Adsorption of Ni2+ on the surface of molecularly imprinted adsorbent from Penicillium chysogenum mycelium

The adsorption capacity for Ni²⁺ on to the surface molecular imprinting adsorbent on Penicillium chysogenum mycelium (the surface-imprinted adsorbent) was 40–45 mg g^–1 (using 200 mg Ni²⁺ l^–1), two times of the mycelium adsorbent. The surface-imprinted adsorbent had good stability at pH 28. The optimal concentration of EDTA for desorption was 0.1 to 0.5 g l^–1. The surface imprinted adsorbent could be reused 15 times without losing its uptake.     

Ni2+ binds to active site of hen egg-white lysozyme and quenches fluorescence of Trp62 and Trp108

We found that the maximum emission of the tryptophyl fluorescence of hen egg-white lysozyme is shifted from 337 to 323 nm and quenched to the extent of 55% with an increase in concentrations of NiCl2 from 0 to 2M in 50 mM Na acetate buffer (pH 4.7). In contrast, NaCl does not influence the fluorescence of lysozyme up to 2M. To elucidate the particular effects of Ni2+ on the tryptophyl fluorescence of lysozyme, we have measured the assembly behavior and secondary structure of lysozyme in various concentrations of NiCl2, and determined the structures of lysozyme crystals grown in 0.3, 0.5, and 1.0M NiCl2, respectively. The results of analytical centrifugation and circular dichroism experiments show that lysozyme keeps a monomer state and has an identical secondary structure, irrespective of NiCl2 concentrations. The crystal structures show that all crystals grown in different concentrations of NiCl2 have an identical main chain and side chain conformation. And one Ni2+ binding with Odelta atom of Asp52 in the active site and coordinating with five water molecules to form hexagonal coordination has been determined for each crystal structure. Based on these results, we have proposed that Ni2+ quenches the fluorescence of Trp62 and Trp108 due to the binding of Ni2+ to the active site of lysozyme.     

Ca2+ binding in the active site of HincII: implications for the catalytic mechanism

The 2.8 A crystal structure of the type II restriction endonuclease HincII bound to Ca(2+) and cognate DNA containing GTCGAC is presented. The DNA is uncleaved, and one calcium ion is bound per active site, in a position previously described as site I in the related blunt cutting type II restriction endonuclease EcoRV [Horton, N. C., Newberry, K. J., and Perona, J. J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95 (23), 13489-13494], as well as that found in other related enzymes. Unlike the site I metal in EcoRV, but similar to that of PvuII, NgoMIV, BamHI, BglII, and BglI, the observed calcium cation is directly ligated to the pro-S(p) oxygen of the scissile phosphate. A calcium ion-ligated water molecule is well positioned to act as the nucleophile in the phosphodiester bond cleavage reaction, and is within hydrogen bonding distance of the conserved active site lysine (Lys 129), as well as the pro-R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these groups in the catalytic mechanism. Kinetic data consistent with an important role for the 3'-phosphate group in DNA cleavage by HincII are presented. The previously observed sodium ion [Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47] persists in the active sites of the Ca(2+)-bound structure; however, kinetic data show little effect on the single-turnover rate of DNA cleavage in the absence of Na(+) ions.     

Functional mimicry of the active site of glutathione peroxidase by glutathione imprinted selenium-containing protein

For imitating the active site of antioxidant selenoenzyme glutathione peroxidase (GPx), an artificial enzyme selenosubtilisin was employed as a scaffold for reconstructing substrate glutathione (GSH) specific binding sites by a bioimprinting strategy. GSH was first covalently linked to selenosubtilisin to form a covalent complex GSH-selenosubtilisin through a Se-S bond, then the GSH molecule was used as a template to cast a complementary binding site for substrate GSH recognition. The bioimprinting procedure consists of unfolding the conformation of selenosubtilisin and fixing the new conformation of the complex GSH-selenosubtilisin. Thus a new specificity for naturally occurring GPx substrate GSH was obtained. This bioimprinting procedure facilitates the catalytic selenium moiety of the imprinted selenosubtilisin to match the reactive thiol group of GSH in the GSH binding site, which contributes to acceleration of the intramolecular catalysis. These imprinted selenium-containing proteins exhibited remarkable rate enhancement for the reduction of H2O2 by GSH. The average GPx activity was found to be 462 U/micromol, and it was approximately 100 times that for unimprinted selenosubtilisin. Compared with ebselen, a well-known GPx mimic, an activity enhancement of 500-fold was observed. Detailed steady-state kinetic studies demonstrated that the novel selenoenzyme followed a ping-pong mechanism similar to the naturally occurring GPx.     

