Can Co(II) or Cd(II) substitute for Zn(II) in zinc fingers?

Zinc finger domains consist of sequences of amino acids containing cysteine and histidine residues tetrahedrally coordinated to a zinc ion. The role of zinc in a DNA binding finger was considered purely structural due to the absence of redox chemistry in zinc. However, whether other metals e.g. Co(II) or Cd(II) can substitute Zn(II) is not settled. For an answer the detailed interaction of Co(II) and Cd(II) with cysteine methylester and histidine methylester has been investigated as a model for the zinc core in zinc fingers. The study was extended to different temperatures to evaluate the thermodynamic parameters associated with these interactions. The results suggest that zinc has a unique role.     

Identification of redox sensitive thiols of protein disulfide isomerase using isotope coded affinity technology and mass spectrometry

Regulation of the redox state of protein disulfide isomerase (PDI) is critical for its various catalytic functions. Here we describe a procedure utilizing isotope-coded affinity tag (ICAT) technology and mass spectrometry that quantitates relative changes in the dynamic thiol and disulfide states of human PDI. Human PDI contains six cysteine residues, four present in two active sites within the a and a' domains, and two present in the b' domain. ICAT labeling of human PDI indicates a difference between the redox state of the two active sites. Furthermore, under auto-oxidation conditions an approximately 80% decrease in available thiols within the a domain was detected. Surprisingly, the redox state of one of the two cysteines, Cys-295, within the b' domain was altered between the fully reduced and the auto-oxidized state of PDI while the other b' domain cysteine remained fully reduced. An interesting mono- and dioxidation modification of an invariable tryptophan residue, Trp-35, within the active site was also mapped by tandem mass spectrometry. Our findings indicate that ICAT methodology in conjunction with mass spectrometry represents a powerful tool to monitor changes in the redox state of individual cysteine residues within PDI under various conditions.     

Potentiometric detection of thiols: a mechanistic evaluation of quinone–thiol interactions

The potentiometric response resulting from the sequential addition of reduced thiols to a benzoquinone/hydroquinone couple has been investigated. The system has been shown to offer a simple route through which thiol could be quantified but a discrepancy in the reaction stoichiometry between glutathione and cysteine was observed. A mechanistic appraisal of the quinone–thiol interactions has been conducted and the proposed reaction pathways corroborated by spectroscopic analysis.     

Spectroscopy and electronic structure of electron deficient zinc phthalocyanines

The effect of introduction of perfluoro alkyl groups into phthalocyanines, as evidenced by the spectroscopic properties of 1,4,8,11,15,18,22,25-octa-fluoro-2,3,9,10,16,17,23,24-octa-perfluoro isopropyl zinc phthalocyanine, ZnF(64)Pc(-2) and its ring-reduced radical anion species, [ZnF(64)Pc(-3)](-), are reported. A combination of UV-visible absorption and magnetic circular dichroism (MCD) spectroscopy, ESI and MALDI-TOF mass spectrometry, cyclic and differential pulse voltammetry, and complete theoretical calculations using INDO/S and DFT techniques reveals that the substitution of all sixteen hydrogen atoms in protio ZnPc(-2) by eight F and eight i-C(3)F(7) groups red shifts the Q and pi --> pi transitions and narrows the HOMO-LUMO gap while simultaneously preventing ring photooxidation and stabilizing the radical anion. The [ZnF(64)Pc(-3)](-) species, which is in equilibrium in solution with the neutral complex when a reducing agent is present, is unusually stable. The above effects are attributed to the strong electron withdrawing properties of the peripheral substituents, which render ZnF(64)Pc extremely electron deficient.     

