Comparison of cysteine and penicillamine ligands in a Co(II) maquette

l-Penicillamine (Pen) has been investigated as a ligand for metalloprotein design by examining the binding of Co(II) to the sequence NH(2)-KL(Pen)EGG.(Pen)IG(Pen)GA(Pen).GGW-CONH(2). For comparison, we have studied Co(II) binding to the analogous sequence with Cys ligands, the ferredoxin maquette ligand IGA that was originally designed to bind a [4Fe-4S] cluster. The Co(II) affinity and UV-vis spectroscopic properties of IGA indicate formation of a pseudotetrahedral tetrathiolate ligated Co(II). In contrast, IGA-Pen showed formation of a pseudotetrahedral complex with Co(II) bound by three Pen ligands and an exogenous H(2)O. EXAFS data on both Co(II) complexes confirms not only the proposed primary coordination spheres but also shows six Co(II)-C(beta) methyl group distances in Co(II)-IGA-Pen. These results demonstrate that ligand sterics in simple peptides can be designed to provide asymmetric coordination spheres such as those commonly observed in natural metalloproteins.     

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.     

Coupling of native IEF and extended X-ray absorption fine structure to characterize zinc-binding sites from pI isoforms of SOD1 and A4V pathogenic mutant

Extended X-ray absorption fine structure (EXAFS) has already provided high-resolution structures of metal-binding sites in a wide variety of metalloproteins. Usually, EXAFS is performed on purified metalloproteins either in solution or crystallized form but purification steps are prone to modify the metallation state of the protein. We developed a protocol to couple EXAFS analysis to metalloprotein separation using native gel electrophoresis. This coupling opens a large field of applications as metalloproteins can be characterized in their native state avoiding purification steps. Using native isoelectric focusing, the method enables the EXAFS analysis of metalloprotein pI isoforms. We applied this methodology to SOD1, wild-type, and Ala4Val mutant (A4V), a mutation found in amyotrophic lateral sclerosis (ALS) because decreased Zn affinity to SOD1 mutants is suggested to be involved in the pathogenesis of this neurodegenerative disease. We observed similar coordination structures for Zn in wild-type and mutant proteins, in all measured pI isoforms, demonstrating the feasibility of EXAFS on electrophoresis gels and suggesting that the Zn-binding site is not structurally modified in A4V SOD1 mutant.     

1,4,7,10-tetraazacyclododecane metal complexes as potent promoters of carboxyester hydrolysis under physiological conditions

New 1,4,7,10-tetrazacyclododecane ([12]aneN4 or cyclen) ligands with different heterocyclic spacers (triazine and pyridine) of various lengths (bi- and tripyridine) or an azacrown pendant and their mono- and dinuclear Zn(II), Cu(II), and Ni(II) complexes have been synthesized and characterized. The pKa values of water molecules coordinated to the complexed metal ions were determined by potentiometric pH titrations and vary from 7.7 to 11.2, depending on the metal-ion and ligand properties. The X-ray structure of [Zn2L2]mu-OH(ClO4)3.CH3CN.H2O shows each Zn(II) ion in a tetrahedral geometry, binding to three N atoms of cyclen (the average distance of Zn-N = 2.1 A) and having a mu-OH bridge at the apical site linking the two metal ions (the average distance of Zn-O- = 1.9 A). The distance between the Zn(II) ion and the fourth N atom is 2.6 A. All Zn(II) complexes promote the hydrolysis of 4-nitrophenyl acetate (NA) under physiological conditions, while those of Cu(II) and Ni(II) do not have a significant effect on the hydrolysis reaction. The kinetic studies in buffered solutions (0.05 M Tris, HEPES, or CHES, I = 0.1 M, NaCl) at 25 degrees C in the pH range of 6-11 under pseudo-first-order reaction conditions (excess of the metal complex) were analyzed by applying the method of initial rates. Comparison of the second-order pH-independent rate constants (kNA, M-1 s-1) for the mononuclear complexes ZnL1, ZnL3, and ZnL8, which are 0.39, 0.27, and 0.38, respectively, indicates that the heterocyclic moiety improves the rate of hydrolysis up to 4 times over the parent Zn([12]aneN4) complex (kNA = 0.09 M-1 s-1). The reactive species is the Zn(II)-OH- complex, in which the Zn(II)-bound OH- acts as a nucleophile, which attacks intermolecularly the carbonyl group of the acetate ester. For dinuclear complexes Zn2L2, Zn2L4, Zn2L5, Zn2L6, and Zn2L7, the mechanism of the reaction is defined by the degree of cooperation between the metal centers, determined by the spacer length. For Zn2L7, having the longest triaryl spacer, the two metal centers act independently in the hydrolysis; therefore, the reaction rate is twice as high as the rate of the mononuclear analogue (kNA = 0.78 M-1 s-1). The complexes with a monoaryl spacer show saturation kinetics with the formation of a Michaelis-Menten adduct. Their hydrolysis rates are 40 times higher than that of the Zn[12]aneN4 system (kNA approximately 4 M-1 s-1). Zn2L6 is a hybrid between these two mechanisms; a clear saturation curve is not visible nor are the metal cores completely independent from one another. Some of the Zn(II) complexes show a higher hydrolytic activity under physiological conditions compared to other previously reported complexes of this type.     

