The RNA-binding heme protein DiGeorge critical region 8 (DGCR8) and its ribonuclease partner Drosha cleave primary transcripts of microRNA (pri-miRNA) as part of the canonical microRNA (miRNA) processing pathway. Previous studies show that bis-cysteine thiolate-coordinated Fe(III) DGCR8 supports pri-miRNA processing activity, while Fe(II) DGCR8 does not. In this study, we further characterized Fe(II) DGCR8 and tested whether CO or NO might bind and restore pri-miRNA processing activity to the reduced protein. Fe(II) DGCR8 RNA-binding heme domain (Rhed) undergoes a pH-dependent transition from 6-coordinate to 5-coordinate, due to protonation and loss of a lysine ligand; the ligand bound throughout the pH change is a histidine. Fe(II) Rhed binds CO and NO from 6- and 5-coordinate states, forming common CO and NO adducts at all pHs. Fe(II)–CO Rhed is 6-coordinate, low-spin, and pH insensitive with the histidine ligand retained, suggesting that the protonatable lysine ligand has been replaced by CO. Fe(II)–NO Rhed is 5-coordinate and pH insensitive. Fe(II)–NO also forms slowly upon reaction of Fe(III) Rhed with excess NO via a stepwise process. Heme reduction by NO is rate-limiting, and the rate would be negligible at physiological NO concentrations. Importantly, in vitro pri-miRNA processing assays show that both CO- and NO-bound DGCR8 species are inactive. Fe(II), Fe(II)–CO, and Fe(II)–NO Rhed do not bear either of the cysteine ligands found in the Fe(III) state. These data support a model in which the bis-cysteine thiolate ligand environment of Fe(III) DGCR8 is necessary for establishing proper pri-miRNA binding and enabling processing activity.

Both Met104 and Met105 are involved, either directly or indirectly, in the redox mediated ligand switch of the heme-dependent transcription factor, RcoM-1. Recent studies of Burkholderia xenovorans RcoM identified Cys94 as the thiolate ligand in the Fe(III) state of the heme cofactor. Upon reduction, a neutral donor replaces Cys94 trans to His74. Homology modelling implicated either Met104 or Met105 as the possible ligand in the Fe(II) state. We spectroscopically compared wild type (WT) RcoM-1 to three Met-to-Leu variants (M104L, M105L, and M104L/M105L) to identify which Met residue acts as the ligand. All proteins were isolated as admixtures of Fe(III) and Fe(II)–CO heme; oxidation by ferricyanide enables study of homogeneous oxidation and coordination states. Met104 is the CO-replaceable Fe(II) heme ligand. The magnetic circular dichroism (MCD) spectrum of Fe(II) M105L resembled WT. M104L and M104L/M105L, however, showed spectra arising from the formation of a high-spin, five-coordinate species indicating the loss of the ligand. The electron paramagnetic resonance (EPR) spectra of WT Fe(III) RcoM-1, oxidized Fe(III) M104L, and as-isolated M105L exhibited narrow, rhombic low-spin signals typical of thiolate-bound hemes. In contrast, oxidized Fe(III) M105L and oxidized Fe(III) M104L/M105L revealed a broad, rhombic low-spin, six-coordinate signal indicative of replacement of the thiolate by a neutral ligand. Thus, we conclude that Met105 is important to the stability of the Fe(III) heme pocket during oxidation.

