Proton coupling to [4Fe-4S](2+/+) and [4Fe-4Se](2+/+) oxidation and reduction in a designed protein

The coupling of a single proton to [4Fe-4S]2+/+ oxidation/reduction in a de novo designed iron-sulfur protein maquette is presented. The reduced state pKared is 9.3, and the oxidized state pKaox is <6.5. The reduced state pKared shifts to 8.3 upon incorporation of a [4Fe-4Se]2+/+ cluster, implicating the cluster itself or its primary coordination sphere as the proton-coupling site.     

Electrospray mass spectrometry of

There has been a substantial growth in the application of mass spectrometry (MS) methods for the analysis of inorganic materials, due to the inherent sensitivity of mass spectrometry ionization to the specific composition and structure of the analyzed materials. To date, few mass spectrometry studies have focused on metal-chalcogenide materials, an important class of semiconductor materials at the nanoscale, that exhibit interesting optical and electronic properties as a function of size. In this study, we report the application of a correlated electrospray mass spectrometry (ESMS) study between negative-ion and positive-ion mode under low-cone voltage to probe size, composition, and stability of metal-chalcogenide materials at the <1 nm scale. This correlation approach provides insight into the ionization behavior and thermodynamic stability of clusters in the <1.0 nm size domain of the form [Zn4(SPh)10][Me4N]2, [Cd4(SPh)10][Me4N]2, [E4Zn10(SPh)16][Me4N]4, [E4Cd10(SPh)16][Me4N]4 (E = S, Se). It is demonstrated that application of low-cone voltage ESMS can be a useful technique for the rapid analysis of intact solid state nanomaterials when both negative and positive ionic modes are analyzed, with a potential for extrapolation to other classes of nanoscale materials.     

Analysis of single nucleotide polymorphism sites in exon 4 of the p53 gene using high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry

Three groups of four oligonucleotides with special single nucleotide polymorphisms (SNP) sites in exon 4 of the p53 gene were analyzed with ion-pair reversed-phase high-performance liquid chromatography electrospray ionization mass spectrometry tandem mass spectrometry. The retention order of four oligonucleotides with SNPs was C < G < A < T, regardless of whether the polymorphisms were at the 3' end, the 5' end, or the middle of the oligonucleotides. The charge state of the molecular ion affects the MS/MS spectra of the oligonucleotides. SNPs at the 3' end can be easily identified from the fragmentation pattern of the 2- charge state, but not from the 3- charge state, especially from the w1 fragment. The single base may be taken as the symbol of the 5' end SNP site derived from [M3H]2, but not from the [M3H]2 charge state. The oligonucleotides with SNPs in the middle were also determined from the [M2H]2 precursor ion.     

Probing the intrinsic electronic structure of the cubane [4Fe-4S] cluster: nature's favorite cluster for electron transfer and storage

The cubane [4Fe-4S] is the most common multinuclear metal center in nature for electron transfer and storage. Using electrospray, we produced a series of gaseous doubly charged cubane-type complexes, [Fe4S4L4]2- (L = -SC2H5, -SH, -Cl, -Br, -I) and the Se-analogues [Fe4Se4L4]2- (L = -SC2H5, -Cl), and probed their electronic structures with photoelectron spectroscopy and density functional calculations. The photoelectron spectral features are similar among all the seven species investigated, revealing a weak threshold feature due to the minority spins on the Fe centers and confirming the low-spin two-layer model for the [4Fe-4S](2+) core and its "inverted level scheme". The measured adiabatic detachment energies, which are sensitive to the terminal ligand substitution, provide the intrinsic oxidation potentials of the [Fe4S4L4]2- complexes. The calculations revealed a simple correlation between the electron donor property of the terminal thiolate as well as the bridging sulfide with the variation of the intrinsic redox potentials. Our data provide intrinsic electronic structure information of the [4Fe-4S] cluster and the molecular basis for understanding the protein and solvent effects on the redox properties of the [4Fe-4S] active sites.     

