Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies

Zn(2+) in the tumor-suppressor protein p53 DNA-binding domain (DBD) is essential for its structural stability and DNA-binding specificity. Mg(2+) has also been recently reported to bind to the p53DBD and influence its DNA-binding activity. In this contribution, the binding geometry of Mg(2+) in the p53DBD and the mechanism of how Mg(2+) affects its DNA-binding activity were investigated using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Various possible coordination geometries of Mg(2+) binding to histidines (His), cysteines (Cys), and water molecules were studied at the B3LYP/6-311+g** level of theory. The protonation state of Cys and the environment were taken into account to explore the factors governing the coordination geometry. The free energy of the reaction to form the Mg(2+) complexes was estimated, suggesting that the favorable binding mode changes from a four- to six-coordinated geometry as the number of the protonated Cys increases. Furthermore, MD simulations were employed to explore the binding modes of Mg(2+) in the active site of the p53DBD. The simulation results of the Mg(2+) system and the native Zn(2+) system show that the binding affinity of Mg(2+)to the p53DBD is weaker than that of Zn(2+), in agreement with the DFT calculation results and experiments. In addition, the two metal ions are found to make a significant contribution to maintain a favorable orientation for Arg248 to interact with putative DNA, which is critically important to the sequence-specific DNA-binding activity of the p53DBD. However, the effect of Mg(2+) is less marked. Additionally, analysis of the natural bond orbital (NBO) charge transfer reveals that Mg(2+) has a higher net positive charge than Zn(2+), leading to a stronger electrostatic attractive interaction between Mg(2+) and putative DNA. This may partly explain the higher sequence-independent DNA-binding affinity of p53DBD-Mg(2+) compared to p53DBD-Zn(2+) observed in experiment.     

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.     

Kinetics of thermal unfolding of phenylalanine hydroxylase variants containing different metal cofactors (FeII, CoII, and ZnII) and their isokinetic relationship

The kinetics of thermal unfolding of apo- and holo-Chromobacterium violaceum phenylalanine hydroxylase (cPAH) was investigated using circular dichroism (CD) over the temperature range 44-76 degrees C. In addition to the native cofactor (FeII), the unfolding kinetics of holo-cPAH was characterized using ZnII and CoII as cofactors. Kinetic profiles for apo- and holo-cPAH showed a single-phase exponential rise in the CD signal at lambda=222 nm and a first-order dependence on protein concentration. The extrapolated unfolding rate constants (ku) at ambient temperature followed the order apo>Fe>Zn>Co. Transition-state analysis of the activation parameters revealed an isokinetic correlation, which suggests a common mechanism for the enzyme variants. The values of the entropy of activation (DeltaS++) for apo- and Fe-cPAH were negative but small: -34+/-24 and -32+/-18 J mol(-1) K(-1), respectively. On the other hand, DeltaS++ values for Zn- and Co-cPAH were large and positive: 54+/-9 and 175+/-27 J mol(-1) K(-1), respectively. Therefore, at higher temperatures the unfolding rates of Zn- and Co-cPAH are affected significantly by entropy, while the unfolding rates of apo- and Fe-cPAH are dominated by enthalpy even at higher temperatures. The rate of unfolding of holo-cPAH did not depend on excess metal concentrations and maintained single-phase kinetic profiles, refuting the occurrence of adventitious metal binding and the notion that unfolding occurs via apo-cPAH exclusively. Isothermal titration calorimetry (ITC) was employed to measure cPAH binding affinities for Fe, Zn, and Co as well as the enthalpy of metal coordination. Dissociation constants (Kd) decreased in the order Fe>Zn>Co. The non-native metals, Zn and Co, were bound more tightly than Fe. The activation enthalpy for unfolding (DeltaH++) displayed a linear correlation with the enthalpy of metal binding obtained from ITC measurements (DeltaHITC). On this basis, a common mechanism (transition state) is suggested for this family of metal cofactors, and the varying enthalpy of activation arises from the differing stabilities of enzyme variants having different metal cofactors.     

Polythiol binding to biologically relevant metal ions

The coordination properties of three peptides with CXXC motif: Ac-GCASCDNCRACKK-NH(2), Ac-GCASCDNCRAAKK-NH(2) and Ac-GCASCDNARAAKK-NH(2) as donors of four, three and two thiol ligands for Ni(2+),Cd(2+), Zn(2+) and Bi(3+) were studied by potentiometric titrations, UV-Vis and CD spectra measurements. Since the stability of the complexes is closely connected with the amount of the metal-bound cysteine sulfurs, competition plots of the complexes of peptides with 2, 3 and 4 cysteines further prove the involvement of all thiols in the metal ion binding. Furthermore, the sulfur-bound zinc complexes appear to be much more stable than the sulfur-bound nickel ones. The stabilities of the studied complexes decreases in the series Bi(3+) ? Cd(2+) > Zn(2+) > Ni(2+).     

