Factors governing the metal coordination number in metal complexes from Cambridge Structural Database analyses

The metal coordination number (CN) is a key determinant of the structure and properties of metal complexes. It also plays an important role in metal selectivity in certain metalloproteins. Despite its central role, the preferred CN for several metal cations remains ambiguous, and the factors determining the metal CN are not fully understood. Here, we evaluate how the CN depends on (1) the metal's size, charge, and charge-accepting ability for a given set of ligands, and (2) the ligand's size, charge, charge-donating ability, and denticity for a given metal by analyzing the Cambridge Structural Database (CSD) structures of metal ions in the periodic table. The results show that for a given ligand type, the metal's size seems to affect its CN more than its charge, especially if the ligand is neutral, whereas, for a given metal type, the ligand's charge and charge-donating ability appear to affect the metal CN more than the ligand's size. Interestingly, all 98 metal cations surveyed could adopt more than than one CN, and most of them show an apparent preference toward even rather than odd CNs. Furthermore, as compared to the preferred metal CNs observed in the CSD, those in protein binding sites generally remain the same. This implies that the protein matrix (excluding amino acid residues in the metal's first and second coordination shell) does not impose severe geometrical restrictions on the bound metal cation.     

Factors controlling the reactivity of zinc finger cores

Although the Zn(2+) cation in Zn·Cys(4), Zn·Cys(3)His, Zn·Cys(2)His(2), and Zn(2)Cys(6) cores of zinc finger (Zf) proteins typically plays a structural role, the Zn-bound thiolates in some Zf cores are reactive. Such labile Zf cores can serve as drug targets for retroviral or cancer therapies. Previous studies showed that the reactivity of a Zn-bound thiolate toward electrophiles is significantly reduced if it forms S---NH hydrogen bonds with the backbone amide. However, we found several well-known inactive Zf cores containing Cys ligands with no H-bonding interactions. Here, we show that H bonds from the peptide backbone or bonds from a second Zn cation to Zn-bound S atoms suppress the reactivity not only of these S atoms, but also of Zn-bound S* atoms with no interactions. Indeed, two or more indirect NH---S hydrogen bonds raise the free energy barrier for methylation of a Zn-bound S* in a Cys(4) core more than a direct NH---S* hydrogen bond. These findings help to elucidate why several well-known Zf cores have Cys ligands with no H bonds, but are unreactive. They also help to provide guidelines for distinguishing labile Cys-rich Zn sites from structural ones, which in turn help to identify novel potential Zf drug targets.     

All-electron calculations of the nucleation structures in metal-induced zinc-finger folding: role of the Peptide backbone

Although the folding of individual protein domains has been extensively studied both experimentally and theoretically, protein folding induced by a metal cation has been relatively understudied. Almost all folding mechanisms emphasize the role of the side-chain interactions rather than the peptide backbone in the protein folding process. Herein, we focus on the thermodynamics of the coupled metal binding and protein folding of a classical zinc-finger (ZF) peptide, using all-electron calculations to obtain the structures of possible nucleation centers and free energy calculations to determine their relative stability in aqueous solution. The calculations indicate that a neutral Cys first binds to hexahydrated Zn2+ via its ionized sulfhydryl group and neutral backbone oxygen, with the release of four water molecules and a proton. Another nearby Cys then binds in the same manner as the first one, yielding a fully dehydrated Zn2+. Subsequently, two His ligands from the C-terminal part of the peptide successively dislodge the Zn-bound backbone oxygen atoms to form the native-like Zn-(Cys)2(His)2 complex. Each successive Zn complex accumulates increasingly favorable and native interactions, lowering the energy of the ZF polypeptide, which concomitantly becomes more compact, reducing the search volume, thus guiding folding to the native state. In the protein folding process, not only the side chains but also the backbone peptide groups play a critical role in stabilizing the nucleation structures and promoting the hydrophobic core formation.     

Differences in the conformational state of a zinc-finger DNA-binding protein domain occupied by zinc and copper revealed by electrospray ionization mass spectrometry.