A [4Fe-4S] cluster dimer bridged by bis(2,2':6',2'-terpyridine-4'-thiolato)iron(II)

The use of 2,2':6',2'-terpyridine-4'-thiol (tpySH) was explored as a bridging ligand for the formation of stable assemblies containing both [4Fe-4S] clusters and single metal ions. Reaction of tpySH (2 equiv) with (NH4)2Fe(SO4)(2).6H2O generated the homoleptic complex [Fe(tpySH)2](2+), which was isolated as its PF6(-) salt. The compound could be fully deprotonated to yield neutral [Fe(tpyS)2], and the absorption spectrum is highly dependent on the protonation state. Reaction of [Fe(tpySH)2](PF6)2 with the new 3:1 site-differentiated cluster (n-Bu4N)2[Fe4S4(TriS)(SEt)] yielded the first metal-bridged [4Fe-4S] cluster dimer, (n-Bu4N)2[{Fe4S4(TriS)(mu-Stpy)}2Fe]. Electrochemical studies indicate that the [4Fe-4S] clusters in the dimer act as independent redox units, while UV-vis spectroscopy provides strong evidence for a thioquinonoid electron distribution in the bridging tpyS(-) ligand. TpySH thus acts as a directional bridging ligand between [4Fe-4S] clusters and single metal ions, thereby opening the way to the synthesis of larger, more complex assemblies.     

Noncovalent complexes of APS reductase from <Emphasis Type="Italic">M. tuberculosis</Emphasis>: Delineating a mechanistic model using ESI-FTICR MS

ESI-FTICR MS was utilized to characterize a 4Fe-4S containing protein Mycobacterium tuberculosis APS reductase. This enzyme catalyzes the reduction of APS to sulfite and AMP with reducing equivalents from the protein cofactor, thioredoxin. Under nondenaturing conditions, a distribution of the apoprotein, a 2Fe-2S intermediate, and the 4Fe-4S holoprotein were observed. Accurate mass measurements indicated an oxidation state of +2 for the 4Fe-4S cluster, with no disulfide bond in the holoenzyme. Gas-phase stability of the 4Fe-4S cluster was investigated using both in-source and collision induced dissociation, which provided information regarding the relative gas-phase binding strength of iron towards protein ligands and inorganic sulfides. Noncovalent complexes of the holoprotein with several ligands, including APS, thioredoxin, and AMP, were also investigated. Calculated values of dissociation constants for the complexes indicate that AMP binds with a higher affinity to the enzyme intermediate than to the free enzyme. The implications of the binary and ternary complexes observed by gas-phase noncovalent interactions in the mechanism of APS reduction are discussed.     

Electrospray ionization ion trap mass spectrometry of a tetrahedral supramolecular Ti4L4 cluster

The analysis of self-assembled supramolecular clusters held together by metal-ligand interactions is a relatively new area in mass spectrometry. These complexes may have molecular weights exceeding several kDa, are often highly charged and their composition is most sensitive to their chemical environment. Electrospray ionization appears to be the ionization technique of choice for their mass spectral characterization. The analysis (positive and negative ion detection mode) of the prototype compound [Ti₄L₄]^8? (L = a catechol-based tris-bidentate ligand; MW of cluster = 2293 u) using a Paul trap mass analyzer is reported. The combination of electrospray ionization and high resolution ion trap technology is a powerful tool which provides the unambiguous solution state characterization of this supramolecular cluster. The results are correlated with the known solid state structure of the cluster and reactions previously reported for mononuclear Ti(IV) catecholates.     

Carbon monoxide induced decomposition of the active site [Ni-4Fe-5S] cluster of CO dehydrogenase

During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, and Moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni-4Fe-5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII(Ch)) at 1.6 A resolution contains a characteristic mu(2)-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni-4Fe-4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 A and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 A resolution, respectively, do not contain the mu(2)-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni-4Fe-4S] cluster is composed of a cubane [Ni-3Fe-4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni-4Fe-4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni-4Fe-5S] cluster C of CODHII(Ch). In addition, the latter was converted into a [Ni-4Fe-4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII(Ch) and the functionality of the protein. We have determined the CO oxidation activity of CODHII(Ch) under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N(2) or CO, and solved the corresponding structures at 1.1 to 1.6 A resolutions. Fully active CODHII(Ch) obtained after incubation of the enzyme with dithionite under N(2) revealed the [Ni-4Fe-5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII(Ch) with a CO-reduced [Ni-4Fe-5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni-4Fe-4S] cluster, which did not contain a mu(2)-S. These data suggest that the [Ni-4Fe-4S] cluster of CODHII(Ch) is an inactivated decomposition product originating from the [Ni-4Fe-5S] cluster.     