Thermodynamic studies on the recognition of flexible peptides by transition-metal complexes

Strong and selective binding to a trihistidine peptide has been achieved employing Cu(2+)-histidine interactions in aqueous medium (25 mM HEPES buffer, pH 7.0). When the pattern of cupric ions on a complex matched with the pattern of histidines on the peptide, a strong and selective binding was observed. UV-vis spectroscopic studies show that the cupric ions coordinate to the histidines of the peptides. Thermodynamic studies reveal that the binding process is enthalpy driven over the entire range of working temperature (25-40 degrees C). An enthalpy-entropy compensation effect was also observed.     

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.     

1H and (113)Cd NMR Investigations of Cd(2+) and Zn(2+) Binding Sites on Serum Albumin: Competition with Ca(2+), Ni(2+), Cu(2+), and Zn(2+)

1H and (113)Cd NMR studies are used to investigate the Cd(2+) binding sites on serum albumin (67 kDa) in competition with other metal ions. A wide range of mammalian serum albumins possess two similar strong Cd(2+) binding sites (site A 113-124 ppm; site B 24-28 ppm). The two strong sites are shown not to involve the free thiol at Cys34. Ca(2+) influences the binding of Cd(2+) to isolated human albumin, and similar effects due to endogenous Ca(2+) are observed for intact human blood serum. (1)H NMR studies show that the same two His residues of human serum albumin are perturbed by Zn(2+) and Cd(2+) binding alike. Zn(2+) displaces Cd(2+) from site A which leads to Cd(2+) occupation of a third site (C, 45 ppm). The N-terminus of HSA is not the locus of the two strong Cd(2+) binding sites, in contrast to Cu(2+) and Ni(2+). After saturation of the N-terminal binding site, Cu(2+) or Ni(2+) also displaces Cd(2+) from site A to site C. The effect of pH on Cd(2+) binding is described. A common Cd(2+)/Zn(2+) binding site (site A) involving interdomain His residues is discussed.     

Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules

The pathogenesis of Alzheimer's disease (AD) has been suggested to be related with the aggregation of amyloid β (Aβ) peptides. Metal ions (e.g. Cu, Fe, and Zn) are supposed to induce the aggregation of Aβ. Recent development of bifunctional molecules that are capable of interacting with Aβ and chelating biometal ions provides promising therapeutics to AD. However, the molecular mechanism for how Aβ, metal ions, and bifunctional molecules interact with each other is still elusive. In this study, the binding mode of Zn(2+)-bound Aβ with bifunctional molecules was investigated by the combination of conformational sampling of full-length Aβ peptides using replica exchange molecular dynamics simulations (REMD) and conformational selection using molecular docking and classical MD simulations. We demonstrate that Zn(2+)-bound Aβ((1-40)) and Aβ((1-42)) exhibit different conformational ensemble. Both Aβ peptides can adopt various conformations to recognize typical bifunctional molecules with different binding affinities. The bifunctional molecules exhibit their dual functions by first preferentially interfering with hydrophobic residues 17-21 and/or 30-35 of Zn(2+)-bound Aβ. Additional interactions with residues surrounding Zn(2+) could possibly disrupt interactions between Zn(2+) and Aβ, which then facilitate these small molecules to chelate Zn(2+). The binding free energy calculations further demonstrate that the association of Aβ with bifunctional molecules is driven by enthalpy. Our results provide a feasible approach to understand the recognition mechanism of disordered proteins with small molecules, which could be helpful to the design of novel AD drugs.     

Versatile trifunctional chemosensor of rhodamine derivative for Zn2+, Cu2+ and His/Cys in aqueous solution and living cells

On the basis of rhodamine, a versatile trifunctional chemosensor RP has been synthesized. It can selectively and sensitively recognize Cu(2+) and Zn(2+) in different solutions. Based on the zinc-containing [RP@Zn(2+)] complex, it shows highly selective recognition for His/Cys. Fluorescent imaging of Zn(2+) in living cells was also obtained.     