Development of the active site model for calcium-containing quinoprotein alcohol dehydrogenases

A new PQQ model compound [dimethyl 7-(1,4,7,10-tetraoxa-13-azacyclopentadec-13-yl)carbonyl-4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,9-dicarboxylate, 1], in which a 1-aza-15-crown-5 group is attached through an amide linkage at the 7-position, has been synthesized in order to develop an efficient model system of calcium-containing quinoprotein alcohol dehydrogenases. It has been found that Ca²⁺ binds to the quinone most strongly among the alkaline earth metal ions examined (Ca²⁺+>Sr²⁺+≫Ba²⁺+≫Mg²⁺) and the binding constant (K_M) for Ca²⁺ is as large as 2.1×10⁵ M⁻¹. Formation of the C-5 hemiacetal derivatives with ethanol is also investigated spectrophotometrically to show that the alcohol-addition to the quinone is enhanced in the presence of the metal ions. In this case, Ca²⁺ and Sr²⁺ show a similar efficiency that is several times larger than that of Ba²⁺. Addition of a strong base such as DBU (1,8-diazabicyclo[5.4.0]undec-7-ene) into a MeCN solution containing the metal ion complex of 1 and ethanol leads to redox reactions to give the Ca²⁺ complex of 1H₂ (quinol form) and acetaldehyde. Kinetic studies on the redox reactions have been performed to gain insight into the mechanism of the alcohol-oxidation reaction catalyzed by the metal complexes of coenzyme PQQ.     

A model for the active site of skeletal muscle myosin.

A model for a main element of the active site of skeletal muscle myosin is presented that relates directly to the 92 amino acid fragment (p₁₀) of myosin recently described by Elzinga &; Collins (1977). In this model, the substrate, an eight-membered cyclic complex of MgATP, fits tightly into a 16 amino acid segment of p₁₀ and interacts with seven of its amino acids. A main feature of the model is the important role played by the one molecule of N^τ-methylhistidine² that is present in each myosin heavy chain. At the site, it is postulated that this rare amino acid functions as a donor ligand to Mg²⁺. Once N^τ-methylhistidine is put in place next to the metal, the other amino acids that appear to form a pocket come easily into position around the MgATP. These amino acids with their postulated functions are: tyrosine 72, which through a Mg-bound water, or perhaps directly, is attached to the Mg; histidine 76, which donates a proton to the P_γ of ATP; lysine 78, which binds electrostatically to P_β of ATP; phenylalanines 80 and 81, which flank the purine ring of ATP; and aspartate 66, which forms a hydrogen bond to the 6-amino group of adenine. The Mg-coordination role ascribed to N^τ-methylhistidine 69 in skeletal muscle myosin could be taken by histidine 69 in cardiac myosin and in other muscle myosins that do not contain the methylated amino acid.The choice of p₁₀ to contain a main element of the active site is based on: (a) the presence in p₁₀ of the essential sulfhydryl groups, SH1 and SH2, whose modification affects the ATPase activity of myosin; (b) the presence in ρ₁₀ of N^τ-methylhistidine, an unusual amino acid whose methylation in skeletal muscle we take as an indicator for a special function at the active site; (c) the position of p₁₀ in the primary structure near the junction between subfragment 1 and subfragment 2 (the hinge region) where, we postulate, enzymatic events at the active site are coupled to movements of the hinge that occur during contraction; (d) indications that the DTNB light chain, probably involved in regulation, is also near the hinge; (e) the effects of MgATP at the active site on the chemical reactivity of three SH groups (SH1, SH2 and SH3) located near the hinge; and (f) the effect of hinge cleavage on the oxygen exchange reaction catalyzed at the active site. The correlation of all these observations forms the basis for our placement of part of the active site on p₁₀ near the subfragment 1-subfragment 2 hinge.     