Cystathionine β-synthase (CBS) is the first and rate-limiting enzyme in the transsulfuration pathway, which is critical for the synthesis of cysteine from methionine in eukaryotes. CBS uses coenzyme pyridoxal 5′-phosphate (PLP) for catalysis, and S-adenosylmethionine regulates the activity of human CBS, but not yeast CBS. Human and fruit fly CBS contain heme; however, the role for heme is not clear. This paper reports biochemical and spectroscopic characterization of CBS from fruit fly Drosophila melanogaster (DmCBS) and the CO/NO gas binding reactions of DmCBS and human CBS. Like CBS enzymes from lower organisms (e.g., yeast), DmCBS is intrinsically highly active and is not regulated by AdoMet. The DmCBS heme coordination environment, the reactivity, and the accompanying effects on enzyme activity are similar to those of human CBS. The DmCBS heme bears histidine and cysteine axial ligands, and the enzyme becomes inactive when the cysteine ligand is replaced. The Fe(II) heme in DmCBS is less stable than that in human CBS, undergoing more facile reoxidation and ligand exchange. In both CBS proteins, the overall stability of the protein is correlated with the heme oxidation state. Human and DmCBS Fe(II) hemes react relatively slowly with CO and NO, and the rate of the CO binding reaction is faster at low pH than at high pH. Together, the results suggest that heme incorporation and AdoMet regulation in CBS are not correlated, possibly providing two independent means for regulating the enzyme.

Luminescent oligomers and polymers doped with silver(I) salts were used as optical sensors for ethylene and other gaseous small molecules. Films of poly(vinylphenylketone) (PVPK) or 1,4-bis(methylstyryl)benzene (BMSB) impregnated with AgBF4, AgSbF6, or AgB(C6F5)4 respond to ethylene exposures with a reversible emission quenching that is proportional to the pressure of the gas. Experiments with various analytes revealed that only gases capable of forming coordinate bonds with Ag(I) ions (i.e., ethylene, propylene, and ammonia) produced a sensing response. Comparison of the effects of ethylene and tetradeuterioethylene revealed that the emission quenching was due to enhanced vibrational relaxation. The Ag(I) ions are essential to the observed optical response. The oligomer/polymer support enhances the response characteristics of the impregnated salt by promoting separation of Ag(I) from its anion, a separation that improves accessibility of the Ag(I) ion to the gaseous analytes. Salts with large lattice energies, where the anion is not dissociated from Ag(I) in the matrix, fail to sensitize film responses. Photoluminescence experiments with Ag(I)-impregnated BMSB films established that the Ag(I) ions serve to communicate the analyte-binding signal to the support by altering the support-based emission. These experiments demonstrate a sensing paradigm where simultaneous coordination of Ag(I) ions to the support matrix and to a gaseous analyte enables the optical response.

Cystathionine β-synthase (CBS) is an essential pyridoxal 5′-phosphate (PLP)-dependent enzyme of the transsulfuration pathway that condenses serine with homocysteine to form cystathionine; intriguingly, human CBS also contains a heme b cofactor of unknown function. Herein we describe the enzymatic and spectroscopic properties of a disease-associated R266K hCBS variant, which has an altered hydrogen-bonding environment. The R266K hCBS contains a low-spin, six-coordinate Fe(III) heme bearing a His/Cys ligation motif, like that of WT hCBS; however, there is a geometric distortion that exists at the R266K heme. Using rR spectroscopy, we show that the Fe(III)-Cys(thiolate) bond is longer and weaker in R266K, as evidenced by an 8 cm–1 downshift in the ν(Fe–S) resonance. Presence of this longer and weaker Fe(III)–Cys(thiolate) bond is correlated with alteration of the fluorescence spectrum of the active PLP ketoenamine tautomer. Activity data demonstrate that, relative to WT, the R266K variant is more impaired in the alternative cysteine-synthesis reaction than in the canonical cystathionine-synthesis reaction. This diminished cysteine synthesis activity and a greater sensitivity to exogenous PLP correlate with the change in PLP environment. Fe–S(Cys) bond weakening causes a nearly 300-fold increase in the rate of ligand switching upon reduction of the R266K heme. Combined, these data demonstrate cross talk between the heme and PLP active sites, consistent with previous proposals, revealing that alteration of the Arg266–Cys52 interaction affects PLP-dependent activity and dramatically destabilizes the ferrous thiolate-ligated heme complex, underscoring the importance of this hydrogen-bonding residue pair.

