Conversion of antennapedia homeodomain to zinc finger-like domain: Zn(II)-induced change in protein conformation and DNA binding

From the standpoint of protein dynamics and metalloprotein design, it is interesting to create an artificial protein which induces structural change and regulates its function by metal-ion binding. We engineered a novel protein, "Antennafinger (Ant-F)", whose structure and function can be controlled with Zn(II), by introducing the consensus sequence of a Cys(2)His(2)-type zinc finger protein into a non-metalloprotein scaffold, an Antennapedia homeodomain mutant (Ant-wt), selected using a motif-searching system. The circular dichroism studies demonstrate that Ant-F has secondary structures similar to Ant-wt and also changes its conformation due to Zn(II)-binding. The optical absorption spectra of the Co(II) complexes of Ant-F and its derivative proteins suggest that the geometry of the metal center of holo-Ant-F is tetrahedral and that the mutated Cys(2)His(2) residues are involved in the complex formation. In addition, the gel mobility shift assay reveals that the DNA binding activity of Ant-F can be regulated through Zn(II)-induced structural alteration. These results provide valuable information about the dynamic properties of proteins and a novel concept for metalloprotein design.     

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.     

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.     

Creation of a type 1 blue copper site within a de novo coiled-coil protein scaffold

Type 1 blue copper proteins uniquely coordinate Cu(2+) in a trigonal planar geometry, formed by three strong equatorial ligands, His, His, and Cys, in the protein. We designed a stable Cu(2+) coordination scaffold composed of a four-stranded α-helical coiled-coil structure. Two His residues and one Cys residue were situated to form the trigonal planar geometry and to coordinate the Cu(2+) in the hydrophobic core of the scaffold. The protein bound Cu(2+), displayed a blue color, and exhibited UV-vis spectra with a maximum of 602-616 nm, arising from the thiolate-Cu(2+) ligand to metal charge transfer, depending on the exogenous axial ligand, Cl(-) or HPO(4)(2-). The protein-Cu(2+) complex also showed unresolved small A(∥) values in the electron paramagnetic resonance (EPR) spectral analysis and a 328 mV (vs normal hydrogen electrode, NHE) redox potential with a fast electron reaction rate. The X-ray absorption spectrum revealed that the Cu(2+) coordination environment was identical to that found in natural type 1 blue copper proteins. The extended X-ray absorption fine structure (EXAFS) analysis of the protein showed two typical Cu-N(His) at around 1.9-2.0 ?, Cu-S(Cys) at 2.3 ?, and a long Cu-Cl at a 2.66 ?, which are also characteristic of the natural type 1 blue copper proteins.     

The active-site structure of umecyanin, the stellacyanin from horseradish roots

The type 1 copper sites of cupredoxins typically have a His(2)Cys equatorial ligand set with a weakly interacting axial Met, giving a distorted tetrahedral geometry. Natural variations to this coordination environment are known, and we have utilized paramagnetic (1)H NMR spectroscopy to study the active-site structure of umecyanin (UMC), a stellacyanin with an axial Gln ligand. The assigned spectra of the Cu(II) UMC and its Ni(II) derivative [Ni(II) UMC] demonstrate that this protein has the typical His(2)Cys equatorial coordination observed in other structurally characterized cupredoxins. The NMR spectrum of the Cu(II) protein does not exhibit any paramagnetically shifted resonances from the axial ligand, showing that this residue does not contribute to the singly occupied molecular orbital (SOMO) in Cu(II) UMC. The assigned paramagnetic (1)H NMR spectrum of Ni(II) UMC demonstrates that the axial Gln ligand coordinates in a monodentate fashion via its side-chain amide oxygen atom. The alkaline transition, a feature common to stellacyanins, influences all of the ligating residues but does not alter the coordination mode of the axial Gln ligand in UMC. The structural features which result in Cu(II) UMC possessing a classic type 1 site as compared to the perturbed type 1 center observed for other stellacyanins do not have a significant influence on the paramagnetic (1)H NMR spectra of the Cu(II) or Ni(II) proteins.     