Sequential oxidation of the cubane [4Fe--4S] cluster from [4Fe--4S](-) to [4Fe--4S](3+) in Fe(4)S(4)L(n)(-) complexes

Gaseous Fe(4)S(n)(-) (n = 4-6) clusters and synthetic analogue complexes, Fe(4)S(4)L(n)(-) (L = Cl, Br, I; n = 1-4), were produced by laser vaporization of a solid Fe/S target and electrospray from solution samples, respectively, and their electronic structures were probed by photoelectron spectroscopy. Low binding energy features derived from minority-spin Fe 3d electrons were clearly distinguished from S-derived bands. We showed that the electronic structure of the simplest Fe(4)S(4)(-) cubane cluster can be described by the two-layer spin-coupling model previously developed for the [4Fe] cubane analogues. The photoelectron data revealed that each extra S atom in Fe(4)S(5)(-) and Fe(4)S(6)(-) removes two minority-spin Fe 3d electrons from the [4Fe--4S] cubane core and each halogen ligand removes one Fe 3d electron from the cubane core in the Fe(4)S(4)L(n)(-) complexes, clearly revealing a behavior of sequential oxidation of the cubane over five formal oxidation states: [4Fe--4S](-) --> [4Fe--4S](0) --> [4Fe--4S](+) --> [4Fe-4S](2+) --> [4Fe-4S](3+). The current work shows the electron-storage capability of the [4Fe--4S] cubane, contributes to the understanding of its electronic structure, and further demonstrates the robustness of the cubane as a structural unit and electron-transfer center.     

Laser desorption mass spectrometry of squaric acid and its salts

The laser desorption mass spectrometry of the oxocarbon squaric acid (3,4-dihydroxy-3-cyclobutene-1,2-dione) and its salts of the form A₂C₄O₄ (A = cation) is described. Both positive and negative ion spectra were obtained. The positive ion spectrum of the acid is characterized by an ion corresponding to loss of CO from [M + H]⁺. The negative ion spectrum shows an intense [M ? H]^? peak in addition to a dimer species. The alkali salt spectra contain [M + A]⁺ in the positive mode and [M ? A]^? and an intense [C₄HO₄]^? in the negative mode. The smaller alkali salts also have an [M + H]⁺ adduct ion. Unlike the alkali squarates, the ammonium salt shows ions corresponding to losses of neutrals from the molecular adduct in the positive ion spectrum and a dimer species in the negative ion spectrum. Molecular weight information was obtained in all cases. A (bis) dicyanomethylene derivative of potassium squarate was also studied. Some field desorption mass spectrometry results are presented for comparison.     

Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation

The radical SAM (RS) proteins RlmN and Cfr catalyze methylation of carbons 2 and 8, respectively, of adenosine 2503 in 23S rRNA. Both reactions are similar in scope, entailing the synthesis of a methyl group partially derived from S-adenosylmethionine (SAM) onto electrophilic sp(2)-hybridized carbon atoms via the intermediacy of a protein S-methylcysteinyl (mCys) residue. Both proteins contain five conserved Cys residues, each required for turnover. Three cysteines lie in a canonical RS CxxxCxxC motif and coordinate a [4Fe-4S]-cluster cofactor; the remaining two are at opposite ends of the polypeptide. Here we show that each protein contains only the one "radical SAM" [4Fe-4S] cluster and the two remaining conserved cysteines do not coordinate additional iron-containing species. In addition, we show that, while wild-type RlmN bears the C355 mCys residue in its as-isolated state, RlmN that is either engineered to lack the [4Fe-4S] cluster by substitution of the coordinating cysteines or isolated from Escherichia coli cultured under iron-limiting conditions does not bear a C355 mCys residue. Reconstitution of the [4Fe-4S] cluster on wild-type apo RlmN followed by addition of SAM results in rapid production of S-adenosylhomocysteine (SAH) and the mCys residue, while treatment of apo RlmN with SAM affords no observable reaction. These results indicate that in Cfr and RlmN, SAM bound to the unique iron of the [4Fe-4S] cluster displays two reactivities. It serves to methylate C355 of RlmN (C338 of Cfr), or to generate the 5'-deoxyadenosyl 5'-radical, required for substrate-dependent methyl synthase activity.     

Synthesis of the P-cluster inorganic core of nitrogenases

The [8Fe-7S] core of the P-clusters in nitrogenases is unique among the known [Fe-S] clusters which are essential to electron-transfer processes in nature. The [8Fe-7S] cluster has been thought unstable and to exist only in protein environments. We found that this unusual [8Fe-7S] structure can be self-assembled from the reaction of Fe(II) bis-amide, tetramethylthiourea, 2,4,6-triisopropylbenzenethiol, and elemental sulfur in a specific mole ratio. The structure of the complex isolated therefrom closely resembles that of the reduced form (PN) of the P-clusters, while the 6Fe(II)2Fe(III) oxidation state was manifested by the M?ssbauer study.     