The inorganic perspective of nerve growth factor: interactions of Cu2+ and Zn2+ with the N-terminus fragment of nerve growth factor encompassing the recognition domain of the TrkA receptor

There is a significant overlap between brain areas with Zn(2+) and Cu(2+) pathological dys-homeostasis and those in which the nerve growth factor (NGF) performs its biological role. The protein NGF is necessary for the development and maintenance of the sympathetic and sensory nervous systems. Its flexible N-terminal region has been shown to be a critical domain for TrkA receptor binding and activation. Computational analyses show that Zn(2+) and Cu(2+) form pentacoordinate complexes involving both the His4 and His8 residues of the N-terminal domain of one monomeric unit and the His84 and Asp105 residues of the other monomeric unit of the NGF active dimer. To date, neither experimental data on the coordination features have been reported, nor has one of the hypotheses according to which Zn(2+) and Cu(2+) may have different binding environments or the Ser1 α-amino group could be involved in coordination been supported. The peptide fragment, encompassing the 1-14 sequence of the human NGF amino-terminal domain (NGF(1-14)), blocked at the C terminus, was synthesised and its Cu(2+) and Zn(2+) complexes characterized by means of potentiometric and spectroscopic (UV/Vis, CD, NMR, and EPR) techniques. The N-terminus-acetylated form of NGF(1-14) was also investigated to evaluate the involvement of the Ser1 α-amino group in metal-ion coordination. Our results demonstrate that the amino group is the first anchoring site for Cu(2+) and is involved in Zn(2+) coordination at physiological pH. Finally, a synergic proliferative activity of both NGF(1-14) and the whole protein on SHSY5Y neuroblastoma cell line was found after treatment in the presence of Cu(2+). This effect was not observed after treatment with the N-acetylated peptide fragment, demonstrating a functional involvement of the N-terminal amino group in metal binding and peptide activity.     

Molecular design of specific metal-binding peptide sequences from protein fragments: theory and experiment

A novel strategy is presented for designing peptides with specific metal-ion chelation sites, based on linking computationally predicted ion-specific combinations of amino acid side chains coordinated at the vertices of the desired coordination polyhedron into a single polypeptide chain. With this aim, a series of computer programs have been written that 1) creates a structural combinatorial library containing Z(i)-(X)(n)-Z(j) sequences (n=0-14; Z: amino acid that binds the metal through the side chain; X: any amino acid) from the existing protein structures in the non-redundant Protein Data Bank; 2) merges these fragments into a single Z(1)-(X)(n(1) )-Z(2)-(X)(n(2) )-Z(3)-(X)(n(3) )--Z(j) polypeptide chain; and 3) automatically performs two simple molecular mechanics calculations that make it possible to estimate the internal strain in the newly designed peptide. The application of this procedure for the most M(2+)-specific combinations of amino acid side chains (M: metal; see L. Rulísek, Z. Havlas J. Phys. Chem. B 2003, 107, 2376-2385) yielded several peptide sequences (with lengths of 6-20 amino acids) with the potential for specific binding with six metal ions (Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+) and Hg(2+)). The gas-phase association constants of the studied metal ions with these de novo designed peptides were experimentally determined by MALDI mass spectrometry by using 3,4,5-trihydroxyacetophenone as a matrix, whereas the thermodynamic parameters of the metal-ion coordination in the condensed phase were measured by isothermal titration calorimetry (ITC), chelatometry and NMR spectroscopy methods. The data indicate that some of the computationally predicted peptides are potential M(2+)-specific metal-ion chelators.     

Spectroscopic characterizations of bridging cysteine ligand variants of an engineered Cu2(Scys)2 CuA azurin

Bridging cysteine ligands of the Cu(A) center in an engineered Cu(A) azurin were replaced with serine, and the variants (Cys116Ser and Cys112Ser Cu(A) azurin) were characterized by mass spectrometry, as well as UV-vis and electron paramagnetic resonance (EPR) spectroscopic techniques. The replacements resulted in dramatically perturbed spectroscopic properties, indicating that the cysteines play a critical role in maintaining the structural integrity of the Cu center. The replacements at different cysteine residues resulted in different perturbations, even though the two cysteines are geometrically symmetrical in the primary coordination sphere with respect to the two copper ions. The Cys112Ser variant contains two distinct type 2 copper centers, while the Cys116Ser variant has one type 1 copper center with slight tetragonal distortion. Both the UV-vis and EPR spectra of the Cys116Ser variant change with pH, and the pK(a) of the transition is 6.0. A type 1 copper EPR spectrum with A(||) = 26 G was obtained at pH 7.0, while a type 2 copper EPR spectrum with A(||) = 140 G was found at pH 5.0. Interestingly, lowering the temperature from 290 to 85 K resulted in conversion of the Cys116Ser variant from a type 1 copper center to a type 2 copper center, suggesting rearrangement of the ligand around the copper or binding of an exogenous ligand at low temperature. This difference in mutation effects at different cysteines may be due to different constraints exerted on the two cysteines by hydrogen-bonding patterns in the ligand loop.     

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.     