Affinity labeling of the active site of the Ca2+-ATPase of sarcoplasmic reticulum

The inactivation of sarcoplasmic reticulum ATPase by fluorescein isothiocyanate (FITC) was shown to have a hyperbolic dependence on the concentration of FITC. The results were quantitatively accounted for by a model in which the reagent first binds reversibly (Kf = 70 microM) to the ATPase and then reacts irreversibly (kmax = 0.8 and 2 min-1 in the absence and presence of 1 mM Mg2+, respectively) to form inactive enzyme. Comparison with the rate constant for the reaction of the model compound alpha-acetyllysine with FITC showed that the FITC-reactive lysyl side-chain of the ATPase is not unusually reactive, indicating that the specificity of the reaction is due to affinity labeling behavior of the reagent. This was supported by protection experiments using ATP, ADP, AdoPP[NH]P, ITP, and TNP-ATP, all of which displayed protection constants similar to their known binding constants to the active site of the ATPase. Both inorganic phosphate and orthovanadate were effective in preventing inactivation by FITC, and calcium only partially reversed the effect of these anions, implying the existence of a ternary complex such as Ca2.E.Pi. Since all ligands (ATP, ADP and Pi) which bind or react at the catalytic site protect it, only the unliganded form appears to bind and react with FITC. Addition of calcium to the MgATP complex of the ATPase caused an increase in the FITC inactivation rate, implying that during turnover there is a larger fraction of unliganded enzyme present, i.e., substrate binding is weaker (Ks is larger). Protection was also observed with fluorescein and two related dyes, eosin and erythrosin. Like FITC, the isothiocyanates of these dyes were effective inactivators. In separate experiments, these two dyes were shown to promote photoinactivation of the ATPase. ATP exerted a protective effect with a concentration dependence consistent with high-affinity active-site binding.     

A model for the salt effect on adsorption equilibrium of basic protein to dye-ligand affinity adsorbent

A model describing the salt effect on adsorption equilibrium of a basic protein, lysozyme, to Cibacron Blue 3GA-modified Sepharose CL-6B (CB-Sepharose) has been developed. In this model, it is assumed that the presence of salt causes a fraction of dye-ligand molecules to lodge to the surface of the agarose gel, resulting from the induced strong hydrophobic interaction between dye ligand and agarose matrix. The salt effect on the lodging of dye-ligand is expressed by the equilibrium between salt and dye-ligand. For the interactions between protein and vacant binding sites, stoichiometric equations based either on cation exchanges or on hydrophobic interactions are proposed since the CB dye can be regarded as a cation exchanger contributed by the sulfonate groups on it. Combining with the basic concept of steric mass-action theory for ion exchange, which considers both the multipoint nature and the macromolecular steric shielding of protein adsorption, an explicit isotherm for protein adsorption equilibrium on the dye-ligand adsorbent is formulated, involving salt concentration as a variable. Analysis of the model parameters has yielded better understanding of the mechanism of salt effects on adsorption of the basic protein. Moreover, the model predictions are in good agreement with the experimental data over a wide range of salt and ligand concentrations, indicating the predictive nature of the model.     

Independent bindings of Mn2+ and Mg2+ to the active site of B. cereus glutamine synthetase

Glutamine synthetase purified from Bacillus cereus IFO 3131 was modified by iodoacetamide and the ATP analog 5'-p-fluorosulfonylbenzoyladenosine (FSBA). Only Mg2+-dependent activity was inactivated by iodoacetamide, whereas only Mn2+-dependent activity was inactivated by FSBA. When iodoacetamide-treated enzyme was reacted with FSBA, Mn2+-dependent activity was also inactivated. Mg2+ plus Mn2+-dependent activity was inactivated in any case. The results suggested that the binding sites of Mn2+ and Mg2+ are separate from each other in the active site of B. cereus glutamine synthetase and that bindings of Mg2+ and Mn2+ to each site are required for normal activity in vivo.     