The CO-responsive transcriptional regulator RcoM from Burkholderia xenovorans (BxRcoM) was recently identified as a Cys(thiolate)-ligated heme protein that undergoes a redox-mediated ligand switch; however, the Cys bound to the Fe(III) heme was not identified. To that end, we generated and purified three Cys-to-Ser variants of BxRcoM-2—C94S, C127S, and C130S—and examined their spectroscopic properties in order to identify the native Cys(thiolate) ligand. Electronic absorption, resonance Raman, and electron paramagnetic resonance (EPR) spectroscopies demonstrate that the C127S and C130S variants, like wild-type BxRcoM-2, bind a six-coordinate low-spin Fe(III) heme using a Cys/His ligation motif. In contrast, electronic absorption and resonance Raman spectra of the C94S variant are most consistent with a mixture of five-coordinate high-spin and six-coordinate low-spin Fe(III) heme, neither of which are ligated by a Cys(thiolate) ligand. The EPR spectrum of C94S is dominated by a large, axial high-spin Fe(III) signal, confirming that the native ligation motif is not maintained in this variant. Together, these data reveal that Cys94 is the distal Fe(III) heme ligand in BxRcoM-2; by sequence alignment, Cys94 is also implicated as the distal Fe(III) heme ligand in BxRcoM-1, another homologue found in the same organism.

Human cystathionine β-synthase (hCBS), a key enzyme in the trans-sulfuration pathway, catalyzes the condensation of serine with homocysteine to produce cystathionine. CBS from higher organisms is the only known protein that binds pyridoxal-5′-phosphate (PLP) and heme. Intriguingly, the function of the heme in hCBS has yet to be elucidated. Herein, we describe the characterization of a cobalt-substituted variant of hCBS (Co hCBS) in which CoPPIX replaces FePPIX (heme). Co(III) hCBS is a unique Co-substituted heme protein: the Co(III) ion is 6-coordinate, low-spin, diamagnetic, and bears a cysteine(thiolate) as one of its axial ligands. The peak positions and intensities of the electronic absorption and MCD spectra of Co(III) hCBS are distinct from those of previously Co-substituted heme proteins; TD-DFT calculations reveal that the unique features arise from the 6-coordinate Co bound axially by cysteine(thiolate) and a neutral donor, presumably histidine. Reactivity of Co(III) hCBS with HgCl2 is consistent with a loss of the cysteine(thiolate) ligand. Co(III) hCBS is slowly reduced to Co(II) hCBS, which contains a 5-coordinate, low-spin, S = 1/2 Co-porphyrin that does not retain the cysteine(thiolate) ligand; this form of Co(II) hCBS binds NO(g) but not CO(g). Co(II) hCBS is reoxidized in the air to form a new Co(III) form, which does not contain a cysteine(thiolate) ligand. Canonical and alternative CBS assays suggest that maintaining the native heme ligation motif of wild-type Fe hCBS (Cys/His) is essential in maintaining maximal activity in Co hCBS. Correlation between the coordination structures and enzyme activity in both native Fe and Co-substituted proteins implicates a structural role for the heme in CBS.

The recently synthesized sterically constrained copper(I) complex [Cu(dtbp)2]+ (1), where dtbp is 2,9-di-tert-butyl-1,10-phenanthroline, exhibits unique photophysical and reactivity properties. Complex 1 (λabs, 425 nm; ε, 3100 L M−1 cm−1; λemission, 599 nm) has the longest metal-to-ligand charge-transfer (MLCT) emission lifetime (τ, 3260 ns) and largest quantum yield (ϕ, 5.6%) of all [Cu(R2phen)2]+ complexes. Complex 1 also exhibits a large positive reduction potential for the [Cu2+(dtbp)2]|[Cu+(dtbp)2] couple (E1/2 = 0.70 V vs Fc+/0) and a large negative excited-state reduction potential for the [Cu2+(dtbp)(dtbp−•)]|[Cu2+(dtbp)2] couple (E1/2 = −1.66 V vs Fc+/0), indicating that this complex is a potent photoreductant in the excited state. The steric constraint imposed by the t-butyl substituents in 1 enables unusual ligand replacement reactivity. Either CH3CN or CO replaces one of the dtbp ligands, a reaction that is readily followed by loss of the unique emission signature of 1. Monodentate CH3CN binds to the copper(I) center with an affinity 2 orders of magnitude greater than that of the displaced dtbp, despite the fact that the displaced ligand is bidentate. CO-induced displacement of dtbp from 1 is reversible, but only in the presence of 1 equiv of unbound dtbp. The exceptionally strong donor ligand CH3NC displaces both dtbp ligands from 1. In contrast to the facile ligand displacement reactivity with good donor ligands, 1 does not react readily with O2, by either a ligand displacement or an oxidative pathway. Rather, O2 induces partial quenching of emission via an outer-sphere interaction with 1.

