Steric and counterion effects on the structure of dipicolylamine nickel complexes

Four nickel complexes each containing an R-2,2′-dipicolylamine ligand species (RDPA; R = benzyl, isopropyl, or tert-butyl) were synthesized and structurally characterized. In the absence of an interfering coordinating counterion, BzDPA and iPrDPA form 1:2 nickel:ligand complexes, with two facial ligands completing an pseudooctahedral nickel(II) coordination environment. In contrast, the sterically hindered tBuDPA ligand instead forms 1:1 metal:ligand complexes, even in the absence of associating counterions. Two novel tBuDPA nickel complexes with different counterions are described: nickel(II) chloride gives rise to an unusual 2Ni-3Cl dimer complex, while nickel(II) nitrate affords a 1:1 nickel:ligand complex which crystallizes with both fac and mer conformations in the same unit cell.     

Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the beta5-alpha2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7.     

Steric effects, solvent effects, and turnover in hydrolytic cleavage of peptides promoted by palladium(II) aqua complexes

 Dipeptides and tripeptides AcMet-aaH containing N-acetyl methionine, in which the group aaH is GlyH, AlaH, ValH, or Gly-GlyH, undergo hydrolytic cleavage of the Met-aaH peptide bond in the presence of the following complexes of palladium(II): cis-[Pd(en)(H₂O)₂]²⁺, cis-[Pd(tn)(H₂O)₂]²⁺, cis-[Pd(en)(CH₃OH)₂]²⁺, cis-[Pd(S,N-MetH)(H₂O)₂]²⁺, cis-[Pd(S,N-Met-GlyH)(H₂O)₂]²⁺, and cis-[Pd(S,N-Met-AlaH)(H₂O)₂]²⁺. These mononuclear complexes are precursors of binuclear palladium(II) complexes containing the substrates AcMet-aaH as bridging thioether ligands. The rate constant for cleavage is higher when the bidentate ligand in the precursor complex is ethylenediamine (which is completely displaced) than S,N-methionine (of which only the amino group is displaced), because the number of aqua ligands available for cleavage is greater in the former than in the latter case. The demonstrated dependence of the rate constant on the steric bulk (volume) of the leaving group, aaH, points the way toward achieving a degree of sequence selectivity in cleavage of peptide bonds by palladium(II) aqua complexes. One equivalent of cis-[Pd(en)(H₂O)₂]²⁺ cleaves as many as ten equivalents of AcMet-GlyH, but the rate constant decreases as the molar excess of the dipeptide over the catalyst increases. This demonstration of catalytic turnover points the way to our ultimate goal – artificial metallopeptidases. Received: 13 June 1997 / Accepted: 24 September 1997     

Steric effects in antibody reactions with polyvalent antigen

Antigen valency has been defined (Singer, 1965) as the maximum number of epitopes per antigen which can be simultaneously occupied by antibody. If the epitopes are closely spaced, steric hindrance prevents the simultaneous occupancy of all epitopes. Current methods of estimating both the antigen valency and the association constant (Ka) from equilibrium binding data do not allow for the effects of steric hindrance. We have developed a theory which accounts rigorously for steric hindrance when monovalent ligands of quite general shape (antibodies) react reversibly with multivalent acceptor molecules (antigens). The surfaces of the acceptors are modelled by completely general two-dimensional lattices. Using this theory we demonstrate that curvature of Scatchard plots can arise from steric effects alone in the absence of other known causes such as cross-linking, cooperativity and heterogeneous epitope affinities. Our results generalize the conclusions of McGhee & von Hippel (1974) who dealt with one-dimension acceptor molecules such as DNA. We discuss inaccuracies in the estimation of both Ka and antigen valency using the traditional approach of fitting straight lines to Scatchard plots.     

Toxic and biochemical effects of zinc in Caco-2 cells

Zinc (in relatively high concentrations) can be toxic to intestinal cells. The aim of the present study was to quanitfy cellular injury in preconfluent, colonic cancerous cells and in postconfluent, differentiating human intestinal Caco-2 cells. Cellular damage was measured by using cell proliferation, lactate dehydrogenase (LDH)-release, and apoptosis studies. Furthermore, the activities of the major antioxidative enzymes [superoxide dismutase (SOD), glutathione peroxidase (GPx) and catalase] and differentiation markers (alkaline phosphatase and aminopeptidase-N) were determined after exposure of the cells to increasing amounts of zinc sulfate. Proliferation and viability decreased in a concentration-dependent manner. A noticeable increase of LDH-release correlated to cell rounding and detachment at relatively high zinc levels (200 muM) was observed in both groups of cells. Above 100 muM of zinc, significant apoptotic activity was found in the preconfluent cells. Zinc supplementation did not alter SOD activities. However, GPx and, in part, catalase activities tended to be higher in zinc-treated cells (nevertheless the results were not significant). Differentiation markers were noticeably induced by increasing amounts of zinc, especially in the preconfluent cells. In conclusion, we suggest that the susceptibility to zinc induced damage is equal in both confluentation groups of Caco-2 cells. Risk assessment for high concentrations seems recommendable.     