A topographical model for the c-AMP phosphodiesterase III active site.

With this minireview, concepts about how c-AMP and various inhibitor molecules interact with the phosphodiesterases seem to have come full-circle. It will be proposed and elaborated herein that an understanding of SAR for the newest, "second generation" PDE inhibitors is best accomplished by adopting a model that supposes that these compounds are transition state inhibitors. The analysis finds an interesting parallel with early studies where it was recognized that c-AMP adopts a trigonal bipyramid transition state during hydrolysis. The dynamic interaction of ligands with the phosphodiesterase enzymes will also be made evident when simple algebraic expressions are shown to be inadequate for predicting inhibitor potencies. The latter are apparently complicated by cooperative or synergistic relationships that occur among the various binding sites within the receptor. Finally, implications that can be derived from certain topographical features of the model are discussed relative to a range of potential therapeutic indications.     

Role of surface adsorption and porosity features in the molecular recognition ability of imprinted sol-gels

Organically modified molecularly imprinted silicas (MIS) for nafcillin recognition were prepared using a simple sol-gel procedure. Molecular recognition of the template was observed by tuning the chemical and structural properties of the MIS. The relative amounts of organically modified alkoxysilane precursors were found to be key in the textural and morphological characteristics of the MIS as well as for developing an imprinting effect in the materials. The recognition properties of the imprinted materials were found to be strongly influenced by the hydrolytic stability of the alkoxysilanes and their inductive effects during sol-gel hydrolysis/condensation stages. The concept was to combine properties of organic groups with those of glass-like materials in order to develop synergetic properties through variations in the composition. Results from batch rebinding experiments as well as from the thorough study of the N(2) adsorption properties and the textural and structural characteristics of the MIS revealed that an imprint effect could be attributed to the presence of the template during the synthesis of MIS.     

A model of the rabies virus glycoprotein active site

The glycoprotein from the neurotropic rabies virus shows a significant homology with the α neurotoxin that binds to the nicotinic acetylcholine receptor. The crystal structure of the α neurotoxins suggests that the Arg 37 guanidinium group and the Asp 31 side-chain carboxylate of the erabutoxin have stereochemical features resembling those of acetylcholine. Conformational studies on the Asn194-Ser195-Arg196-Gly197 tetrapeptide, an essential part of the binding site of the rabies virus glycoprotein, indicate that the side chains of Asn and Arg could also mimic the acetylcholine structure. This observation is consistent with the recently proposed mechanism of the viral infection. © 1993 John Wiley & Sons, Inc.     

Studies of adsorption for heavy metal ions and degradation of methyl orange based on the surface of ion-imprinted adsorbent

In order to prepare a novel adsorbent which can not only degrade organic compound, but also adsorb the heavy metal ions, immobilization of nanometer titanium dioxide on ion-imprinted chitosan carries was investigated. The amount of TiO₂, different kinds and amounts of dispersants, adding methods of TiO₂, different kinds of cross-linking agents and target metal ions are important factors influencing the degradation of Methyl Orange (MO) and the adsorption for Ni²⁺. When 15% amount of TiO₂ was added in preparation, the removal of MO was highly increased to nearly 90%, which was about eight times higher than that without TiO₂, at the same time, the effect of TiO₂ on the adsorption capacity was not obvious. The results show that in the presence of Ni²⁺ and MO, the MO could be removed effectively and the removal of MO reached 95.4%. At the initial concentration of Ni²⁺ of 200 mg/L, the adsorption capacity of Ni²⁺ reached 33 mg/g in the presence of MO.     