Investigation of the interaction between arsenic species and thiols via electrospray ionization tandem mass spectrometry

Arsenic species have been known to participate in a number of chemical and biological reactions, including oxidation-reduction reactions, acid-base reactions, covalent interactions, and methylation-demethylation reactions because of the element's multiple and interconvertible oxidation states. Little is known about the structure or bonding behavior between arsenic species and thiolcontaining biomolecules. Therefore, a better understanding of the bonding behavior and detailed information on the molecular structure for arsenic-thiol complexes is needed. As a result, we have investigated the interaction between arsenic species (arsenate (As^V), arsenite (As^III), monomethylarsonic acid (MMA^V), and dimethylarsinic acid (DMA^V)) with biomolecules containing thiol groups (glutathione and cysteine) by electrospray ionization mass spectrometry (ESI-MS). These compounds were dissolved in methanol/water solution and introduced into the MS instrument in order to elucidate the direct bonding behavior of thiol group of biomolecules with arsenic species. In addition, further detailed structural information on this complex was obtained by collision-induced dissociation (CID) measurements.In each mass spectrum for mixture solutions between arsenic species and thiol compounds, various peaks such as protonated arsenic-thiol complexes, protonated noncomplexed thiol compounds, sodium bound cluster ions, and proton bound cluster ions were observed. In these mass spectra, the arsenic complexes were formed by interaction with thiol groups on the cysteine residues. These arsenic-thiol complexes produced a variety of fragment ions by cleavage of chemical bonds, and by interaction of other binding site on thiol compounds in tandem mass spectrometry experiments.     

Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function

Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.     

Site-specific amide hydrogen/deuterium exchange in E. coli thioredoxins measured by electrospray ionization mass spectrometry

Mass spectrometry as an analytical tool to study protein folding and structure by hydrogen/deuterium exchange is a relatively new approach. In this study, site-specific amide deuterium content was measured in oxidized and reduced E. coli thioredoxins by using the b(n) ions in electrospray ionization CID MS/MS experiments after 20-s incubation in D(2)O phosphate-buffered solution (pH 5.7). The deuterium levels correlated well with reported NMR-determined H/D exchange rate constants. The deuterium measured by y(n) ions, however, showed much less reliable correlation with rate exchange data. In general, residues in alpha helices and beta sheets, when measured by b(n) ions, showed low incorporation of deuterium while loops and turns had high deuterium levels. Most amide sites in the two protein forms showed similar deuterium levels consistent with the expected similarity of their structures, but there were some differences. The turn consisting of residues 18-22 in particular showed more variability in deuterium content consistent with reported structural differences in the two forms. The deuterium uptake by thioredoxins alkylated at Cys-32 by S-(2-chloroethyl)glutathione and S-(2-chloroethyl)cysteine, in peptides 1-24 and 45-58, was similar to that observed for oxidized and reduced thioredoxins, but several residues, particularly Leu-53 and Thr-54, showed slightly elevated deuterium levels, suggesting that structural changes had occurred from alkylation of the protein at Cys-32. It is concluded that b(n) ions are reliable for determining the extent of site-specific amide hydrogen isotope exchange and that mass spectrometry is useful as a complementary technique to NMR and other analytical methods for probing regional structural characteristics of proteins.     

Contribution of individual zinc ligands to metal binding and peptide folding of zinc finger peptides

Little is known about the contribution of individual zinc-ligating amino acid residues for coupling between zinc binding and protein folding in zinc finger domains. To understand such roles of each zinc ligand, four zinc finger mutant peptides corresponding to the second zinc finger domain of Sp1 were synthesized. In the mutant peptides, glycine was substituted for one of four zinc ligands. Their metal binding and folding properties were spectroscopically characterized and compared to those of the native zinc finger peptide. In particular, the electronic charge-transfer and d-d bands of the Co(II)-substituted peptide complexes were used to examine the metal coordination number and geometry. Fluorescence emission studies revealed that the mutant peptides are capable of binding zinc despite removing one ligand. Circular dichroism results clearly showed the induction of an alpha-helix by zinc binding. In addition, the structures of certain mutant zinc finger peptides were simulated by molecular dynamics calculation. The information indicates that His23 and the hydrophobic core formed between the alpha-helix and the beta-sheet play an essential role in alpha-helix induction. This report demonstrates that each ligand does not contribute equally to alpha-helix formation and coordination geometry in the zinc finger peptide.     

