Thermodynamics of metal ion binding. 2. Metal ion binding by carbonic anhydrase variants

The ability to construct molecular motifs with predictable properties in aqueous solution requires an extensive knowledge of the relationships between structure and energetics. The design of metal binding motifs is currently an area of intense interest in the bioorganic community. To date synthetic motifs designed to bind metal ions lack the remarkable affinities observed in biological systems. To better understand the structural basis of metal ion affinity, we report here the thermodynamics of binding of divalent zinc ions to wild-type and mutant carbonic anhydrases and the interpretation of these parameters in terms of structure. Mutations were made both to the direct His ligand at position 94 and to indirect, or second-shell, ligands Gln-92, Glu-117, and Thr-199. The thermodynamics of ligand binding by several mutant proteins is complicated by the development of a second zinc binding site on mutation; such effects must be considered carefully in the interpretation of thermodynamic data. In all instances modification of the protein produces a complex series of changes in both the enthalpy and entropy of ligand binding. In most cases these effects are most readily rationalized in terms of ligand and protein desolvation, rather than in terms of changes in the direct interactions of ligand and protein. Alteration of second-shell ligands, thought to function primarily by orienting the direct ligands, produces profoundly different effects on the enthalpy of binding, depending on the nature of the residue. These results suggest a range of activities for these ligands, contributing both enthalpic and entropic effects to the overall thermodynamics of binding. Together, our results demonstrate the importance of understanding relationships between structure and hydration in the construction of novel ligands and biological polymers.     

Metal binding specificity in carbonic anhydrase is influenced by conserved hydrophobic core residues.

The role of highly conserved aromatic residues surrounding the zinc binding site of human carbonic anhydrase II (CAII) in determining the metal ion binding specificity of this enzyme has been examined by mutagenesis. Residues F93, F95, and W97 are located along a beta-strand containing two residues that coordinate zinc, H94 and H96, and these aromatic amino acids contribute to the high zinc affinity and slow zinc dissociation rate constant of CAII [Hunt, J. A., and Fierke, C. A. (1997) J. Biol. Chem. 272, 20364-20372]. Substitutions of these aromatic amino acids with smaller side chains enhance the copper affinity (up to 100-fold) while decreasing the affinity of both cobalt and zinc, thereby altering the metal binding specificity up to 10(4)-fold. Furthermore, the free energy of the stability of native CAII, determined by solvent-induced denaturation, correlates positively with increased hydrophobicity of the amino acids at positions 93, 95, and 97 as well as with cobalt and zinc affinity. Conversely, increased copper affinity correlates with decreased protein stability. Zinc specificity is therefore enhanced by formation of the native enzyme structure. These data suggest that the hydrophobic cluster in CAII is important for orienting the histidine residues to stabilize metals bound with a distorted tetrahedral geometry and to destabilize the trigonal bipyramidal geometry of bound copper. Knowledge of the structural factors that lead to high metal ion specificity will aid in the design of metal ion biosensors and de novo catalytic sites.     

Interaction of acetazolamide and 4-nitrothiophenolate ion with bivalent metal ion derivatives of bovine carbonic anhydrase.

The stability and rate constants for the interaction of acetazolamide (diamox) and 4-nitrothiophenolate ion (NTP) with the bivalent Mn, Co, Ni, Cu and Cd forms of bovine carbonic anhydrase have been measured by utilizing the distinct visible spectra of each metalloenzyme-NTP adduct. Differing stabilities of the various NTP and (particularly) diamox complexes reside mainly in varying values for the dissociation rate constants (kd). Intrinsic formation rate constants (for the acid form of the enzyme reacting with the basic form of the ligand) are uniformly high (greater than or equal 2 X 10(7) M-1 s-1 at 25 degrees C). Invariance of kd with pH and a bell-shaped log K-pH profile with the Cu-enzyme adducts are features observed previously with the native enzyme. Binding of NTP with the Cu and Cd metalloenzymes is stronger than to the native form.     

Metal poison inhibition of carbonic anhydrase

Carbonic anhydrase is inhibited by the “metal poison” cyanide. Several spectroscopic investigations of carbonic anhydrase where the natural zinc ion has been replaced by cobalt have further strengthened the view that cyanide and cyanate bind directly to the metal. We have determined the structure of human carbonic anhydrase II inhibited by cyanide and cyanate, respectively, by X-ray crystallography. It is shown that the inhibitors replace a molecule of water, which forms a hydrogen bond to the peptide nitrogen of Thr-199 in the native structure. The coordination of the zinc ion is hereby left unaltered compared to the native crystal structure, so that the zinc coordinates three histidines and one molecule of water or hydroxyl ion in a tetrahedral fashion. The binding site of the two inhibitors is identical to what earlier has been suggested to be the position of the substrate (CO₂) when attacked by the zinc bound hydroxyl ion. The peptide chain undergoes no significant alterations upon binding of either inhibitor. © 1993 Wiley-Liss, Inc.     