A series of silica-bound Cu(II) triazacyclononane materials was prepared to study the effect of linker length and surface hydrophobicity on the hydrolysis of phosphate esters. The general synthetic approach for these heterogeneous reagents was rhodium-catalyzed hydrosilation between an alkenyl-modified triazacyclononane and hydride-modified silica followed by metallation with a Cu(II) salt. Elemental analysis confirmed that organic functionalization of the silica gel was successful and provided an estimate of the surface concentration of triazacyclononane. EPR spectra were consistent with square pyramidal Cu(II), indicating that Cu(II) ions were bound to the immobilized macrocycles. The hydrolytic efficacies of these heterogeneous reagents were tested with bis(p-nitrophenyl)phosphate (BNPP) and diethyl 4-nitrophenyl phosphate (paraoxon). The agent that performed best was an octyl-linked, propanol-blocked material. This material had the most hydrophilic surface and the most accessible active site, achieving a rate maximum on par with the other materials, but in fewer cycles and without an induction period.

CooA is a heme-dependent CO-sensing transcription factor that has three observable heme coordination states. There is some evidence that each CooA heme state has a distinct protein conformation; the goal of this study was to characterize these conformations by measuring their structural stabilities through guanidine hydrochloride (GuHCl) denaturation. By studying the denaturation processes of the Fe(III) state of WT CooA and several variants, we were able to characterize independent unfolding processes for each domain of CooA. This information was used to compare the unfolding profiles of various CooA heme activation states [Fe(III), Fe(II), and Fe(II)-CO] to show that the heme coordination state changes the stability of the effector binding domain. A mechanism consistent with the data predicts that all CooA coordination states and variants undergo unfolding of the DNA-binding domain between 2 and 3 M GuHCl with a free energy of unfolding of ∼17 kJ/mol, while unfolding of the heme domain is variable and dependent on the heme coordination state. The findings support a model in which changes in heme ligation alter the structural stability of the heme domain and dimer interface but do not alter the stability of the DNA-binding domain. These studies provide evidence that the domains of transcription factors are modular and that allosteric signaling occurs through changes in the relative positions of the protein domains without affecting the structure of the DNA-binding region.

Nuclear receptors E75, which regulates development in Drosophila melanogaster, and Rev-erbβ, which regulates circadian rhythm in humans, bind heme within their ligand binding domains (LBD). The heme-bound ligand binding domains of E75 and Rev-erbβ were studied using electronic absorption, MCD, resonance Raman, and EPR spectroscopies. Both proteins undergo redox-dependent ligand switching and CO- and NO-induced ligand displacement. In the Fe(III) oxidation state, the nuclear receptor hemes are low spin and 6-coordinate with cysteine(thiolate) as one of the two axial heme ligands. The sixth ligand is a neutral donor, presumably histidine. When the heme is reduced to the Fe(II) oxidation state, the cysteine(thiolate) is replaced by a different neutral donor ligand, whose identity is not known. CO binds to the Fe(II) heme in both E75(LBD) and Rev-erbβ(LBD) opposite a sixth neutral ligand, plausibly the same histidine that served as the sixth ligand in the Fe(III) state. NO binds to the heme of both proteins; however, the NO−heme is 5-coordinate in E75 and 6-coordinate in Rev-erbβ. These nuclear receptors exhibit coordination characteristics that are similar to other known redox and gas sensors, suggesting that E75 and Rev-erbβ may function in heme-, redox-, or gas-regulated control of cellular function.

