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.     

Hydrolytic reaction by zinc finger mutant peptides: successful redesign of structural zinc sites into catalytic zinc sites

To redesign a metal site originally required for the stabilization of a folded protein structure into a functional metal site, we constructed a series of zinc finger mutant peptides such as zf(CCHG) and zf(GCHH), in which one zinc-coordinating residue is substituted into a noncoordinating one. The mutant peptides having water bound to the zinc ion catalyzed the hydrolysis of 4-nitrophenyl acetate as well as the enantioselective hydrolysis of amino acid esters. All the zinc complexes of the mutant peptides showed hydrolytic activity, depending on their peptide sequences. In contrast, the zinc complex of the wild-type, zf(CCHH), and zinc ion alone exhibited no hydrolytic ability. These results clearly indicate that the catalytic abilities are predominantly attributed to the zinc center in the zinc complexes of the mutant peptides. Kinetic studies of the mutant peptides demonstrated that the catalytic hydrolysis is affected by the electron-donating ability of the protein ligands and the coordination environment. In addition, the pH dependence of the hydrolysis strongly suggests that the zinc-coordinated hydroxide ion participates the catalytic reaction. This report is the first successful study of catalytically active zinc finger peptides.     

Expanding the DNA-recognition repertoire for zinc finger proteins beyond 20 amino acids

The design of DNA binding domains based on the Cys2His2 zinc finger motif has proven to be a successful strategy for the specific recognition of novel DNA sequences. Although considerable effort has been devoted to the generation of zinc finger proteins with widely varying DNA-binding preferences, only a limited number of potential DNA binding sites have been targeted with a high degree of specificity. These restrictions on zinc finger design appear to be a consequence of the limited repertoire of side-chain lengths and functionalities available with the 20 proteinogenic amino acids. To demonstrate that these limitations can be overcome through the use of "unnatural" amino acids, expressed protein ligation was employed to incorporate the amino acid citrulline into a single position within a three-zinc finger protein. As anticipated, the resulting semisynthetic protein specifically recognizes adenine in the appropriate position of its binding site.     

Coordination properties of zinc finger peptides revisited: ligand competition studies reveal higher affinities for zinc and cobalt

Zinc fingers are ubiquitous small protein domains which have a Zn(Cys)(4-x)(His)(x) site. They possess great diversity in their structure and amino acid composition. Using a family of six peptides, it was possible to assess the influence of hydrophobic amino acids on the metal-peptide affinities and on the rates of metal association and dissociation. A model of a treble-clef zinc finger, a model of the zinc finger site of a redox-switch protein, and four variants of the classical ββα zinc finger were used. They differ in their coordination set, their sequence length, and their hydrophobic amino acid content. The speciation, metal binding constants, and structure of these peptides have been investigated as a function of pH. The zinc binding constants of peptides, which adopt a well-defined structure, were found to be around 10(15) at pH 7.0. The rates of zinc exchange between EDTA and the peptides were also assessed. We evidenced that the packing of hydrophobic amino acids into a well-defined hydrophobic core can have a drastic influence on both the binding constant and the kinetics of metal exchange. Notably, well-packed hydrophobic amino acids can increase the stability constant by 4 orders of magnitude. The half-life of zinc exchange was also seen to vary significantly depending on the sequence of the zinc finger. The possible causes for this behavior are discussed. This work will help in understanding the dynamics of zinc exchange in zinc-containing proteins.     

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.     

The recognition of a noncanonical RNA base pair by a zinc finger protein.

BACKGROUND: The zinc finger (ZF) is the most abundant nucleic-acid-interacting protein motif. Although the interaction of ZFs with DNA is reasonably well understood, little is known about the RNA-binding mechanism. We investigated RNA binding to ZFs using the Zif268-DNA complex as a model system. Zif268 contains three DNA-binding ZFs; each independently binds a 3 base pair (bp) subsite within a 9 bp recognition sequence. RESULTS: We constructed a library of phage-displayed ZFs by randomizing the alpha helix of the Zif268 central finger. Successful selection of an RNA binder required a noncanonical base pair in the middle of the RNA triplet. Binding of the Zif268 variant to an RNA duplex containing a G.A mismatch (rG.A) is specific for RNA and is dependent on the conformation of the mismatched middle base pair. Modeling and NMR analyses revealed that the rG.A pair adopts a head-to-head configuration that counterbalances the effect of S-puckered riboses in the backbone. We propose that the structure of the rG.A duplex is similar to the DNA in the original Zif268-DNA complex. CONCLUSIONS: It is possible to change the specificity of a ZF from DNA to RNA. The ZF motif can use similar mechanisms in binding both types of nucleic acids. Our strategy allowed us to rationalize the interactions that are possible between a ZF and its RNA substrate. This same strategy can be used to assess the binding specificity of ZFs or other protein motifs for noncanconical RNA base pairs, and should permit the design of proteins that bind specific RNA structures.     

The role of zinc finger linkers in zinc finger protein binding to DNA

Journal of Computer-Aided Molecular Design - Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains...     

Interaction of trivalent antimony with a CCHC zinc finger domain: potential relevance to the mechanism of action of antimonial drugs

Sb(III) competes with Zn(II) for its binding to the CCHC zinc finger domain of the NCp7 protein of HIV-1, indicating that zinc finger proteins may be targets for antimony-based drugs and thus responsible for their important pharmacological actions.     

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.     