Probing determinants of the metal ion selectivity in carbonic anhydrase using mutagenesis

Few studies measuring thermodynamic metal ion selectivity of metalloproteins have been performed, and the major determinants of metal ion selectivity in proteins are not yet well understood. Several features of metal ion binding sites and metal coordination have been hypothesized to alter the transition metal selectivity of chelators, including (1) the polarizability of the coordinating atom, (2) the relative sizes of the binding site and the metal ion, and (3) the metal ion binding site geometry. To test these hypotheses, we have measured the metal ion affinity and selectivity of a prototypical zinc enzyme, human carbonic anhydrase II (CAII), and a number of active site variants where one of the coordinating ligands is substituted by another side chain capable of coordinating metal. CAII and almost all of the variants follow the inherent metal ion affinity trend suggested by the Irving-Williams series, demonstrating that this trend operates within proteins as well as within small molecule chelators and may be a dominant factor in metal ion selectivity in biology. Neither the polarizability of the liganding side chains nor the size of the metal ion binding site correlates strongly with metal ion specificity; instead, changes in metal ion specificity in the variants correlate with the preferred coordination number and geometry of the metal ion. This correlation suggests that a primary feature driving deviations from the inherent ligand affinity trend is the positioning of active site groups such that a given metal ion can adopt a preferred coordination number/geometry.     

Effect of metal binding on the intrinsic fluorescence of bovine carbonic anhydrase

Bovine carbonic anhydrase shows an intrinsic fluorescence which results from tryptophans located in different microenvironments. It is possible to attribute the whole fluorescence to at least two types of tryptophan.This fluorescence is differently affected by the binding of different metals. In fact while Zn²⁺ causes an increase of the fluorescence yield, the binding of Co²⁺, Cu²⁺ and Hg²⁺ is followed by a quenching of the fluorescence. The quenching is about 40% for the cobalt, 80% for the copper and 60% for the mercury derivative. The binding of Cu²⁺ and Hg²⁺ induces also a change in the shape of the fluorescence emission spectrum. This fact suggests a different influence of the metals on the various types of tryptophan.The fluorescence quenching induced by iodide which can bind to the metal and act as a fluorescence perturbing agent is also indicative of the presence of different tryptophans.     

A novel carbonic anhydrase II binding site regulates NHE1 activity

Carbonic anhydrase II (CAII) binds to and regulates transport by the NHE1 isoform of the mammalian Na(+)/H(+) exchanger. We localized and characterized the CAII binding region on the C-terminal tail of the Na(+)/H(+) exchanger. CAII did not bind to acidic sequences in NHE1 that were similar to the CAII binding site of bicarbonate transporters. Instead, by expressing a variety of fusion proteins of the C-terminal region of the Na(+)/H(+) exchanger, we demonstrated that CAII binds to the penultimate group of 13 amino acids of the cytoplasmic tail. Within this region, site-specific mutagenesis demonstrated that amino acids S796 and D797 form part of a novel CAII binding site. Phosphorylation of the C-terminal 26 amino acids by heart cell extracts did not alter CAII binding to this region, but phosphorylation greatly increased CAII binding to a protein containing the C-terminal 182 amino acids of NHE1. This suggested that an upstream region of the cytoplasmic tail acts as an inhibitor of CAII binding to the penultimate group of 13 amino acids. The results demonstrate that a novel phosphorylation-regulated CAII binding site exists in distal amino acids of the NHE1 tail.     

Structural analysis of inhibitor binding to human carbonic anhydrase II.

X-ray crystal structures of carbonic anhydrase II (CAII) complexed with sulfonamide inhibitors illuminate the structural determinants of high affinity binding in the nanomolar regime. The primary binding interaction is the coordination of a primary sulfonamide group to the active site zinc ion. Secondary interactions fine-tune tight binding in regions of the active site cavity >5 A away from zinc, and this work highlights three such features: (1) advantageous conformational restraints of a bicyclic thienothiazene-6-sulfonamide-1,1-dioxide inhibitor skeleton in comparison with a monocyclic 2,5-thiophenedisulfonamide skeleton; (2) optimal substituents attached to a secondary sulfonamide group targeted to interact with hydrophobic patches defined by Phe131, Leu198, and Pro202; and (3) optimal stereochemistry and configuration at the C-4 position of bicyclic thienothiazene-6-sulfonamides; the C-4 substituent can interact with His64, the catalytic proton shuttle. Structure-activity relationships rationalize affinity trends observed during the development of brinzolamide (Azopt), the newest carbonic anhydrase inhibitor approved for the treatment of glaucoma.     