An intercalator-linked macrocycle3,6-bis(dimethylamino)-10-(6-[1,4,7-triazacyclononane]hexyl) acridinium bromide was synthesized, its copper(II) complex was prepared, and the DNA cleavage activity of this metal complex was compared to that of the intercalator-free (Cu[9]aneN3)2+ complex.

Spectroscopic characterization of the newly discovered heme-PAS domain sensor protein BxRcoM-2 reveals that this protein undergoes redox-dependent ligand switching and CO- and NO-induced ligand displacement. The aerobic bacterium Burkholderia xenovorans expresses two homologous heme-containing proteins that promote CO-dependent transcription in vivo. These regulators of CO metabolism, BxRcoM-1 and BxRcoM-2, are gas-responsive heme-PAS domain proteins like mammalian neuronal PAS domain protein 2 (NPAS2) and the direct oxygen sensor from Escherichia coli (EcDos). BxRcoM-2 was studied using electronic absorption, MCD, resonance Raman, and EPR spectroscopies. In the Fe(III) oxidation state, the heme is low-spin and six-coordinate with a cysteine(thiolate) as one of the two ligands. The sixth ligand is a histidine (His74), which is present in all states of the protein that were studied. Reduction to the Fe(II) oxidation state results in replacement of the cysteine(thiolate) with a neutral thioether ligand, Met104. CO and NO bind to the Fe(II)BxRcoM-2 heme opposite the histidine ligand. Thus, BxRcoM-2 employs coordination state changes similar to those known for CO-sensing CooA, with redox-dependent loss of a cysteine(thiolate) ligand and displacement of a relatively weakly bound axial ligand by the effector gas molecule. Like EcDos, the weakly bound axial ligand that is displaced is methionine.

CooA is a transcription factor from Rhodospirillum rubrum that is regulated by the binding of the small molecule effector, CO, to a heme moiety in the protein. The heme in CooA is axially ligated by two endogenous donors in the Fe(III) and Fe(II) states of the protein, and CO binding to the Fe(II) state results in replacement of the distal ligand. Reduction of the heme in the absence of CO results in a ligand switch on the proximal side, in which a cysteine thiolate in the Fe(III) state is replaced by a histidine in the Fe(II) state. Recently, a variant, termed RW CooA, was designed to respond to a new effector; Fe(II) RW CooA shows high specificity and induced DNA-binding activity in the presence of imidazole. Spectroscopic characterization of the imidazole adducts of RW CooA revealed that, unlike CO, imidazole binds to both Fe(III) RW CooA and Fe(II) RW CooA. The spectral characteristics are consistent with normal function of the redox-mediated ligand switch; Fe(III)–imidazole RW CooA bears a thiolate ligand and Fe(II)–imidazole RW CooA bears a neutral donor ligand. Since the effector binds to both redox states, RW CooA was used to probe the role of the redox-mediated ligand switch in the CooA activation mechanism. Functional studies of Fe(III)–imidazole and Fe(II)–imidazole ligated RW CooA demonstrate that only the Fe(II)–imidazole form is active for DNA binding. Thus, the ligand switch is essential for the activating conformational change and may prevent aberrant activation of CooA by other neutral diatomic molecules.