Matrix-assisted laser desorption/ionization mass spectra reflect solution-phase zinc finger peptide complexation

The complexation between an 18-residue zinc finger peptide of CCHC type (CCHC=Cys-X₂-Cys-X₄-His-X₄-Cys, X=variable amino acid) from the gag protein p55 of human immunodeficiency virus type 1 (HIV-1) and various transition metal ions was studied by means of circular dichroism spectroscopy and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). A correlation between the complexation behavior in solution and in MALDI-MS could be established. It was shown that MALDI-MS is a fast method suitable for studying metal binding properties of zinc finger complexes.     

On-line electrochemical tagging of cysteines in proteins during nanospray

An electrochemical modification of free cysteine residues is studied and characterized by means of quinone addition. Taking advantage of the electrolytic nature of electrospray interfaces (ESI), an electrochemical tagging is performed prior to mass spectrometry (MS) analyses. The tagging has been studied by MS and different mechanisms, involving electrochemical and/or chemical steps, could be characterized. It is demonstrated that the present nanospray is a very efficient tool to obtain cysteine modification. Using the high voltage electrode of the nanospray interface to perform protein specific tagging is a novel method that can be associated to analytical or preparative techniques, such as digestion of proteins or capillary electrophoresis, for post-column modifications.     

Direct Zinc Finger Protein Persulfidation by H2S Is Facilitated by Zn2+

H₂S is a gaseous signaling molecule that modifies cysteine residues in proteins to form persulfides (P‐SSH). One family of proteins modified by H₂S are zinc finger (ZF) proteins, which contain multiple zinc‐coordinating cysteine residues. Herein, we report the reactivity of H₂S with a ZF protein called tristetraprolin (TTP). Rapid persulfidation leading to complete thiol oxidation of TTP mediated by H₂S was observed by low‐temperature ESI‐MS and fluorescence spectroscopy. Persulfidation of TTP required O₂ , which reacts with H₂S to form superoxide, as detected by ESI‐MS, a hydroethidine fluorescence assay, and EPR spin trapping. H₂S was observed to inhibit TTP function (binding to TNFα mRNA) by an in vitro fluorescence anisotropy assay and to modulate TNFα in vivo. H₂S was unreactive towards TTP when the protein was bound to RNA, thus suggesting a protective effect of RNA.     

Sequence-selective and hydrolytic cleavage of DNA by zinc finger mutants

We have reported the successful conversion of the structural zinc site in zinc finger peptides to a functional zinc site. A series of resulting zinc finger mutants exhibit the hydrolytic ability of the activated ester depending on the coordination geometry and acidity of the zinc ions. In this study, we explored the hydrolytic ability of DNA by the H4 mutant since the mutant showed the highest hydrolytic ability of the activated ester among the series of mutant peptides. The zinc-bound form of the H4 mutant peptide exhibited the hydrolytic ability of activated phosphoesters and even converted the supercoiled plasmid to the nicked circular form. An increasing ionic strength leads to a loss in the nuclease ability of the zinc finger mutants due to the nonspecific interaction between the zinc finger peptide and DNA. In sharp contrast, the three-tandem H4-type zinc finger protein performed the specific DNA hydrolysis at the GC box even at a high ionic strength. Thus, the present study demonstrated that converting the native zinc site to the hydrolytic zinc site in the zinc finger protein is a novel approach for creating artificial nucleases with sequence selectivity.     

Covalent attachment and dissociative loss of sinapinic acid to/from cysteine-containing proteins from bacterial cell lysates analyzed by MALDI-TOF-TOF mass spectrometry