Determination of ionization state by resonance Raman spectroscopy Sulfonamide binding to carbonic anhydrase.

Resonance Raman (RR) spectroscopy has been used to study the ionization state of the sulfonamide, 4'-sulfamylphenyl-2-azo-7-acetamido-1-hydroxynaphthalene-3,-6-disulfonate (Neoprontosil), bound to carbonic anhydrase. The correlation of effects of pH and deuteration on the spectra of model compounds with these effects on the Neoprotosil spectrum allows us to assign spectral bands in the 900-1000 and 100-1200 cm-1 regions to the SO2NH2 group. Large shifts in these bands occur upon ionization of the sulfonamide. On the basis of the positions of bands in the enzyme complex, it was determined that the sulfonamide was bound to the enzyme as SO2NH2, rather than as SO2NH-. Rates of association and dissociation and the dissociation equilibrium constant were measured as a function of pH. The rate behavior for Neoprontosil is consistent with that observed for other sulfonamides and kdissoc/kassoc = kdissoc, suggesting a one-step binding mechanism. Since RR spectroscopy establishes that the final ionization state of the sulfonamide in the enzyme complex is SO2NH2, protonated sulfonamide must bind directly to basic form of the enzyme. These conclusions suggest that sulfonamides form "outer-space" complexes with metal at the enzyme active site.     

Thermodynamics of carbonic anhydrase catalysis. A comparison between human isoenzymes B and C

The CO2 hydration and HCO3- dehydration activities of human red cell carbonic anhydrase isozymes B and C (HCAB and HCAC) have been studied as a function of temperature from 0 degrees to 37 degrees C. The Arrhenius plots of ln kcat versus 1/T are linear for both isozymes in both hydration and dehydration reactions, indicating that the rate-determining steps remain unchanged over this temperature range. The 37 degrees C hydration kcat, at pH 7.5, is 13 X 10(5) s-1 for isozyme C and 0.71 X 10(5) s-1 for isozyme B. Km, for hydration, is 10 mM for C and 5 mM for B, and invariant with temperature. The uncatalyzed reactions are significantly affected by temperature, 30- to 40-fold rate enhancements being observed from 0 degrees to 37 degrees C. The enzyme-catalyzed processes are much less sensitive to temperature, the rate enhancements being 2- to 3-fold for HCAB and 5- to 6-fold for HCAC in this temperature range. These observations are consistent with a significant lowering of the free energy of activation by both isozymes. This effect is greater for C accounting for its higher catalytic power. The enthalpy of activation, at pH 7.5 and 8.2, in the rate-limiting step is considerably less for the B enzyme compared to C. This is, however, more than offset by a large negative entropy of activation in the case of HCAB. This observation indicates either a mechanistic difference in the rate-limiting events or a difference in the structural organizations of the active sites of the two isozymes, or both.     

Structural influence of hydrophobic core residues on metal binding and specificity in carbonic anhydrase II

Aromatic residues in the hydrophobic core of human carbonic anhydrase II (CAII) influence metal ion binding in the active site. Residues F93, F95, and W97 are contained in a beta-strand that also contains two zinc ligands, H94 and H96. The aromatic amino acids contribute to the high zinc affinity and slow zinc dissociation rate constant of CAII [Hunt, J. A., and Fierke, C. A. (1997) J. Biol. Chem. 272, 20364-20372]. Substitution of these aromatic amino acids with smaller side chains enhances Cu(2+) affinity while decreasing Co(2+) and Zn(2+) affinity [Hunt, J. A., Mahiuddin, A., & Fierke, C. A. (1999) Biochemistry 38, 9054-9062]. Here, X-ray crystal structures of zinc-bound F93I/F95M/W97V and F93S/F95L/W97M CAIIs reveal the introduction of new cavities in the hydrophobic core, compensatory movements of surrounding side chains, and the incorporation of buried water molecules; nevertheless, the enzyme maintains tetrahedral zinc coordination geometry. However, a conformational change of direct metal ligand H94 as well as indirect (i.e., "second-shell") ligand Q92 accompanies metal release in both F93I/F95M/W97V and F93S/F95L/W97M CAIIs, thereby eliminating preorientation of the histidine ligands with tetrahedral geometry in the apoenzyme. Only one cobalt-bound variant, F93I/F95M/W97V CAII, maintains tetrahedral metal coordination geometry; F93S/F95L/W97M CAII binds Co(2+) with trigonal bipyramidal coordination geometry due to the addition of azide anion to the metal coordination polyhedron. The copper-bound variants exhibit either square pyramidal or trigonal bipyramidal metal coordination geometry due to the addition of a second solvent molecule to the metal coordination polyhedron. The key finding of this work is that aromatic core residues serve as anchors that help to preorient direct and second-shell ligands to optimize zinc binding geometry and destabilize alternative geometries. These geometrical constraints are likely a main determinant of the enhanced zinc/copper specificity of CAII as compared to small molecule chelators.     

