Crystal Structure Analysis of the Repair of Iron Centers Protein YtfE and Its Interaction with NO.

Molecular mechanisms underlying the repair of nitrosylated [Fe-S] clusters by the microbial protein YtfE remain poorly understood. The X-ray crystal structure of YtfE, in combination with EPR, magnetic circular dichroism (MCD), UV, and (17) O-labeling electron spin echo envelope modulation measurements, show that each iron of the oxo-bridged Fe(II) -Fe(III) diiron core is coordinatively unsaturated with each iron bound to two bridging carboxylates and two terminal histidines in addition to an oxo-bridge. Structural analysis reveals that there are two solvent-accessible tunnels, both of which converge to the diiron center and are critical for capturing substrates. The reactivity of the reduced-form Fe(II) -Fe(II) YtfE toward nitric oxide demonstrates that the prerequisite for N2 O production requires the two iron sites to be nitrosylated simultaneously. Specifically, the nitrosylation of the two iron sites prior to their reductive coupling to produce N2 O is cooperative. This result suggests that, in addition to any repair of iron centers (RIC) activity, YtfE acts as an NO-trapping scavenger to promote the NO to N2 O transformation under low NO flux, which precedes nitrosative stress.

Water-Soluble Dinitrosyl Iron Complex (DNIC): a Nitric Oxide Vehicle Triggering Cancer Cell Death via Apoptosis.

Nitric oxide (NO) is an important cellular signaling molecule that modulates various physiological activities. Angiogenesis-promoting activities of NO-donor drugs have been explored in both experimental and clinical studies. In this study, a structurally well characterized and water-soluble neutral {Fe(NO)2}(9) DNIC [(S(CH2)2OH)(S(CH2)2NH3)Fe(NO)2] (DNIC 2) was synthesized to serve as a NO-donor species. The antitumor activity of DNIC 2 was determined by MTT assay, confocal imaging, and Annexin-V/PI staining. The IC50 values of DNIC 2 were 18.8, 42.9, and 38.6 µM for PC-3, SKBR-3, and CRL5866 tumor cells, respectively. Moreover, DNIC 2 promoted apoptotic cell death via activation of apoptosis-associated proteins and inhibition of survival associated proteins. In particular, DNIC 2 treatment suppressed PC-3 tumor growth by 2.34- and 19.3-fold at 7 and 21 days, in comparison with the control group. These results indicate that water-soluble DNIC 2 may serve as a promising drug for cancer therapy.

Ambient Stable Trigonal Bipyramidal Copper(III) Complexes Equipped with an Exchangeable Axial Ligand.

A stable trigonal bipyramidal copper(III) complex, [PPN][Cu((TMS)PS3)Cl] (1, wherein PPN represents bis(triphenylphosphine)iminium), was synthesized from CuCl2/PPNCl via intramolecular copper(II) disproportionation. Under ambient conditions, the axial chloride of 1 is exchangeable in solution thus making 1 serve as an intermediate to prepare trigonal bipyramidal copper(III) derivatives, e.g., [PPN][Cu((TMS)PS3)(N3)] (2) and [Cu((TMS)PS3)(DABCO)] (3). Diamagnetic complexes 1-3 were fully characterized by X-ray crystallography, NMR, UV-vis, and Cu K-edge absorption spectroscopy. A series of UV-vis titrations were performed to investigate the relative ligand affinity toward the [Cu((TMS)PS3)] moiety, verifying the 1:1 binding equilibrium between various ligands. Compared to known copper(III) compounds, Cu K-edge absorptions of 1-3 possess lower pre-edge energy and higher shakedown transition energy, which, respectively, attribute to the electron donation from (TMS)PS3(3-) ligand and their trigonal ligand field.

Insight into the reactivity and electronic structure of dinuclear dinitrosyl iron complexes.