Transition metal ions are important in biological regulation partly because they can bind to and stabilize protein surface domain structures in specific conformations that are involved in key molecular recognition events. There are two C2-C2 type zinc-finger sequences within the highly conserved DNA-binding domain of the estrogen receptor protein (ERDBD). Electrospray ionization (ESI) mass spectrometry has been used to demonstrate that the metal-binding sites within the 71-residue ERDBD can bind either Zn (up to 2) or Cu (up to 4). Evidence for the induction and/or stabilization of a different conformational state with bound Cu is revealed by a characteristic shift in the ESI charge envelope. The 10+ charge state is most abundant for the fully reduced ERDBD apopeptide and the ERDBD-Zn holopeptide (bound Zn does not alter the charge envelope). In contrast, the 8+ charge state is typically the optimum charge state observed for the ERDBD-Cu holopeptide; indeed, the entire charge envelope is frame-shifted to lower charge states with bound Cu. Interpretation of the altered charge states is simplified because (i) a single type of metal-binding ligand (sulfur) is involved in the case of both Zn and Cu binding, and (ii) the two different metal cations are both divalent. Thus, it is likely that the dissimilar charge envelopes represent different peptide conformers, each of which is stabilized by a different type of bound metal ion.(ABSTRACT TRUNCATED AT 250 WORDS)     

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 Stability Versus Kinetic Lability of ZnS4 Core

Density Functional Theory and post‐Hartree Fock calculations reveal an unusual energy profile for Zn? S and Zn? N bond dissociation reactions in several [Zn(SR)₄]^2? and [Zn(Im)(SR)₃]^? complexes. The Zn? S bond dissociation in tetrathiolate dianions, which is highly exothermic in the gas phase, proceeds through a late transition state which can be rationalized on the basis of an avoided crossing resulting from Coulomb repulsion between the anionic fragments and ligand‐to‐metal charge‐transfer in the [Zn(SR)₄]^2? complexes. When solvation models for water, DMSO, or acetonitrile are included, some complexes become stable while others are metastable, so this constitutes the first theoretical model which is in full agreement with the experimental data for various [Zn(SR)₄]^2?, [Zn(SR)₃]^?, and [Zn(Im)(SR)₃]^? complexes. The analysis given here indicates that the Zn(Cys)₄ and Zn(His)(Cys)₃ cores of numerous proteins are metastable with respect to Zn? S and Zn? N bond dissociation, respectively. This is consistent with the kinetic lability at the zinc‐centers and illustrates that in nature, thermodynamic stability is imparted upon the zinc cores by the protein environment.     

Gas-phase dehydrogenation of methanol with mononuclear vanadium-oxide cations

The reactions of methanol with mass-selected V+, VOH+, VO+, and VO2(+) cations are studied by Fourier-transform ion-cyclotron resonance (FT-ICR) mass spectrometry in order to investigate the influence of the formal oxidation state of the metal on the reactivity of vanadium-oxide compounds. Interestingly, the most reactive species is the low-valent hydroxide cation VOH+, for which a formal condensation reaction prevails to afford VOCH3(+). In contrast, atomic V+ is oxidized and the high-valent dioxide cation VO2(+) is reduced by methanol. The dehydrogenation of methanol mediated by VO+ does not involve any change of the metal's oxidation state. For the latter reaction, the experimental results are complemented by a theoretical investigation by using density functional theory.     

Mononuclear versus binuclear metal-binding sites: metal-binding affinity and selectivity from PDB survey and DFT/CDM calculations

Binuclear metal centers in metalloenzymes are involved in a number of hydrolytic, hydration, isomerization, and redox processes. Despite the growing number of studies elucidating their structure, properties, and function, questions regarding certain aspects of the bimetallic proteins' biochemistry still remain, e.g., the following: (i) What are the general characteristics of binuclear sites found in 3D structures such as the range of metal-metal distances and the most common ligand bridging the two metal cations? (ii) How does the presence of a metal cation in one of the binuclear sites affect the metal-binding affinity/selectivity of the other site? (iii) How do the characteristics and metal-binding affinity/selectivity of binuclear sites compare with those of their mononuclear counterparts? Here we address these questions by combining a Protein Data Bank survey of binuclear sites with density functional theory (DFT) combined with continuum dielectric method (CDM) calculations. The results reveal that, for homobinuclear sites, the metal separation depends on the metal's charge and electron-accepting ability, and Asp-/Glu-, bidentately bound to the two cations, is the most common bridging ligand. They also reveal that Mg2+ occupying one of the binuclear sites attenuates the metal-binding affinity but enhances the selectivity of its neighboring site, compared to the corresponding mononuclear counterparts. These findings are consistent with available experimental data. The weak metal binding of one of the binuclear sites would enhance the metal cofactor mobility in achieving the transition state, whereas the enhanced selectivity of Mg2+-Mg2+ centers helps protect against unwanted substitutions by transition metal ions, which are generally stronger Lewis acids compared to Mg2+.     