Crystal structures of oxidized and reduced stellacyanin from horseradish roots

Umecyanin (UMC) is a type 1 copper-containing protein which originates from horseradish roots and belongs to the stellacyanin subclass of the phytocyanins, a ubiquitous family of plant cupredoxins. The crystal structures of Cu(II) and Cu(I) UMC have been determined at 1.9 and 1.8 A, respectively. The protein has an overall fold similar to those of other phytocyanins. At the active site the cupric ion is coordinated by the N(delta1) atoms of His44 and His90, the S(gamma) of Cys85, and the O(epsilon)(1) of Gln95 in a distorted tetrahedral geometry. Both His ligands are solvent exposed and are surrounded by nonpolar and polar side chains on the protein surface. Thus, UMC does not possess a distinct hydrophobic patch close to the active site in contrast to almost all other cupredoxins. UMC has a large surface acidic patch situated approximately 10-30 A from the active site. The structure of Cu(I) UMC is the first determined for a reduced phytocyanin and demonstrates that the coordination environment of the cuprous ion is more trigonal pyramidal. This subtle change in geometry is primarily due to the Cu-N(delta1)(His44) and Cu-O(epsilon1)(Gln95) bond lengths increasing from 2.0 and 2.3 A in Cu(II) UMC to 2.2 and 2.5 A, respectively, in the reduced form, as a consequence of slight rotations of the His44 and Gln95 side chains. The limited structural changes upon redox interconversion at the active site of this stellacyanin are analogous to those observed in a typical type 1 copper site with an axial Met ligand and along with its surface features suggest a role for UMC in interprotein electron transfer.     

Classical Cys2His2 zinc finger peptides are rapidly oxidized by either H2O2 or O2 irrespective of metal coordination

ZIF268, a member of the classical zinc finger protein family, contains three Cys(2)His(2) zinc binding domains that together recognize the DNA sequence 5'-AGCGTGGGCGT-3'. These domains can be fused to an endonuclease to make a chimeric protein to target and cleave specific DNA sequences. A peptide corresponding to these domains, named ZIF268-3D, has been prepared to determine if the zinc finger domain itself can promote DNA cleavage when a redox active metal ion, Fe(II), is coordinated. The UV-vis absorption spectrum of Fe(II)-ZIF268-3D is indicative of Fe(II) coordination. Using fluorescence anisotropy, we demonstrate that Fe(II)-ZIF268-3D binds selectively to its target DNA in the same manner as Zn(II)-ZIF268-3D. In the presence of added oxidant, H(2)O(2) or O(2), DNA cleavage is not observed by Fe(II)-ZIF268-3D. Instead, the peptide itself is rapidly oxidized. Similarly, Zn(II)-ZIF268-3D and apo-ZIF268-3D are rapidly oxidized by H(2)O(2) or O(2), and we propose that ZIF268-3D is highly susceptible to oxidation.     

Zn protein simulations including charge transfer and local polarization effects

Nearly half of all proteins contain metal ions, which perform a wide variety of specific functions associated with life processes. However, insights into the local/global, structural and dynamical fluctuations in metalloproteins from molecular dynamics simulations have been hampered by the "conventional" potential energy function (PEF) used in nonmetalloprotein simulations, which does not take into the nonnegligible charge transfer and polarization effects in many metal complexes. Here, we have carried out molecular dynamics simulations of Zn(2+) bound to Cys(-) and/or His(0) in proteins using both the conventional PEF and a novel PEF that accounts for the significant charge transfer and polarization effects in these Zn complexes. Simulations with the conventional PEF yield a nontetrahedral Cys(2)His(2) Zn-binding site and significantly overestimate the experimental Zn-S(Cys(-)) distance. In contrast, simulations with the new PEF accurately reproduce the experimentally observed tetrahedral structures of Cys(2)His(2) and Cys(4) Zn-binding sites in proteins, even when the simulation started from a nontetrahedral Zn(2+) configuration. This suggests that simulations with the new PEF could account for coordinational changes at Zn, which occurs during the folding/unfolding of Zn-finger proteins and certain enzymatic reactions The strategy introduced here can easily be applied to investigate Zn(2+) interacting with protein ligands other than Cys(-) and His(0). It can also be extended to study the interaction of other metals that have significant charge transfer and polarization effects.     