A combination of N/S/Fe K-edge X-ray absorption spectroscopy (XAS), X-ray diffraction data, and density functional theory (DFT) calculations provides an efficient way to unambiguously delineate the electronic structures and bonding characters of Fe-S, N-O, and Fe-N bonds among the direduced-form Roussin's red ester (RRE) [Fe2(µ-SPh)2(NO)4](2-)(1) with {Fe(NO)2}(10)-{Fe(NO)2}(10) core, the reduced-form RRE [Fe2(µ-SPh)2(NO)4](-)(3) with {Fe(NO)2}(9)-{Fe(NO)2}(10) core, and RRE [Fe2(µ-SPh)2(NO)4] (4) with {Fe(NO)2}(9)-{Fe(NO)2}(9) core. The major contributions of highest occupied molecular orbital (HOMO) 113α/ß in complex 1 is related to the antibonding character between Fe(d) and Fe(d), Fe(d), and S atoms, and bonding character between Fe(d) and NO(π*). The effective nuclear charge (Zeff) of Fe site can be increased by removing electrons from HOMO to shorten the distances of Fe···Fe and Fe-S from 1 to 3 to 4 or, in contrast, to increase the Fe-N bond lengths from 1 to 3 to 4. The higher IR νNO stretching frequencies (1761, 1720 cm(-1) (4), 1680, 1665 cm(-1) (3), and 1646, 1611, 1603 cm(-1) (1)) associated with the higher transition energy of N1s →σ*(NO) (412.6 eV (4), 412.3 eV (3), and 412.2 eV (1)) and the higher Zeff of Fe derived from the transition energy of Fe1s → Fe3d (7113.8 eV (4), 7113.5 eV (3), and 7113.3 eV (1)) indicate that the N-O bond distances of these complexes are in the order of 1 > 3 > 4. The N/S/Fe K-edge XAS spectra as well as DFT computations reveal the reduction of complex 4 yielding complex 3 occurs at Fe, S, and NO; in contrast, reduction mainly occurs at Fe site from complex 3 to complex 1.

The metal core structures in the recombinant Escherichia coli transcriptional factor SoxR.

X-ray absorption, circular dichroism, and EPR spectroscopy were employed to investigate the metal-core structures in the Escherichia coli transcriptional factor SoxR under reduced, oxidized, and nitrosylated conditions. The spectroscopic data revealed that the coordination environments of the metal active centers varied only very slightly between the reduced and oxidized states, similar to most other proteins containing iron-sulfur clusters. Upon nitrosylation of oxidized SoxR, however, we observed a low-temperature EPR spectrum characteristic of a protein dinitrosyl iron complex (DNIC), with an intensity corresponding to about two DNICs per iron sulfur cluster in the protein, according to spin quantification relative to a low-molecular-weight DNIC standard. In addition, there was no evidence for dichroic spectral features in the responsive region of the nitrosyl iron complexes, as well as for Fe-Fe back-scattering in the fitting of the Fe extended X-ray absorption fine structure (EXAFS) spectrum. Instead the Fe EXAFS spectrum of the nitrosylated SoxR core exhibited the same first- and second-shell coordination environments characteristic of modeled small molecular DNICs, indicating that each of the [2 Fe-2 S] cores in the homodimeric SoxR was dissociated into two individual DNICs. Similar nitrosylation of the reduced mixed-valence SoxR for 1 min led to degradation of the iron-sulfur clusters to give several iron species, including one with EPR signals characteristic of a reduced Roussin's red ester (rRRE), a diamagnetic species, presumably Roussin's red ester (RRE), and a small amount of DNIC. We also undertook in vivo time-course studies of E. coli cells containing recombinant SoxR after rapid purging of the cells with exogenous NO gas. Rapid freeze-quenched EPR experiments demonstrated rapid formation of the SoxR rRRE species, followed by fast breakup of this precursor intermediate to form the stable protein-bound DNIC species. Accordingly, under nitrosative stress, we believe that the response of SoxR to NO could depend on the intracellular redox state of E. coli, the central modulator of which could be exploited to deduce the appropriate mechanism to sense the presence of NO for physiological regulation.

Tuning the regio- and stereoselectivity of C-H activation in n-octanes by cytochrome P450 BM-3 with fluorine substituents: evidence for interactions between a C-F bond and aromatic π systems.

We employed the water-soluble cytochrome P450 BM-3 to study the activity and regiospecificity of oxidation of fluorinated n-octanes. Three mutations, A74G, F87V, and L188Q, were introduced into P450 BM-3 to allow the system to undergo n-octane oxidation. In addition, the alanine at residue 328 was replaced with a phenylalanine to introduce an aromatic residue into the hydrophobic pocket to examine whether or not van der Waals interactions between a C-F substituent in the substrate and the polarizable π system of the phenylalanine may be used to steer the positioning of the substrate within the active-site pocket of the enzyme and control the regioselectivity and stereoselectivity of hydroxylation. Interestingly, not only was the regioselectivity controlled when the fluorine substituent was judiciously positioned in the substrate, but the electron input into the iron-heme group became tightly coupled to the formation of product, essentially without abortive side reactions. Remarkable enhancement of the coupling efficiency between electron input and product formation was observed for a range of fluorinated octanes in the enzyme even without the A328F mutation, presumably because of interactions of the C-F substituent with the π system of the porphyrin macrocycle within the active-site pocket. Evidently, tightening the protein domain containing the heme pocket tunes the distribution of accessible enzyme conformations and the associated protein dynamics that activate the iron porphyrin for substrate hydroxylation to allow the reactions mediated by the high-valent Fe(IV)=O to become kinetically more commensurate with electron transfer from the flavin adenine dinucleotide (FAD)/flavin mononucleotide (FMN) reductase. These observations lend compelling evidence to support significant van der Waals interactions between the CF(2) group and aromatic π systems within the heme pocket when the fluorinated octane substrate is bound.