Effects of metal cation coordination on fluorescence properties of a diethylenetriamine bearing two end pyrene fragments

Fluorescence properties of a diethylenetriamine bearing two end pyrene fragments (L) have been studied in water, where effects of adding metal cations (Zn2+, Cd2+, Cu2+, Hg2+, Ag+) on the emission properties of L have been studied. Without metal cations, L shows dual-mode fluorescence consisting of monomer and excimer emissions. The monomer emission intensity (I(M)) is strong at acidic pH but decreases with a pH increase because of an electron transfer (ET) from the unprotonated nitrogen atoms to the excited pyrene fragment. The excimer emission is due to the static excimer formed via a direct photoexcitation of the intramolecular ground-state dimer (GSD) of the end pyrene fragments. The excimer emission intensity (I(E)) is weak at acidic pH but increases with a pH increase because of the GSD stability increase associated with the deprotonation of the polyamine chain. Addition of metal cations leads to I(M) decrease, where chelation-driven I(M) enhancement does not occur even with diamagnetic Zn2+ and Cd2+ at any pH. This is because a pyrene-metal cation pi-complex, formed via a donation of pi-electron of the pyrene fragment to the adjacent metal center, suppresses the monomer photoexcitation. I(E) also decreases upon addition of metal cations because the pyrene-metal cation pi-complex weakens pi-stacking interaction of the end pyrene fragments, leading to GSD stability decrease. The emission properties of L-Zn2+ complexes were studied by means of time-resolved fluorescence decay measurements, and the effects of adding a less-polar organic solvent were also studied to clarify the detailed emission properties.     

A comparison of the electrophilic reactivities of Zn2+ and acetic acid as catalysts of enolization: imperatives for enzymatic catalysis of proton transfer at carbon

The deprotonation of the alpha-CH3 and alpha-CH2OD groups of hydroxyacetone and the alpha-CH3 groups of acetone in the presence of acetate buffer and zinc chloride in D2O at 25 degrees C was followed by monitoring the incorporation of deuterium by 1H NMR spectroscopy, and the rate laws for catalysis of these reactions by acetate anion and zinc dication were evaluated. Relative to solvent water at a common standard state of 1 M, Zn2+ provides 6.3 and 4.4 kcal/mol stabilizations, respectively, of the transition states for deprotonation of the alpha-CH2OD and alpha-CH3 groups of hydroxyacetone by acetate anion, and a smaller 3.3 kcal/mol stabilization of the transition state for deprotonation of the alpha-CH3 group of acetone. There is only a 1.4 kcal/mol smaller stabilization of the transition state for the acetate-ion-promoted deprotonation of acetone by the Br?nsted acid acetic acid than by Zn2+, which shows that, in the absence of a chelate effect, there is no large advantage to the use of a metal dication rather than a Br?nsted acid to stabilize the transition state for deprotonation of alpha-carbonyl carbon.     

Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study

Many of the essential metalloproteins are located in the cell, whose cytoplasmic fluid contains several small inorganic anions, such as Cl-, NO2-, NO3-, H2PO4-, and SO4(2-), that play an indispensable role in determining the cell's volume, regulating the cell's pH, signal transduction, muscle contraction, as well as cell growth and metabolism. However, the physical principles governing the competition between these abundant, intracellular anions and protein or nucleic acid residues in binding to cytoplasmic metal cations such as Na+, K+, Mg2+, and Ca2+ are not well understood; hence, we have delineated the physicochemical basis for this competition using density functional theory in conjunction with the continuum dielectric method. The results show that the metal cation can bind to its target protein against a high background concentration of inorganic anions because (i) desolvating a negatively charged Asp/Glu carboxylate in a protein cavity costs much less than desolvating an inorganic anion in aqueous solution and (ii) the metal-binding site acts as a polydentate ligand that uses all its ligating entities to bind the metal cation either directly or indirectly. The results also show that the absolute hydration free energy of the "alien" anion as well as the net charge and relative solvent exposure of the metal-binding protein cavity are the key factors governing the competition between protein and inorganic ligands for a given cytoplasmic metal cation. Increasing the net negative charge of the protein cavity, while decreasing the number of available amide groups for metal binding, protects the metal-bound ligands from being dislodged by cellular anions, thus revealing a "protective" role for carboxylate groups in a protein cavity, in addition to their role in high affinity metal-binding.     

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.     

Modulation of boradiazaindacene emission by cation-mediated oxidative PET

[reaction: see text] Bright green boradiazaindacene fluorescence is quenched by an oxidative photoinduced electron transfer (PET) from the excited state fluorophore to the bipyridyl unit complexed to metal cations. The closed shell diamagnetic cation Zn(II) is one of the most effective quenchers of fluorescence in this system, demonstrating that the quenching is not simply related to the facilitated intersystem crossing. The molecule also acts as a NOR logic gate with two chemical inputs, TFA and Zn(II).     

Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry

The binding of a series of benzoxazole analogs with different amide- and ester-linked side chains to duplex DNA in the absence and presence of divalent metal cations is examined. All ligands were found to form complexes with Ni2+, Cu2+, and Zn2+, with 2:1 ligand/metal cation binding stoichiometries dominating for ligands containing shorter side chains (2, 6, 7, and 8), while 1:1 complexes were the most abundant for ligands with long side chains (9, 10, and 11). Ligand binding with duplex DNA in the absence of metal cations was assessed, and the long side-chain ligands were found to form low abundance complexes with 1:1 ligand/DNA binding stoichiometries. The ligands with the shorter side chains only formed DNA complexes in the presence of metal cations, most notably for 7 and 8 binding to DNA in the presence of Cu2+. The binding of long side-chain ligands was enhanced by Cu2+ and to a lesser degree by Ni2+ and Zn2+. The cytotoxicities of all of the ligands against the A549 lung cancer and MCF7 breast cancer cell lines were also examined. The ligands exhibiting the most dramatic metal-enhanced DNA binding also demonstrated the greatest cytotoxic activity. Both 7 and 8 were found to be the most cytotoxic against the A549 lung cancer cell line and 8 demonstrated moderate cytotoxicity against MCF7 breast cancer cells. Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds.     

Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.     

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.     

Molecular Machines: Stimulation of Cation Motion in Molecular Switches

The theoretical aspects of the mechanism of the motion of cations and ligands in molecular machines referred to as redox switches are presented. The interrelated properties of cations—the energetic, electrochemical, spectral, and magnetic properties; their propensity to form either covalent or ionic bonds; and the relative softness and hardness of cations and ligands—stimulate molecular motion. These properties determine the thermal stability and stability to destruction caused by electrochemical processes and, eventually, the maximal number of transformation cycles. The maximal efficiency of redox switches is attained when the redox reaction involves a cation with a half-filled (d ⁵, f ⁷) or complete (d ¹⁰, f ¹⁴) electronic shell. The role of the Jahn-Teller effect is considered: it is responsible for geometry distortion, which stimulates cation motion. The properties of nd and 4f cations are compared from the standpoint of their use for designing redox switches. In switches constructed on the basis of supramolecular compounds containing hard and soft moieties, softer cations (Fe²⁺, Co²⁺, Cu⁺, etc.) prefer to coordinate to soft ligands and harder cations (Fe³⁺, Co³⁺, Cu²⁺, etc.) prefer to coordinate to hard ligands. A cation moves due to the soft-hard change of its coordination sphere in the course of the redox reaction. Design of redox switches based on solid compounds with a cation in mixed oxidation state is shown to be promising. Cations can change their oxidation state with a change in temperature or pressure. The possibility of designing “magnetic switches” is considered.