Ethylenediamine as active site probe for Na+/K+-ATPase

(1) Ethylenediamine is an inhibitor of Na+- and K+-activated processes of Na+/K+-ATPase, i.e. the overall Na+/K+-ATPase activity, Na+-activated ATPase and K+-activated phosphatase activity, the Na+-activated phosphorylation and the Na+-free (amino-buffer associated) phosphorylation. (2) The I50 values (I50 is the concentration of inhibitor that half-maximally inhibits) increase with the concentration of the activating cations and the half-maximally activating cation concentrations (Km values) increase with the inhibitor concentration. (3) Ethylenediamine is competitive with Na+ in Na+-activated phosphorylation and with the amino-buffer (triallylamine) in Na+-free phosphorylation. Significant, though probably indirect, effects can also be noted on the affinity for Mg2+ and ATP, but these cannot account for the inhibition. (4) Inhibition parallels the dual protonated or positively charged ethylenediamine concentration (charge distance 3.7 A). (5) Direct investigation of interaction with activating cations (Na+, K+, Mg+, triallylamine) has been made via binding studies. All these cations drive ethylenediamine from the enzyme, but K+ and Mg+ with the highest efficiency and specificity. Ethylenediamine binding is ouabain-insensitive, however. (6) Ethylenediamine neither inhibits the transition to the phosphorylation enzyme conformation, nor does it affect the rate of dephosphorylation. Hence, we provisionally conclude that ethylenediamine inhibits the phosphoryl transfer between the ATP binding and phosphorylation site through occupation of cation activation sites, which are 3-4 A apart.     

Structural basis for Ni(2+) transport and assembly of the urease active site by the metallochaperone UreE from Bacillus pasteurii

Bacillus pasteurii UreE (BpUreE) is a putative chaperone assisting the insertion of Ni(2+) ions in the active site of urease. The x-ray structure of the protein has been determined for two crystal forms, at 1.7 and 1.85 A resolution, using SIRAS phases derived from a Hg(2+)-derivative. BpUreE is composed of distinct N- and C-terminal domains, connected by a short flexible linker. The structure reveals the topology of an elongated homodimer, formed by interaction of the two C-terminal domains through hydrophobic interactions. A single Zn(2+) ion bound to four conserved His-100 residues, one from each monomer, connects two dimers resulting in a tetrameric BpUreE known to be formed in concentrated solutions. The Zn(2+) ion can be replaced by Ni(2+) as shown by anomalous difference maps obtained on a crystal of BpUreE soaked in a solution containing NiCl(2). A large hydrophobic patch surrounding the metal ion site is surface-exposed in the biologically relevant dimer. The BpUreE structure represents the first for this class of proteins and suggests a possible role for UreE in the urease nickel-center assembly.     

A revised model of the active site of alternative oxidase

The plant mitochondrial protein alternative oxidase catalyses dioxygen dependent ubiquinol oxidation to yield ubiquinone and water. A structure of this protein has previously been proposed based on an assumed structural homology to the di-iron carboxylate family of proteins. However, these authors suggested the protein has a very different topology than the known structures of di-iron carboxylate proteins. We have re-examined this model and based on comparison of recent sequences and structural data on di-iron carboxylate proteins we present a new model of the alternative oxidase which allows prediction of active site residues and a possible membrane binding motif.     

The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site

In eukaryotic organisms, initiation of mRNA turnover is controlled by progressive shortening of the poly-A tail, a process involving the mega-Dalton Ccr4-Not complex and its two associated 3′-5′ exonucleases, Ccr4p and Pop2p (Caf1p). RNA degradation by the 3′-5′ DEDDh exonuclease, Pop2p, is governed by the classical two metal ion mechanism traditionally assumed to be dependent on Mg²⁺ ions bound in the active site. Here, we show biochemically and structurally that fission yeast (Schizosaccharomyces pombe) Pop2p prefers Mn²⁺ and Zn²⁺ over Mg²⁺ at the concentrations of the ions found inside cells and that the identity of the ions in the active site affects the activity of the enzyme. Ion replacement experiments further suggest that mRNA deadenylation could be subtly regulated by local Zn²⁺ levels in the cell. Finally, we use site-directed mutagenesis to propose a mechanistic model for the basis of the preference for poly-A sequences exhibited by the Pop2p-type deadenylases as well as their distributive enzymatic behavior.     