CooA, the CO-sensing heme protein from Rhodospirillum rubrum, regulates the expression of genes that encode a CO-oxidation system, allowing R. rubrum to use CO as a sole energy source. To better understand the gas-sensing regulation mechanism used by R. rubrum CooA and its homologs in other organisms, we characterized spectroscopically and functionally the Fe(II), Fe(II)-NO, and Fe(II)-CO forms of CooA from Carboxydothermus hydrogenoformans. Surprisingly, and unlike R. rubrum CooA, C. hydrogenoformans CooA binds NO to form a six-coordinate Fe(II)-NO heme that is active for DNA binding in vitro and in vivo. In contrast, R. rubrum CooA, which is exquisitely specific for CO, forms a five-coordinate Fe(II)-NO adduct that is inactive for DNA binding. Based on analyses of protein variants and temperature studies, NO-dependent DNA binding by C. hydrogenoformans CooA is proposed to result from a greater apparent stability of the six-coordinate Fe(II)-NO adduct at room temperature. Results from the present study strengthen the proposal that CO specificity in the CooA activation mechanism is based on the requirement for a small, neutral distal ligand, which in turn affects the relative positioning of the ligand-bound heme.

Copper(II) triazacyclononane, a catalyst for the hydrolysis of phosphate esters, has been covalently immobilized onto a silica surface and the resulting compound is a robust material that can effect heterogeneous phosphodiester hydrolysis.

The syntheses and characterizations by X-ray crystallography, EPR, and electronic absorption spectroscopy are reported for [Cu([9]aneN3)2][CF3SO3]2·H2O (1) [Cu([9]aneN2O)2][BF4]2 (2), and [Cu([9]aneN2O)2][NO3]2 (3). The dynamic Jahn–Teller distortion present in the Cu([9]aneN3)2 2+ cation is removed upon replacement of one nitrogen donor with oxygen. The pseudo-octahedral structures of 2 and 3, determined crystallographically, exhibit a strong tetragonal distortion with the two oxygen atoms in the elongated axial positions. In contrast, crystallographic characterizations of a number of Cu([9]aneN3)2 2+ salts reveal that the octahedral-like coordination about the Cu(II) is dependent on crystal packing forces, and the degree of tetragonal distortion varies with the identity of the counter ion. A room temperature powder EPR spectrum of [Cu([9]aneN2O)2]Br2 exhibits a static Jahn–Teller distortion while that of [Cu([9]aneN3)2][CF3SO3]2 is dynamically averaged. Solution EPR and electronic absorption spectra of [Cu([9]aneN2O)2][CF3SO3]2 indicate a strong interaction between the equatorial nitrogen atoms and the Cu(II) as evidenced by the observation of nitrogen hyperfine splitting in gx and a shift of the ligand-field absorption to higher energy. The absence of a dynamic Jahn–Teller effect in the presence of the [9]aneN2O ligand correlates with a lowered reactivity for phosphodiester hydrolysis, suggesting that ligand fluxionality may be important in accessing the transition state in copper-promoted hydrolysis.

An intercalator-linked macrocycle3,6-bis(dimethylamino)-10-(6-[1,4,7-triazacyclononane]hexyl) acridinium bromide was synthesized, its copper(II) complex was prepared, and the DNA cleavage activity of this metal complex was compared to that of the intercalator-free (Cu[9]aneN3)2+ complex.

A series of silica-bound Cu(II) triazacyclononane materials was prepared to study the effect of linker length and surface hydrophobicity on the hydrolysis of phosphate esters. The general synthetic approach for these heterogeneous reagents was rhodium-catalyzed hydrosilation between an alkenyl-modified triazacyclononane and hydride-modified silica followed by metallation with a Cu(II) salt. Elemental analysis confirmed that organic functionalization of the silica gel was successful and provided an estimate of the surface concentration of triazacyclononane. EPR spectra were consistent with square pyramidal Cu(II), indicating that Cu(II) ions were bound to the immobilized macrocycles. The hydrolytic efficacies of these heterogeneous reagents were tested with bis(p-nitrophenyl)phosphate (BNPP) and diethyl 4-nitrophenyl phosphate (paraoxon). The agent that performed best was an octyl-linked, propanol-blocked material. This material had the most hydrophilic surface and the most accessible active site, achieving a rate maximum on par with the other materials, but in fewer cycles and without an induction period.