An unsymmetrical tripodal ligand with NOS2-donor set: coordination chemistry with nickel(II) and zinc(II)

The synthesis of the novel tripodal ligand [N(CH2CH2CH2OH)(CH2CH2SH)2] H3-4 is reported. The aliphatic tetradentate ligand is equipped with an unsymmetrical NOS2 donor set. It reacts with Ni(OAc)2 x 4H2O or Zn(BF4)2 x xH2O to give the complexes [Ni(H-4)]2 5 and [Zn(H-4)]4 6, respectively. The molecular structures of 5 and 6 have been determined by X-ray diffraction. In both cases multinuclear, mu-thiolato-bridged complexes, wherein the ligand coordinates with only three (NS2) of the four donor groups, had formed. The dinuclear complex 5 adopts a butterfly geometry and contains nickel(II) ions in a square-planar NS3 coordination environment. Cyclic voltammetry experiments indicate that the nickel centers in 5 are electron-rich but not overly sensitive toward oxidation. Complex 6 is tetranuclear and the four thiolato-bridged metal centers form a ring. It shows a distorted tetrahedral coordination geometry for the zinc(II) ions in an NS3 coordination sphere. In both complexes the hydroxyl functionalized ligand arm of the tripodal ligand remains uncoordinated.     

Syntheses and crystal structures of nickel(II), copper(II), and zinc(II) complexes with a biphenyl-bridged bis(pyrrole-2-yl-methyleneamine) ligand

The reactions of nickel(II), copper(II), and zinc(II) acetate salts with a potentially tetradentate biphenyl-bridged bis(pyrrole-2-yl-methyleneamine) ligand yielded three complexes with different coordination geometries. X-ray crystal structural analysis reveals that in the nickel(II) complex each nickel is five-coordinate, distorted trigonal bipyramid. In the copper(II) complex, each copper is four-coordinate, between square planar and tetrahedral. In the zinc(II) complex, each zinc is four-coordinate with a distorted tetrahedral geometry and the molar ratio of the zinc and ligand is 1 : 2.     

Comparison of the specificity of interaction of cellular and viral zinc-binding domains with 2-mercaptobenzamide thioesters

The interactions of two 2-mercaptobenzamide thioester compounds with six diverse zinc-binding domains (ZBDs) have been analyzed by UV/visible spectroscopy, NMR spectroscopy, and nucleic acid binding assays. These thioester compounds serve as useful tools for probing the intrinsic chemical stability of ZBDs that exist within a variety of cellular and viral proteins. In our studies, the classical (Cys(2)His(2)) zinc finger ZBDs, the interleaved RING like ZBDs of protein kinase C delta (Cys(2)HisCys and HisCys(3)), and the carboxyl-terminal (Cys(2)HisCys) ZBD of Mouse Mammary Tumor Virus nucleocapsid protein (MMTV NCp10) were resistant to reaction with the thioester compounds. In contrast, the thioester compounds were able to efficiently eject zinc from the amino-terminal (Cys(2)HisCys) ZBD of MMTV NCp10, a Cys(2)HisCys ZBD from Friend of GATA-1 (FOG-1), and from both Cys(4) ZBDs of GATA-1. In all cases, zinc ejection led to a loss of protein structure. Interestingly, GATA-1 was resistant to reaction with the thioester compounds when bound to its target DNA sequence. The electronic and steric screening was calculated for select ZBDs to further explore their reactivity. Based on these results, it appears that both first and second zinc-coordination shell interactions within ZBDs, as well as nucleic acid binding, play important roles in determining the chemical stability and reactivity of ZBDs. These studies not only provide information regarding the relative reactivity of cysteine residues within structural ZBDs but also are crucial for the design of future therapeutic agents that selectively target ZBDs, such as those that occur in the HIV-1 nucleocapsid protein.     

Spectroscopic identification of different types of copper centers generated in synthetic four-helix bundle proteins

Using a combined rational-combinatorial approach, stable copper binding sites were implemented in template-assembled synthetic four-helix bundle proteins constructed by three different helices with only 16 amino acid residues. These peptides include two histidines and one cysteine at positions appropriate for coordinating a copper ion. Sequence variations of the helices were made in the second coordination shell or even more remote from the copper binding site (i) to increase the overall stability of the metalloproteins and (ii) to fine-tune the structure and properties of the copper center. As a result, ca. 90% of the 180 proteins that were synthesized were capable to bind copper with a substantially higher specificity than those obtained in the first design cycle (Schnepf, R.; Horth, P.; Bill, E.; Wieghardt, K.; Hildebrandt, P.; Haehnel, W. J. Am. Chem. Soc. 2001, 123, 2186-2195). Furthermore, the stabilities of the copper protein complexes were increased by up to 2 orders of magnitude and thus allowed a UV-vis absorption, resonance Raman, electron paramagnetic resonance, and (magnetic) circular dichroism spectroscopic identification and characterization of three different types of copper binding sites. It could be shown that particularly steric perturbations in the vicinity of the His(2)Cys ligand set control the formation of either a tetragonal (type II) or a tetrahedral (type I) copper binding site. With the introduction of two methionine residues above the histidine ligands, a mixed-valent dinuclear copper binding site was generated with spectroscopic properties that are very similar to those of Cu(A) sites in natural proteins. The results of the present study demonstrate for the first time that structurally different metal binding sites can be formed and stabilized in four-helix bundle proteins.     