A 1,8-naphthyridine-based fluorescent chemodosimeter for the rapid detection of Zn2+ and Cu2+

A novel fluorescent chemodosimeter based on 1,8-naphthyridine exhibits high selectivity to Zn(2+) and Cu(2+). When 1-(7-acetamino-1,8-naphthyridyl)-2-(6-diacetaminopyridyl)ethene was mixed with CuCl2, hydrolysis of the acetamino group catalyzed by Cu(2+) complex was first observed. Resulting from coordination and hydrolysis catalyzed by the corresponding complex of Zn(2+) or Cu(2+), the highly effective fluorescent detection of Zn(2+) and Cu(2+) is realized with Zn(2+)-selective dual-emission and Cu(2+)-selective ON-OFF behavior.     

Zn(2+) Responsive Bimodal Magnetic Resonance Imaging and Fluorescent Imaging Probe Based on a Gadolinium(III) Complex

A Zn(2+)-responsive bimodal magnetic resonance imaging (MRI) and luminescence imaging probe GdL was synthesized. The relaxivity and luminescence properties were examined. In the presence of 0.5 equiv of Zn(2+), the longitudinal relaxivity is increased from 3.8 mM(-1) s(-1) to 5.9 mM(-1) s(-1) at 23 MHz and 25 °C with 55% enhancement, whereas the fluorescence exhibits a 7-fold increase. The Zn(2+) responsive imaging probe shows favorable selectivity and tolerance over a variety of biologically relevant anions and metal ions in physiological pH range for both relaxivity and luminescence. In vitro phantom images and confocal fluorescence images in living cells show that the bimodal Zn(2+) probe can effectively enhance T(1)-weighted imaging contrast and luminescence imaging effect through Zn(2+) coordination with excellent cellmembrane permeability and biocompatibility. Spectral and electrospray ionization mass spectrometry (ESI-MS) studies indicate that two different Zn(2+)-bound species, (GdL)(2)Zn and GdLZn, are formed when 0.5 and 1 equiv of Zn(2+) are bound to GdL complex, respectively. Crystal structural determination and dysprosium-induced (17)O NMR shift (DIS) experiment demonstrate that the increased molecular weight and the improved molecular rigidity upon complexation of Zn(2+) with GdL is the primary factor for relaxivity enhancement. Significant enhancement of the luminescence is due to a heavy atom effect and much increased molecular rigidity upon Zn(2+) binding to 8-sulfonamidoquinoline chromophore.     

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.     

Thermodynamic studies on the interaction of antibodies with beta-amyloid peptide

Antibodies against beta-amyloid peptides (Abetas) are considered an important therapeutic opportunity in Alzheimer's disease. Despite the vast interest in Abeta no thermodynamic data on the interaction of antibodies with Abeta are available as yet. In the present study we use isothermal titration calorimetry (ITC) and surface plasmon resonance to provide a quantitative thermodynamic analysis of the interaction between soluble monomeric Abeta(1-40) and mouse monoclonal antibodies (mAb). Using four different antibodies directed against the N-terminal, middle, and C-terminal Abeta epitopes, we measured the thermodynamic parameters for the binding to Abeta. Each antibody species was found to have two independent and equal binding sites for Abeta with binding constants in the range of 10(7) to 10(8) M(-1). The binding reaction was essentially enthalpy driven with a reaction enthalpy of DeltaH(0)(Abeta) approximately -19 to -8 kcal/mol, indicating the formation of tight complexes. The loss in conformational freedom was supported by negative values for the reaction entropy DeltaS(0)(Abeta). We also measured the heat capacity change of the 1mAb:2Abeta reaction. DeltaC(0)(p, abeta) was large and negative but could not be explained exclusively by the hydrophobic effect. The free energy of binding was found to be linearly correlated with the size of the epitope.     

Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints,a Case Study on Vascular Endothelial Growth Factor Ligands

Macrocyclization constraints are widely used in the design of protein ligands to stabilize their bioactive conformation and increase their affinities. However, the resulting changes in binding entropy can be puzzling and uncorrelated to affinity gains. Here, the thermodynamic (Isothermal Titration Calorimetry) and structural (X-ray, NMR and CD) analysis of a complete series of lactam-bridged peptide ligands of the vascular endothelial growth factor, and their unconstrained analogs are reported. It is shown that differences in thermodynamics arise mainly from the folding energy of the peptide upon binding. The systematic reduction in conformational entropy penalty due to helix pre-organization can be counterbalanced by an unfavorable vibrational entropy change if the constraints are too rigid. The gain in configurational entropy partially escapes the enthalpy/entropy compensation and leads to an improvement in affinity. The precision of the analytical ITC method makes this study a possible benchmark for constrained peptides optimization.