Kinetics and mechanism of dissociation of zinc ion from carbonic anhydrase.

The kinetics of dissociation of Zn2+ from the metalloenzyme carbonic anhydrase was measured over a range of pH, temperature, and acetate concentration. The rate of dissociation is extremely slow at neutral pH (t1/2 approximately 3) years, 4 degrees C), but increases in almost direct proportion to the hydrogen ion concentration and is enhanced in the presence of 1,10-phenanthroline or acetate. The thermodynamic stability of the zinc-apoenzyme complex was determined over a range of pH from rate data on binding and dissociation (stability constants 10(9)-10(11) M-1, 25 degrees C). The great stability of the complex and slow exchange of the apoenzyme ligand is attributed, at least in part, to the rigidity of the multidentate protein ligand.     

Carbon isotope effect on dehydration of bicarbonate ion catalyzed by carbonic anhydrase

The carbon-13 kinetic isotope effect on the dehydration of HCO3- by bovine carbonic anhydrase has been measured. To accomplish this, bicarbonate was added to a buffer solution at pH 8 containing carbonic anhydrase under conditions where purging of the product CO2 from the solution is rapid. Measurement of the isotopic composition of the purged CO2 as a function of the concentration of carbonic anhydrase permits calculation of the isotope effect on the enzymic reaction. The isotope effect on the dehydration is k12/k13 = 1.0101 +/- 0.0004. This effect is most consistent with a ping-pong mechanism for carbonic anhydrase action, in which proton transfer to or from the enzyme occurs in a step separate from the dehydration step. Substrate and product dissociation steps are at least 2-3-fold faster than the hydration/dehydration step.     

Minireview plant carbonic anhydrase.

This article reviews the literature concerning plant carbonic anhydrase. The following topics are discussed: discovery, molecular weight and structure, zinc content, amino acid composition, mechanism and kinetics of catalytic activity, and function and localization in the plant. Where deficiencies exist in the literature on plant carbonic anhydrase reference is made to articles dealing with mammalian carbonic anhydrase. The theories of carbonic anhydrase function in plants are examined critically and evaluated in the light of existing evidence.     

Steroids interfere with human carbonic anhydrase activity by using alternative binding mechanisms

Bile acids have been shown to inhibit human (h) carbonic anhydrases (CA, EC 4.2.1.1) along the gastrointestinal tract, including hCA II. The elucidation of the hormonal inhibition mechanism of the bile acid cholate to hCA II was provided in 2014 by X-ray crystallography. Herein, we extend the inhibition study to a wealth of steroids against four relevant hCA isoforms. Steroids displaying pendants and functional groups of the carboxylate, phenolic or sulfonate types appended at the tetracyclic ring were shown to inhibit the cytosolic CA II and the tumor-associated, transmembrane CA IX in a medium micromolar range (38.9–89.9?µM). Docking studies displayed the different chemotypes CA inhibition mechanisms. Molecular dynamics (MD) gave insights on the stability over time of hyocholic acid binding to CA II.     

Immunohistochemical demonstration of carbonic anhydrase.

Rabbits were immunized using human erythroxyte carbonic anhydrase B (HCA B) purified by the modified methods of Armstrong et al. (1966) and Bernstein and Schraer (1972). The globulin fraction was isolated by ammonium sulphate precipitation. The anti-HCA B globulin was specific, when judged using the double diffusion technique of Ouchterlony and immunoelectrophoresis. No cross reaction with human erythrocyte carbonic anhydrase C was found, but cross reactions with erythrocyte carbonic anhydrase from rat, mouse and guinea pig were observed. Flurorescein isothiocyanate conjugated goat anti-rabbit globulin was used for the localization of HCA B in tissue sections and erythrocytes on slides.