Determination of the collisionally activated dissociation of a substituted indole by orthogonal acceleration quadrupole time-of-flight mass spectrometry

The use of orthogonal acceleration quadrupole time-of-flight (Q-TOF) mass spectrometry to determine the collisionally activated dissociation (CAD) of a test compound 1-(3-[5-[1,2,4-triazol-4-yl]-1H-indol-3-yl]propyl)-4-(2-[3-fluorophenyl]ethyl)piperazine is described. At unit-mass resolution the identity of many ions is ambiguous because of the complexity of the resulting product ion spectrum. Using the high resolution capabilities of the Q-TOF instrument, exact masses for each fragment were determined. These data were used to infer molecular formulas for each fragment through software interpretation and, by further applying chemical intuition, the majority of ions were fully assigned. Additionally, by utilizing in-source fragmentation at high cone voltage, analyses of second-generation products allowed derivation of a consistent sequential fragmentation pathway. This study clearly demonstrates the power of Q-TOF mass spectrometry to elucidate complex product ion spectra.     

Mechanism on two-electron oxidation of ubiquinol at the Qp site in cytochrome bc1 complex: B3LYP study with broken symmetry

The molecular and electronic structures of the Rieske iron-sulfur [2Fe-2S] cluster with an imidazolate and imidazole were investigated by using usual unrestricted and broken symmetry B3LYP methods for the highest and lowest spin states, respectively. The electronic structures of the lowest spin states were determined by the spin contaminations and natural orbital analyses. It was shown that the spin contamination presents the number of pairs of the antiferromagnetic spin couplings. The oxidation mechanism of the ubquinol at the Q(p) site of the cytochrome bc(1) complex was also examined by the broken symmetry B3LYP methods. In the [2Fe-2S] clusters with an imidazolate, the oxidized and lowest spin state, [(Imz(-))FeS](ox)LS, was lowest in energy among four possible states, consistent with experimental observations. In the examination of the mechanism of the ubquinol oxidation, it was confirmed that the ubiquinol docks between the imidazolate of [2Fe-2S] clusters and Glu272(-) of cytochrome b by the hydrogen bonds before the oxidation proceeds, consistent with the experimental proposals. Our results support a "Glu272-first" mechanism that Glu272 serves as an acceptor of the first proton from the ubiquinol and subsequently the proton-coupled electron transfer (PCET) occurs from the ubisemiquinone anion to the Rieske iron-sulfur [2Fe-2S] cluster.     

Characterization of the O-4 phosphorylated and O-5 substituted Kdo reducing end group and sequencing of the core oligosaccharide of Aeromonas salmonicida ssp salmonicida lipopolysaccharide using tandem mass spectrometry

The molecular structure of the wild strain of the lipopolysaccharide core of Aeromonas salmonicida, ssp salmonicida has been sequenced using tandem mass spectrometry. The core oligosaccharide was determined to contain an O-4 phosphorylated and O-5 substituted Kdo reducing group, and its structure is proposed as the follows: [structure: see text] After the core oligosaccharide of LPS was released from the lipid A portion by conventional treatment with 1% acetic acid, we demonstrated the existence of a homogeneous mixture composed mainly of the native core oligosaccharide containing the Kdo with its O-4 phosphate group intact, and a degraded core oligosaccharide mixture, which eliminated the O-4 phosphate group with extreme facility. The precise molecular structure and glycone sequence of the homogeneous mixture of phosphorylated and dephosphorylated core oligosaccharides was determined by electrospray ionization (ESI) mass spectrometry and tandem mass spectrometric analysis. CID-MS/MS of the homogeneous mixture of permethylated core oligosaccharides afforded a series of diagnostic product ions which confirmed the established sequence of the glycones to be determined. Matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry reconfirmed the molecular structure of the dephosphorylated homogeneous permethylated mixture of the core oligosaccharides containing the diastereomeric 4,8- and 4,7-anhydro-alpha-keto acids.     

Structural redox control in a 7Fe ferredoxin isolated from Desulfovibrio alaskensis

The redox behaviour of a ferredoxin (Fd) from Desulfovibrio alaskensis was characterized by electrochemistry. The protein was isolated and purified, and showed to be a tetramer containing one [3Fe-4S] and one [4Fe-4S] centre. This ferredoxin has high homology with FdI from Desulfovibrio vulgaris Miyazaki and Hildenborough and FdIII from Desulfovibrio africanus. From differential pulse voltammetry the following signals were identified: [3Fe-4S](+1/0) (E(0')=-158±5mV); [4Fe-4S](+2/+1) (E(0')=-474±5mV) and [3Fe-4S](0/-2) (E(0')=-660±5mV). The effect of pH on these signals showed that the reduced [3Fe-4S](0) cluster has a pK'(red)(')=5.1±0.1, the [4Fe-4S](+2/+1) centre is pH independent, and the [3Fe-4S](0/-2) reduction is accompanied by the binding of two protons. The ability of the [3Fe-4S](0) cluster to be converted into a new [4Fe-4S] cluster was proven. The redox potential of the original [4Fe-4S] centre showed to be dependent on the formation of the new [4Fe-4S] centre, which results in a positive shift (ca. 70mV) of the redox potential of the original centre. Being most [Fe-S] proteins involved in electron transport processes, the electrochemical characterization of their clusters is essential to understand their biological function. Complementary EPR studies were performed.     

