enter the P450cam binding pocket, and the resulting substrate-bound system is trapped in an open conformation via a population shift mechanism. Small ligands, which fully enter the binding pocket, cause an induced-fit mechanism, resulting in the formation of an energetically stable closed conformational state. These results are corroborated by recent experimental studies and potentially provide detailed insight into the functional dynamics and conformational behavior of the entire cytochrome-P450 superfamily.     

Oxygen activation by cytochrome p450: a thermodynamic analysis

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 degrees ' (P450FeO(2)2+, 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 (DeltaG degrees ' = +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 degrees ' (P450FeO(2)2+, H+/P450FeOOH2+) = +0.93 V at pH 7 is larger than necessary to effect reduction of cytochrome P450FeO(2)2+, the magnitude of this electrode potential implies that the binding constant for cytochrome P450Fe3+ with hydrogen peroxide is ca. 3 x 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 cytochrome 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.     

Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy

Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.