Determining thermodynamic parameters from isothermal calorimetric isotherms of the binding of macromolecules to metal cations originally chelated by a weak ligand

An accurate data analysis method for determining stoichiometry and thermodynamic parameters from isothermal titration calorimetry data for the binding of macromolecules to metal cations that are solubilized through an association with a weak ligand is presented. This approach is applied to determine the binding constant for the association of Cu(II) to the first 16 residues of the Alzheimer's amyloid beta peptide, Abeta(1-16) under conditions where Cu(II) is rendered soluble through weak binding to glycine. At pH 7.2 and 37 degrees C, a binding constant of 1.5 x 10(9) M-1 (Kd = 0.7 nM) is determined for the association of Cu(II) with Abeta(1-16).     

Control of metal-ion composition in the synthesis of ternary II-II'-VI nanoparticles by using a mixed-metal cluster precursor approach

The ternary molecular nanoclusters [Zn(x)Cd(10-x)Se4(SePh)12(PnPr3)4] (x = 1.8, 1 a; x = 2.6, 1 b) were employed as single-source precursors for the synthesis of high-quality hexagonal Zn(x)Cd(1-x)Se nanocrystals. The tellurium clusters [Zn(x)Cd(10-x)Te4(TePh)12(PnPr3)4] (x = 1.8, 2 a; x = 2.6, 2 b) are equally convenient precursors for the synthesis cubic Zn(x)Cd(1-x)E nanoparticles. The thermolysis of the cluster molecules in hexadecylamine provides an efficient system in which the inherent metal-ion stoichiometry of the clusters is retained in the nanocrystalline products, whilst also affording control of particle size within the 2-5 nm range. In all cases, the nanoparticles are monodisperse, and luminescence spectra exhibit emission energies close to the absorption edge. Analysis of the optical spectra and X-ray diffraction patterns of these materials indicates a metal-ion concentration gradient within the structures of the nanocrystals, with Zn(II) ions predominantly located near the surface of the particles.     

Role of cofactors in folding of the blue-copper protein azurin

Many proteins in living cells coordinate cofactors, such as metal ions, to attain their activity. Since the cofactors in such cases often can interact with their corresponding unfolded polypeptides in vitro, it is important to unravel how cofactors modulate protein folding. In this review, I will discuss the role of cofactors in folding of the blue-copper protein Pseudomonas aeruginosa azurin. In the case of both copper (Cu(II) and Cu(I)) and zinc (Zn(II)), the metal can bind to unfolded azurin. The residues involved in copper (Cu(II) and Cu(I)) coordination in the unfolded state have been identified as Cys112, His117, and Met121. The affinities of Cu(II), Cu(I), and Zn(II) are all higher for the folded than for the unfolded azurin polypeptide, resulting in metal stabilization of the native state as compared to the stability of apo-azurin. Cu(II), Zn(II), and several apo forms of azurin all fold in two-state kinetic reactions with roughly identical polypeptide-folding speeds. This suggests that the native-state beta-barrel topology, not cofactor interactions or thermodynamic stability, determines azurin's folding barrier. Nonetheless, copper binds much more rapidly (i.e., 4 orders of magnitude) to unfolded azurin than to folded azurin. Therefore, the fastest route to functional azurin is through copper binding before polypeptide folding; this sequence of events may be the relevant biological pathway.     