Geometric and electrostatic study of the [4Fe-4S] cluster of adenosine-5'-phosphosulfate reductase from broken symmetry density functional calculations and extended X-ray absorption fine structure spectroscopy

Adenosine-5'-phosphosulfate reductase (APSR) is an iron-sulfur protein that catalyzes the reduction of adenosine-5'-phosphosulfate (APS) to sulfite. APSR coordinates to a [4Fe-4S] cluster via a conserved CC-X(~80)-CXXC motif, and the cluster is essential for catalysis. Despite extensive functional, structural, and spectroscopic studies, the exact role of the iron-sulfur cluster in APS reduction remains unknown. To gain an understanding into the role of the cluster, density functional theory (DFT) analysis and extended X-ray fine structure spectroscopy (EXAFS) have been performed to reveal insights into the coordination, geometry, and electrostatics of the [4Fe-4S] cluster. X-ray absorption near-edge structure (XANES) data confirms that the cluster is in the [4Fe-4S](2+) state in both native and substrate-bound APSR while EXAFS data recorded at ~0.1 ? resolution indicates that there is no significant change in the structure of the [4Fe-4S] cluster between the native and substrate-bound forms of the protein. On the other hand, DFT calculations provide an insight into the subtle differences between the geometry of the cluster in the native and APS-bound forms of APSR. A comparison between models with and without the tandem cysteine pair coordination of the cluster suggests a role for the unique coordination in facilitating a compact geometric structure and "fine-tuning" the electronic structure to prevent reduction of the cluster. Further, calculations using models in which residue Lys144 is mutated to Ala confirm the finding that Lys144 serves as a crucial link in the interactions involving the [4Fe-4S] cluster and APS.     

Study of the oxidation dynamics of ethyl cysteinate dimer in solution by ultra‐performance liquid chromatography with tandem mass spectrometry

Diaminodithiol (N₂S₂)‐type compounds readily oxidize to produce disulfides. We found that some ligands failed to produce a prospective protonated molecular ion peak but gave a peak of [M–2+H]⁺, whereas others produced both [M+H]⁺ and [M–2+H]⁺ peaks in electrospray ionization mass spectra. In this study, an important N₂S₂ ligand, the ethyl cysteinate dimer (ECD), was investigated with high‐resolution accurate mass measurements and tandem mass spectrometric analysis. The elemental compositions of ECD and its oxidized product were analyzed. The oxidation of ECD was confirmed. An ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) method in multiple reaction monitoring mode was developed, and ECD and its oxidized product were quantitated in solution. The dynamic oxidation process of ECD in solution was studied in detail. The full time course of the decrease in ECD and the increase in its oxide was observed; the oxidation procedure followed first‐order kinetics, and the half‐life time of ECD was 51 min. Copyright © 2009 John Wiley & Sons, Ltd.     

Electrochemical properties of capillary electrophoresis-nanoelectrospray mass spectrometry

Electrochemical properties are inherent to the techniques of electrophoresis and electrospray ionization. Interfacing capillary zone electrophoresis (CZE) with electrospray mass spectrometry (ESMS) can lead to the observation of oxidized species generated as a result of the electrochemical nature of this coupling. Using a nanoelectrospray (nES) interface combined with CZE, controlled chemical oxidation of peptides is demonstrated. The electrolysis of water is used to explain the origin of the chemically oxidized species and this is confirmed using experiments with ¹⁸O labeled water. Identification of the oxidized residues was possible using tandem mass spectrometry to sequence the modified peptides. Methionine was found to be the most readily oxidized residue, followed by aromatic amino acids. Surprisingly, oxidation of aliphatic residues (leucine) was also observed. Addition of a reducing agent to the CZE buffer was found to reduce, but not eliminate, the extent of oxidation. The electrochemical generation of protons at the electrosprayer was used to assist in the analysis of monophosphate nucleotides. Nucleotides were separated as anions followed by detection as [M + H]⁺ ions.