Oxidation of Zn(Cys)4 zinc finger peptides by O2 and H2O2: products, mechanism and kinetics

The reactivity of a series of Zn(Cys)(4) zinc finger model peptides towards H(2)O(2) and O(2) has been investigated. The oxidation products were identified by HPLC and ESI-MS analysis. At pH<7.5, the zinc complexes and the free peptides are oxidised to bis-disulfide-containing peptides. Above pH 7.5, the oxidation of the zinc complexes by H(2)O(2) also yields sulfinate- and sulfonate-containing overoxidised peptides. At pH 7.0, monitoring of the reactions between the zinc complexes and H(2)O(2) by HPLC revealed the sequential formation of two disulfides. Several techniques for the determination of the rate constant for the first oxidation step corresponding to the attack of H(2)O(2) by the Zn(Cys)(4) site have been compared. This rate constant can be reliably determined by monitoring the oxidation by HPLC, fluorescence, circular dichroism or absorption spectroscopy in the presence of excess ethyleneglycol bis(2-aminoethyl ether)tetraacetic acid. In contrast, monitoring of the release of zinc with 4-(2-pyridylazo)resorcinol or of the thiol content with 5,5'-dithiobis(2-nitrobenzoate) did not yield reliable values of this rate constant for the case in which the formation of the second disulfide is slower than the formation of the first. The kinetic measurements clearly evidence a protective effect of zinc on the oxidation of the cysteines by both H(2)O(2) and O(2), which points to the fact that zinc binding diminishes the nucleophilicity of the thiolates. In addition, the reaction between the zinc finger and H(2)O(2) is too slow to consider zinc fingers as potential sensors for H(2)O(2) in cells.     

Affinity partitioning of plasmid DNA with a zinc finger protein

The affinity isolation of pre-purified plasmid DNA (pDNA) from model buffer solutions using native and poly(ethylene glycol) (PEG) derivatized zinc finger-GST (Glutathione-S-Transferase) fusion protein was examined in PEG-dextran (DEX) aqueous two-phase systems (ATPSs). In the absence of pDNA, partitioning of unbound PEGylated fusion protein into the PEG-rich phase was confirmed with 97.5% of the PEGylated fusion protein being detected in the PEG phase of a PEG 600-DEX 40 ATPS. This represents a 1322-fold increase in the protein partition coefficient in comparison to the non-PEGylated protein (Kc = 0.013). In the presence of pDNA containing a specific oligonucleotide recognition sequence, the zinc finger moiety of the PEGylated fusion protein bound to the plasmid and steered the complex to the PEG-rich phase. An increase in the proportion of pDNA that partitioned to the PEG-rich phase was observed as the concentration of PEGylated fusion protein was increased. Partitioning of the bound complex occurred to such an extent that no DNA was detected by the picogreen assay in the dextran phase. It was also possible to partition pDNA using a non-PEGylated (native) zinc finger-GST fusion protein in a PEG 1000-DEX 500 ATPS. In this case the native ligand accumulated mainly in the PEG phase. These results indicate good prospects for the design of new plasmid DNA purification methods using fusion proteins as affinity ligands.     

Oligomerization of uniquely folded mini-protein motifs: development of a homotrimeric betabetaalpha peptide.

The discovery of a discretely folded homotrimeric betabetaalpha motif (BBAT1) was recently reported (J. Am. Chem. Soc. 2001, 123, 1002-1003). Herein the design, synthesis, and analysis of a small library of peptides which led to the isolation of BBAT1 is described. betabetaalpha peptides based on the monomeric sequence of BBA5 (Folding Des. 1998, 120, 95-103) were synthesized to include the anthranilic acid/nitrotyrosine fluorescence quenching pair to rapidly detect interpeptide association. In the first generation of peptides synthesized, truncations in the loop region connecting the beta-hairpin to the alpha-helix revealed that a two-residue deletion in the loop promoted an interpeptide association as detected by fluorescence quenching. An additional library of 22 loop-truncated betabetaalpha peptides was subsequently synthesized to include a variety of sequence mutations in an effort to enhance the observed peptide-peptide binding. From the fluorescence quenching screen, peptide B2 was found to possess the strongest fluorescence-quenching response, indicative of a strong peptide-peptide association. Due the poor solubility of peptide B2, the S-methylated cysteine at position 9 in the loop was substituted with a glycine to generate peptide BBAT1 which possessed greatly improved water solubility and formed discrete trimers. The successful design of this oligomeric betabetaalpha structure will likely aid the design of more complex alpha-beta superstructures and further our understanding of the factors controlling protein-protein interactions at alpha-beta protein interfaces.     

A bacterial one-hybrid selection system for interrogating zinc finger-DNA interactions

We have developed two bacterial one-hybrid systems for interrogating and selecting zinc finger-DNA interactions. Our systems utilize two plasmids: a zinc finger-plasmid containing the gene for the zinc finger fused to a fragment of the alpha subunit of RNA polymerase and a reporter plasmid where the zinc finger-binding site is located upstream of a reporter gene-either the gene encoding the green fluorescent protein (GFP) or chloramphenicol acetyltransferase (CAT). Binding of the zinc finger domain to the target binding site results in a 10-fold increase in chloramphenicol resistance with the CAT reporter and an 8- to 22-fold increase in total cell fluorescence with the GFP reporter. The CAT reporter allows for sequence specific zinc fingers to be isolated in a single selection step whereas the GFP reporter enables quantitative evaluation of libraries using flow cytometry and theoretically allows for both negative and positive selection. Both systems have been used to select for zinc fingers that have affinity for the motif 5'-GGGGCAGAA-3' from a library of approximately 2 x 10(5) variants. The systems have been engineered to report on zinc finger-DNA binding with dissociation constants less than about 1 microM in order to be most applicable for evaluating binding specificity in an in vivo setting.