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a₃ in caa₃-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN⁻ ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.     

Design of a new mimochrome with unique topology

Peptide-based metalloprotein models represent useful systems to help understand how metalloproteins can support different functions, by the use of similar metal ion cofactors. In order to shed light on the role of the protein matrix in modulating the heme properties, we developed new models: mimochromes. They are pseudo-C(2) symmetric systems, composed of two helical peptides covalently linked to the deuteroporphyrin. The use of C(2) symmetry is particularly advantageous, because it simplifies the design, synthesis and characterization. However, it leaves the problem of possible diastereomeric forms. In the cobalt complex of the first derivative, mimochrome I, Lambda and Delta isomers were indeed experimentally observed. All the insights derived from the Co(III)-mimochrome I structure were used to obtain a re-designed molecule, mimochrome IV. The spectroscopic characterization of the iron and cobalt derivatives suggested the presence of the Lambda isomer as unique species. The NMR solution structure of the diamagnetic Co(III)-mimochrome IV confirmed the ability of the molecule to adopt a unique topology, and revealed the peptide chains to be in helical conformation, as designed. The insertion of intramolecular, inter-chain interactions was successful in favoring the formation of one of the two possible diastereomers. The stereochemically stable structure of mimochrome IV provides an attractive model for modulating the redox potential of the heme, by simple changing the peptide chain composition around the heme.     

De novo design of a redox-active minimal rubredoxin mimic

Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment.     

Different binding thermodynamics of Ni2+, Cu2+, and Zn2+ to bacitracin A1 determined by capillary electrophoresis

Thermodynamics of the binding of Ni(2+), Cu(2+) and Zn(2+) to bacitracin A(1) was studied by capillary electrophoresis measuring the peptide effective mobility at different pH in the presence of increasing concentration of the three ligands. The affinity follows the order Ni(2+) > Cu(2+) > Zn(2+), with association constant values of (2.3 +/- 0.1)x10(4), (4.9 +/- 0.2)x10(3), and (1.5 +/- 0.1)x10(3) M(-1), respectively. The only model able to rationalize mobility data implies that metal ion binds to the P(0) peptide form. Moreover, mobility values indicated a change of bacitracin A(1) acidic properties on Ni(2+) and Cu(2+) binding, with a shift of the pK(a) of N-terminal Ile-1 from 7.6 to about 5 and of the pK(a) of the delta-amino group of D-Orn-7 from 9.7 to about 7. Even though on Zn(2+) binding a shift of the N-terminal Ile-1 pK(a) was observed, restrictions in the pH range suitable for investigation, due to precipitation phenomena, did not allow establish if the shift of D-Orn-7 lateral chain pK(a) also occurred. Nonetheless, if present, the shift should be limited to the 7.8-9.7 range. Mobility data indicated that the Stokes radius of the complexes is ca. 3 A lower than that of the free peptide. The present results indicate that metal-ion binding to bacitracin A(1) is more complex than previously assumed.     

Fast Detection Allows Analysis of the Electronic Structure of Metalloprotein by X-ray Emission Spectroscopy at Room Temperature

The paradigm of "detection-before-destruction" was tested for a metalloprotein complex exposed at room temperature to the high x-ray flux typical of third generation synchrotron sources. Following the progression of the x-ray induced damage by Mn Kβ x-ray emission spectroscopy, we demonstrated the feasibility of collecting room temperature data on the electronic structure of native Photosystem II, a trans-membrane metalloprotein complex containing a Mn(4)Ca cluster. The determined non-damaging observation timeframe (about 100 milliseconds using continuous monochromatic beam, deposited dose 1*10(7) photons/μm(2) or 1.3*10(4) Gy, and 66 microseconds in pulsed mode using pink beam, deposited dose 4*10(7) photons/μm(2) or 4.2*10(4) Gy) is sufficient for the analysis of this protein's electron dynamics and catalytic mechanism at room temperature. Reported time frames are expected to be representative for other metalloproteins. The described instrumentation, based on the short working distance dispersive spectrometer, and experimental methodology is broadly applicable to time-resolved x-ray emission analysis at synchrotron and x-ray free-electron laser light sources.     