We report covalent attachment via a thiol ester linkage of 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid or SA) to cysteine-containing protein biomarkers from bacterial cell lysates of E. coli analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry when using SA as the matrix. Evidence to support this conclusion is the appearance of additional peaks in the MS spectra when using SA, which are absent when using α-cyano-4-hydroxycinnamic acid (HCCA). The additional peaks appear at a mass-to-charge (m/z) ∼208 greater to the m/z of a more abundant protein ion peak. Protein biomarkers were identified by tandem mass spectrometry (MS/MS) using a MALDI time-of-flight/time-of-flight (TOF-TOF) mass spectrometer and top-down proteomics. Three protein biomarkers, HdeA, HdeB, and homeobox or YbgS (each containing two cysteine residues) were identified as having reactivity to SA. Non-cysteine-containing protein biomarkers showed no evidence of reactivity to SA. MS ions and MS/MS fragment ions were consistent with covalent attachment of SA via a thiol ester linkage to the side-chain of cysteine residues. MS/MS of a protein biomarker ion with a covalently attached SA revealed fragment ion peaks suggesting dissociative loss SA. We propose dissociative loss of SA is facilitated by a pentacyclic transition-state followed by proton abstraction of the β-hydrogen of the bound SA by a sulfur lone pair followed by dissociative loss of 3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-ynal. The apparent reactivity of SA to cysteine/disulfide-containing proteins may complicate identification of such proteins, however the apparent differential reactivity of SA and HCCA toward cysteine/disulfide-containing proteins may be exploited for identification of unknown cysteine-containing proteins.     

Electrochemically initiated tagging of thiols using an electrospray ionization based liquid microjunction surface sampling probe two‐electrode cell

This paper reports on the conversion of a liquid microjunction surface sampling probe (LMJ‐SSP) into a two‐electrode electrochemical cell using a conductive sample surface and the probe as the two electrodes with an appropriate battery powered circuit. With this LMJ‐SSP, two‐electrode cell arrangement, tagging of analyte thiol functionalities (in this case peptide cysteine residues) with hydroquinone tags was initiated electrochemically using a hydroquinone‐doped solution when the analyte either was initially in solution or was sampled from a surface. Efficient tagging (～90%), at flow rates of 5–10 µL/min, could be achieved for up to at least two cysteines on a peptide. The high tagging efficiency observed was explained with a simple kinetic model. In general, the incorporation of a two‐electrode electrochemical cell, or other multiple electrode arrangement, into the LMJ‐SSP is expected to add to the versatility of this approach for surface sampling and ionization coupled with mass spectrometric detection. Published in 2009 by John Wiley & Sons, Ltd.     

Analysis of effect of casein phosphopeptides on zinc binding using mass spectrometry

Phosphorylation is one of the key events in signal transduction and zinc plays an important catalytic and/or structural role in many biological systems. The binding of Zn to a phosphopeptide will alter the physiological functions of a peptide. The binding of casein phosphopeptides (CPPs) to Zn has been analyzed using nanospray mass spectrometry. Electrospray ionization (ESI) spectra of peptides produced by tryptic digestion of alpha-casein incubated with Zn show both free and Zn-bound phosphopeptides. The interaction of CPPs and the corresponding dephosphorylated peptides with zinc is compared. This study demonstrates that the phosphorylation state of a peptide dramatically affects Zn binding, with the decrease in Zn-bound forms of peptide paralleling the decrease in phosphorylation as casein is chemically dephosphorylated, although, in some cases, a small amount of residual Zn-binding capacity remains in the completely dephosphorylated peptide. The observed fragmentation patterns of the Zn-bound CPPs support the thesis that nonphosphorylated residues are involved in the metal binding.     

Identification of cysteine residues in aspartate transaminase from pig-heart cytosol

Summary The two readily accessible cysteine residues (Cys-45 and Cys-82) and one completely masked residue (Cys-252) in the polypeptide chain of aspartate transaminase have been identified. The second completely masked cysteine residue is Cys-191.Institute of Molecular Biology, Academy of Sciences of the USSR. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 761–764, November–December, 1974.     

Spectroscopic evidence for the formation of goldfingers

Gold(I) has long been used in the treatment of rheumatoid arthritis, but the therapeutically relevant biological targets of gold(I) are not well understood. Here, we report the results of a spectroscopic investigation into the formation of goldfingers. By exploiting a thiolate to gold charge-transfer band in the UV, we observed that gold(I) interacts with zinc finger peptides with a stoichiometry of one gold ion for each two cysteine residues, forming 1:1, 1.5:1, and 2:1 adducts with zinc finger peptides containing CCHH, CCHC, and CCCC donor sets, respectively. In addition, circular dichroism experiments provided evidence that goldfingers are more ordered than the corresponding metal-free peptides but do not exhibit the canonical zinc finger structure.