Peptide-bound dinitrosyliron complexes (DNICs) and neutral/reduced-form Roussin's red esters (RREs/rRREs): understanding nitrosylation of [Fe-S] clusters leading to the formation of DNICs and RREs using a de novo design strategy.

This manuscript describes the interaction of low-molecular-weight DNICs with short peptides designed to explore the stability and structure of DNIC-peptide/RRE-peptide constructs. Although characterization of protein-bound and low-molecular-weight DNICs is possible via EPR, XAS, and NRVS, this study demonstrates that the combination of aqueous IR ν(NO) and UV-vis spectra can serve as an efficient tool to characterize and discriminate peptide-bound DNICs and RREs. The de novo chelate-cysteine-containing peptides KC(A)(n)CK-bound (n = 1-4) dinitrosyliron complexes KC(A)(n)CK-DNIC (CnA-DNIC) and monodentate-cysteine-containing peptides KCAAK-/KCAAHK-bound Roussin's red esters (RREs) KCAAK-RRE/KCAAHK-RRE were synthesized and characterized by aqueous IR, UV-vis, EPR, CD, XAS, and ESI-MS. In contrast to the inertness of chelate-cysteine-containing peptide-bound DNICs toward KCAAK/KCAAHK, transformation of KCAAK-RRE/KCAAHK-RRE into CnA-DNIC triggered by CnA and reversible transformation between CnA-DNIC and CnA-RRE via {Fe(NO)(2)}(9)-{Fe(NO)(2)}(10) reduced-form peptide-bound RREs demonstrate that the {Fe(NO)(2)}(9) motif displays a preference for chelate-cysteine-containing peptides over monodentate-cysteine-containing peptides. Also, this study may signify that nitrosylation of [Fe-S] proteins generating protein-bound RREs, reduced protein-bound RREs, or protein-bound DNICs are modulated by both the oxidation state of iron and the chelating effect of the bound proteins of [Fe-S] clusters.

Nitrosylation of the Diiron Core Mediated by the N Domain of YtfE.

The YtfE protein catalyzes the reduction of NO to N2O, protecting iron-sulfur clusters from nitrosylation. The structure of YtfE has a two-domain architecture, with a diiron-containing C-terminal domain linked to an N-terminal domain, in which the function of the latter is enigmatic. Here, by using electron spin resonance (ESR) spectroscopy, we show that YtfE exists in two conformational states, one of which has not been reported. Under high osmotic stress, YtfE adopts a homogeneous conformation (C state) similar to the known crystal structure. In a regular buffer, the N-terminal domain switches between the C state and a previously unidentified conformation (C' state), the latter of which has more space at the domain interface to allow the trafficking of NO molecules and thus is proposed to be a functionally active state. The conformational switch between the C and C' states is pivotal for facilitating NO access to the diiron core.

A study of NO trafficking from dinitrosyl-iron complexes to the recombinant E. coli transcriptional factor SoxR.

SoxR is a transcriptional factor in Escherichia coli that induces the expression of SoxS to initiate the production of enzymes in response to oxidative stress. In addition to superoxide, SoxR is also sensitive to cellular NO to produce a protein-bound dinitrosyl-iron complex (DNIC) with a characteristic electron paramagnetic resonance (EPR) signal at g(av)=2.03. Toward developing a strategy for NO sensing based on this property of SoxR, we have overexpressed and purified the recombinant His-tagged SoxR protein. Upon treatment of the purified protein under anaerobic conditions with (1) NO solution, (2) S-nitrosothiol (RSNO), and (3) chemically synthesized low molecular weight DNICs (LMW-DNICs), we have observed enhancement of the EPR signal at g(av)=2.03 from the protein-bound DNICs over time, reflecting the redistribution of NO from the NO solution, RSNO and LMW-DNICs to the SoxR. We have exploited this NO exchange to investigate the kinetics and mechanisms of release and delivery of NO from various LMW-DNICs to an isopropyl-beta-D-thiogalactopyranoside-dependent SoxR expressed in E. coli cells. These experiments revealed that the NO from RSNO and LMW-DNICs could cross the biological membrane and enter the cytoplasm of the cell to form the SoxR protein-bound DNIC complex. For comparison, we have also studied the direct NO transfer from the LMW-DNICs to the SoxR protein in buffer. The NO transfer was found to be rapid. From the kinetic data derived, we showed that LMW-DNICs with bidentate thiolate ligands displayed greater stability in aqueous solution but exhibited more facile NO delivery to cytoplasmic SoxR in whole cells.