An artificial guanine that binds cytidine through the cooperative interaction of metal coordination and hydrogen bonding

Cd(II) complex of L binds selectively to cytidine in DMSO with an equilibrium constant of 117 M-1 (where LH is 2-aminomethyl-8-hydroxyquinoline). In contrast, the Zn(II) complex of L does not bind appreciably to any of the four nucleobases under the same condition used for the Cd(II) complex.     

Light-harvesting macroring accommodating a tetrapodal ligand based on complementary and cooperative coordinations

A porphyrin macroring, mimicking the light-harvesting complex of photosynthetic purple bacteria, was synthesized by self-assembling trisporphyrinatoZn(II) complexes with imidazolyl substituents at both molecular terminals. Very strong complementary coordination of imidazolyl to Zn(II) afforded exclusively the cyclic trimer of trisporphyrin under dilute conditions at 27 degrees C in CHCl3/MeOH = 9/1 (v/v). 1H NMR spectra of the macroring indicate the existence of two topological isomers, one symmetric and one asymmetric. Use of three noncoordinated porphyrinatoZn(II) sites allows a tetrapodal ligand to be incorporated into the cavity of the macroring. A Job plot and the clear bending behavior on UV-vis titration indicated the formation a 1:1 complex; the heterogeneity of two topological isomers was not observed, and both isomers similarly accommodated the tetrapodal ligand. The association constant obtained by curve fitting analysis was 8 x 108 M-1 in toluene. This large association constant reflects the cooperative nature of three coordination sites.     

2,6-di(pyrimidin-4-yl)pyridine ligands with nitrogen-containing auxiliaries: the formation of functionalized molecular clefts upon metal coordination

A series of ligands (1-4) based on a 2,6-di(pyrimidin-4-yl)pyridine scaffold have been synthesized, and their abilities to form complexes with Zn(II) and Cu(II) have been determined using UV/vis spectroscopy in buffered aqueous solution (0.01 M N-[2-hydroxyethyl]piperazine-N'-[3-ethanesulfonic acid] (HEPES) at pH = 6.8). The Zn(II) complex of 1 was determined to have a formation constant of 8.4 x 10(3) M(-)(1) while the formation constant of the Cu(II) complex was found to be 1 x 10(6) M(-)(1). The presence of auxiliary amines in 2 increased the stability of the Zn(II) complex relative to that of 1 by a factor of over 40, suggesting possible coordination of the auxiliaries to the Zn(II) center. The guanidinium and 2-amino-4,5-dihydro-imidazolinium groups of 3 and 4 considerably diminished the stability of the Zn(II) and Cu(II) complexes relative to those of 1. X-ray crystal structures of 1-Zn, 3-Zn, 4, and 4-Zn were obtained and are discussed. A significant increase in the stability of 3-Zn, but not in the stability 1-Zn, was observed upon the addition of 1 equiv of sodium phosphate, implicating a stabilizing interaction of the guanidinium groups of 3-Zn and the phosphate anion.     

A highly reactive mononuclear Zn(II) complex for phosphodiester cleavage

The activity of a Zn(II) complex of a tetradentate, tripodal ligand for catalyzing phosphodiester cleavage is enhanced 750-fold by introducing three hydrogen bond donors to the ligand. Inhibition studies show that the Zn-aqua complex is the kinetically active form and that it binds the transition state with a formal dissociation constant of 3 x 108 M-1. The effect of these ligand modifications on the transition-state affinity is comparable to the rate acceleration provided by the metal ion itself. Overall, this mononuclear complex is more active than the most reactive dinuclear Zn(II) complexes reported to date.     

Magnetic resonance imaging detects a specific peptide-protein binding event

DOTA was conjugated to the N-terminus of a 12-mer peptide by using standard peptide synthesis chemistry. The peptide, first isolated by phage display, maintained a high affinity for its protein-binding target, Gal-80, even with GdDOTA attached. The high affinity constant (KA = 5 x 105 M-1) combined with the high relaxivity of the resulting GdDOTA-peptide.protein complex (r1bound = 44.8 +/- 1.7 mM-1 s-1) allowed detection of Gal-80 at muM levels using a standard magnetic resonance imaging protocol. This novel peptide-based, binding-activated MRI method could potentially be used to screen a wide variety of biomolecules.     