Metal-ligand interplay in blue copper proteins studied by 1H NMR spectroscopy: Cu(II)-pseudoazurin and Cu(II)-rusticyanin

The blue copper proteins (BCPs), pseudoazurin from Achromobacter cycloclastes and rusticyanin from Thiobacillus ferrooxidans, have been investigated by (1)H NMR at a magnetic field of 18.8 T. Hyperfine shifts of the protons belonging to the coordinated ligands have been identified by exchange spectroscopy, including the indirect detection for those resonances that cannot be directly observed (the beta-CH(2) of the Cys ligand, and the NH amide hydrogen bonded to the S(gamma)(Cys) atom). These data reveal that the Cu(II)-Cys interaction in pseudoazurin and rusticyanin is weakened compared to that in classic blue sites (plastocyanin and azurin). This weakening is not induced by a stronger interaction with the axial ligand, as found in stellacyanin, but might be determined by the protein folding around the metal site. The average chemical shift of the beta-CH(2) Cys ligand in all BCPs can be correlated to geometric factors of the metal site (the Cu-S(gamma)(Cys) distance and the angle between the CuN(His)N(His) plane and the Cu-S(gamma)(Cys) vector). It is concluded that the degree of tetragonal distortion is not necessarily related to the strength of the Cu(II)-S(gamma)(Cys) bond. The copper-His interaction is similar in all BCPs, even for the solvent-exposed His ligand. It is proposed that the copper xy magnetic axes in blue sites are determined by subtle geometrical differences, particularly the orientation of the His ligands. Finally, the observed chemical shifts for beta-CH(2) Cys and Ser NH protons in rusticyanin suggest that a less negative charge at the sulfur atom could contribute to the high redox potential (680 mV) of this protein.     

Preparation, spectral and biological investigation of formaldehyde-based ligand containing piperazine moiety and its various polymer metal complexes

A novel tetradentate salicylic acid-formaldehyde ligand containing piperazine moiety (SFP) was synthesized by condensation of salicylic acid, formaldehyde and piperazine in presence of base catalyst, which was subjected for the preparation of coordination polymers with metal ions like manganese(II), cobalt(II), copper(II), nickel(II) and zinc(II). All the synthesized polymeric compounds were characterized by elemental analysis, IR, (1)H NMR and electronic spectral studies. The thermal stability was determined by thermogravimetric analysis and thermal data revealed that all the polymer metal complexes show good thermal stability than their parent ligand. Electronic spectral data and magnetic moment values revealed that polymer metal complexes of Mn(II), Co(II) and Ni(II) show an octahedral geometry while Cu(II) and Zn(II) show distorted octahedral and tetrahedral geometry respectively. The antimicrobial screening of the ligand and coordination polymers was done by using Agar well diffusion method against various bacteria and fungi. It was evident from the data that antibacterial and antifungal activity increased on chelation and all the polymer metal complexes show excellent antimicrobial activity than their parent ligand.     

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.     

Metal-coupled folding of Cys2His2 zinc-finger

Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles in life processes, depend on the binding of zinc ion for their proper folding. To computationally study the zinc-coupled folding of the zinc-fingers, charge transfer and metal induced protonation/deprotonation effects have to be considered. Here, by attempting to implicitly account for such effects in classical molecular dynamics and performing intensive simulations with explicit solvent for the peptides with and without zinc binding, we investigate the folding of the Cys2His2-type zinc-finger motif and the coupling between the peptide folding and zinc binding. We find that zinc ion not only stabilizes the native structure but also participates in the whole folding process. It binds to the peptide at an early stage of folding and directs or modulates the folding and stabilizations of the component beta-hairpin and alpha-helix. Such a crucial role of zinc binding is mediated by the packing of the conserved hydrophobic residues. We also find that the packing of the hydrophobic residues and the coordination of the native ligands are coupled. Meanwhile, the processes of zinc binding, mis-ligation, ligand exchange, and zinc induced secondary structure conversion as well as the water behavior due to the involvement of zinc ion are characterized. Our results are in good agreement with related experimental observations and provide significant insight into the general mechanisms of the metal cofactor dependent protein folding and other metal-induced conformational changes of biological importance.