Super-high-affinity binding site for [3H]diazepam in the presence of Co2+, Ni2+, Cu2+, OR Zn2+

Chloride salts of Li⁺, Na⁺, K⁺, Mg²⁺, Ca²⁺, Cr³⁺, Mn²⁺, Fe²⁺, and Fe³⁺ had no effect on [³H]diazepam binding. Chloride salts of Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺ increased [³H]diazepam binding by 34 to 68% in a concentration-dependent fashion. Since these divalent cations potentiated the GABA-enhanced [³H]diazepam binding and the effect of each divalent cation was nearly additive with GABA, these cations probably act at a site different from the GABA recognition site in the benzodiazepine-receptor complex. Scatchard plots of [³H]diazepam binding without an effective divalent cation showed a single class of binding, with a Kd value of 5.3 mM. In the presence of 1 mM Co²⁺, Ni²⁺, Cu²⁺, or Zn²⁺, two distinct binding sites were evident with apparent Kd values of 1.0 nM and 5.7 nM. The higher-affinity binding was not detected in the absence of an effective divalent cation and is probably a novel, super-high-affinity binding site.     

Intramolecular cross-linking at the active site of the Ca2+-ATPase of sarcoplasmic reticulum. High and low affinity nucleotide binding and evidence of active site closure in E2-P

Limited reaction of glutaraldehyde with the Ca2+-ATPase (Mr approximately 110,000) of sarcoplasmic reticulum results in intramolecular cross-linking at the active site, which can be detected by an anomalous increase in apparent molecular weight (Mr approximately 125,000) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Ross D.C., and McIntosh D.B. (1987) J. Biol. Chem. 262, 2042-2049). ATP, ADP, AMPPCP, trinitrophenyladenosine triphosphate, and decavanadate inhibited the cross-link in a manner suggestive of a homogeneous class of inhibitory sites, with K0.5 values for inhibition in agreement with Kd values for binding to the active site. Cross-link formation was inhibited in proportion to phosphoenzyme levels formed from Pi (E2-P) whereas stoichiometric phosphorylation from CaATP (E1-P) had no effect. Inhibition was observed at millimolar concentrations of CaATP, indicative of nucleotide binding to E1-P. MgATP, in the presence of Ca2+, inhibited cross-linkage in the micromolar and millimolar concentration ranges, the former attributable to E1 X ATP and E2-P formation and the latter to ATP binding mainly to E1-P. The inability to cross-link the active site only of the E2-P intermediate suggests a unique active site conformation, possibly a closed active site cleft, which we suggest is linked to low affinity, inwardly orientated Ca2+-binding sites.     

Permutation of the active site motif of tryparedoxin 2

Tryparedoxins (TXN) are thioredoxin-related proteins which, as trypanothione:peroxiredoxin oxidoreductases, constitute the trypanothione-dependent antioxidant defense and may also serve as substrates for ribonucleotide reductase in trypanosomatids. The active site motif of TXN2, 40WCPPCR45, of Crithidia fasciculata was mutated by site-directed mutagenesis and eight corresponding muteins were expressed in E. coli as terminally His-tagged proteins, purified to homogeneity by nickel chelate chromatography, and characterized in terms of specific activity, specificity and, if possible, kinetics. Exchange of Cys41 and Cys44 by serine yielded inactive products confirming their presumed involvement in catalysis. Exchange of Arg45 by aspartate resulted in loss of activity, suggesting an activation of active site cysteines by the positive charge of Arg45. Substitution of Trp40 by phenylalanine or tyrosine resulted in moderate decrease of specific activity, as did exchange of Pro42 by glycine. Kinetic analysis of these three muteins revealed that primarilythe reaction with trypanothione is affected by the mutations. Simulation of thioredoxin or glutaredoxin-like active sites in TXN2 (P42G and W40T/P43Y, respectively) did not result in thioredoxin or glutaredoxin-like activities. These data underscore that TXNs, although belonging to the thioredoxin superfamily, represent a group of enzymes distinct from thioredoxins and glutaredoxins in terms of specificity, and appear attractive as molecular targets for the design of trypanocidal compounds.