De novo metallonucleases based on helix-loop-helix motifs

Three new 42-mer peptides (PR I-III) designed to fold into a hairpin helix-loop-helix motif have been prepared. In the peptide sequence two (PR II-III) or four (PR I) copies of an unnatural amino acid bearing a triazacyclononane metal-ion binding site (ATANP) have been inserted in appropriate positions to allow the ligand subunits to face each other either within the same helix or between the two helices of the hairpin motif. Circular dichroism (CD) studies in solution have shown that the apopeptides adopt a well-defined helix-loop-helix tertiary structure that dimerizes in solution at concentrations above 200 microM to form a four-helix bundle. However, the helical content is strongly dependent on pH and metal-ion binding. Both protonation of the amines of the triazacyclononane units present in the ATANP lateral arm and complexation with Zn(II) ions cause a significant decrease of the helical content of the sequences. The Zn(II) complexes of the three peptides catalyze the transesterification of the RNA model substrate 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP) with different efficiency. The best catalyst appears to be PR I-4 Zn(II), that is, the peptide incorporating four ATANP units. Michaelis-Menten saturation kinetics allowed us to estimate that substrate fully bound to the catalyst reacts 380 times faster than in its absence. The kinetic evidence suggests cooperativity between (at least two) metal ions: one activating the nucleophilic species (directly or indirectly) and the other facilitating nucleophilic attack by coordination of the phosphate.     

The dinuclear Zn(II) complex catalyzed cyclization of a series of 2-hydroxypropyl aryl phosphate RNA models: progressive change in mechanism from rate-limiting P-O bond cleavage to substrate binding

A methoxide-bridged dinuclear Zn(II) complex of 1,3-[N,N'-bis(1,5,9-triazacyclododecane)]propane (1-Zn(II)2:(-OCH3)) was prepared, and its catalysis of the cyclization of a series of 2-hydroxypropyl aryl phosphates (4a-g) was investigated in methanol at pH 9.8, T = 25degreesC by stopped-flow spectrophotometry. An X-ray diffraction structure of the hydroxide analogue of 1-Zn(II)2:(-OCH3), namely 1-Zn(II)2:(-OH), reveals that each of the Zn(II) ions is coordinated by the three N's of the triazacyclododecane units and a bridging hydroxide. The cyclizations of substrates 4a-g reveal a progressive change in the observed kinetics from Michaelis-Menten saturation kinetics for the poorer substrates (4-OCH3 (4g); 4-H (4f); 3-OCH3 (4e); 4-Cl (4d); 3-NO2, (4c)) to second-order kinetics (linear in 1-Zn(II)2:(-OCH3)) for the better substrates (4-NO2,3-CH3 (4b); 4-NO2, (4a)). The data are analyzed in terms of a multistep process whereby a first formed complex rearranges to a reactive complex with a doubly activated phosphate coordinated to both metal ions. The kinetic behavior of the series is analyzed in terms of change in rate-limiting step for the catalyzed reaction whereby the rate-limiting step for the poorer substrates (4g-c) is the chemical step of cyclization of the substrate, while for the better substrates (4b,a) the rate-limiting step is binding. The catalysis of the cyclization of these substrates is extremely efficient. The kcat/KM values for the catalyzed reactions range from 2.75 x 10(5) to 2.3 x 10(4) M-1 s-1, providing an acceleration of 1 x 10(8) to 4 x 10(9) relative to the methoxide reaction (k2OCH3, which ranges from 2.6 x 10(-3) to 5.9 x 10(-6) M-1 s-1 for 4a-g). At a pH of 9.8 where the catalyst is maximally active, the acceleration for the substrates ranges from (1 - 4) x 10(12) relative to the background reaction at the same pH. Detailed energetics calculations show that the transition state for the catalyzed reaction comprising 1-Zn(II)2, methoxide, and 4 is stabilized by about -21 to -23 kcal/mol relative to the transition state for the methoxide reaction. The pronounced catalytic activity is attributed to a synergism between a positively charged catalyst that has high affinity for the substrate and for the transition state for cyclization, and a medium effect involving a reduced polarity/dielectric constant that complements a reaction where an oppositely charged reactant and catalyst experience charge dispersal in the transition state.