Characterization of zinc amino acid complexes for zinc delivery in vitro using Caco-2 cells and enterocytes from hiPSC

Zn is essential for growth and development. The bioavailability of Zn is affected by several factors such as other food components. It is therefore of interest, to understand uptake mechanisms of Zn delivering compounds to identify ways to bypass the inhibitory effects of these factors. Here, we studied the effect of Zn amino acid conjugates (ZnAAs) on the bioavailabilty of Zn. We used Caco-2 cells and enterocytes differentiated from human induced pluripotent stem cells from a control and Acrodermatitis enteropathica (AE) patient, and performed fluorescence based assays, protein biochemistry and atomic absorption spectrometry to characterize cellular uptake and absorption of ZnAAs. The results show that ZnAAs are taken up by AA transporters, leading to an intracellular enrichment of Zn mostly uninhibited by Zn uptake antagonists. Enterocytes from AE patients were unable to gain significant Zn through exposure to ZnCl₂ but did not show differences with respect to ZnAAs. We conclude that ZnAAs may possess an advantage over classical Zn supplements such as Zn salts, as they may be able to increase bioavailability of Zn, and may be more efficient in patients with AE.     

Structural studies on zinc(II) complexes with 2-benzoylpyridine-derived hydrazones

2-Benzoylpyridine-phenylhydrazone (H2BzPh), 2-benzoylpyridine-para-chloro-phenylhydrazone (H2BzpClPh), and 2-benzoylpyridine-para-nitro-phenyl (H2BzpNO₂Ph) hydrazone were obtained and fully characterized, as well as their zinc(II) complexes [Zn(H2BzPh)Cl₂] (1), [Zn(H2BzClPh)Cl₂] (2) and [Zn(H2BzpNO₂Ph)Cl₂] (3). During the syntheses of complex 1 a second product crystallized, which was characterized as [Zn(2BzPh)₂] (1a). Upon re-crystallization in 1:9 DMSO:acetone conversion of 2 into [Zn(H2BzpClPh)Cl₂] · H₂O (2a) and of 3 into [Zn(2BzpNO₂Ph)Cl(DMSO)] (3a) occurred. The crystal structures of 1a, 2a and 3a were determined. In 1a the two nearly perpendicular H2BzPh ligands give rise to a distorted octahedral environment around the metal. The 5-fold coordination around the metal is completed with two chloride ions in 2a and with one chloride and one oxygen atom from DMSO in 3a.     

The ligand environment of zinc stored in vesicles

Zinc serves regulatory functions in cells and thus, several mechanisms exist for tight control of its homeostasis. One mechanism is storage in and retrieval from vesicles, so-called zincosomes, but the chemical speciation of zincosomal zinc has remained enigmatic. Here, we determine the intravesicular zinc-coordination in isolated zincosomes in comparison to intact RAW264.7 murine macrophage cells. In elemental maps of a cell monolayer, generated by microbeam X-ray fluorescence, zincosomes were identified as spots of high zinc accumulation. A fingerprint for the binding motif obtained by μXANES (X-ray absorption near edge structure) matches the XANES from isolated vesicles; zinc is not free, but present as a complexed form (average coordination; 1.0 sulfur, 2,5 histidines 30 and 1.0 oxygen), resembling regulatory or catalytic zinc sites in proteins. Such coordination enables reversible binding, acting as a ‘zinc sink’, facilitating the accumulation of high amounts of zinc against a concentration gradient.     

Differential effects of zinc and magnesium ions on mineralization activity of phosphatidylserine calcium phosphate complexes

Mg²⁺ and Zn²⁺ are present in the mineral of matrix vesicles (MVs) and biological apatites, and are known to influence the onset and progression of mineral formation by amorphous calcium phosphate (ACP) and hydroxyapatite (HAP). However, neither has been studied systematically for its effect on mineral formation by phosphatidylserine-Ca²⁺-Pi complexes (PS-CPLX), an important constituent of the MV nucleation core. Presented here are studies on the effects of increasing levels of Mg²⁺ and Zn²⁺ on the process of mineral formation, either when present in synthetic cartilage lymph (SCL), or when incorporated during the formation of PS-CPLX. Pure HAP and PS-CPLX proved to be powerful nucleators, but ACP took much longer to induce mineral formation. In SCL, Mg²⁺ and Zn²⁺ had significantly different inhibitory effects on the onset and amount of mineral formation; HAP and PS-CPLX were less affected than ACP. Mg²⁺ and Zn²⁺ caused similar reductions in the rate and length of rapid mineral formation, but Zn²⁺ was a more potent inhibitor on a molar basis. When incorporated into PS-CPLX, Mg²⁺ and Zn²⁺ caused significantly different effects than when present in SCL. Even low, subphysiological levels of Mg²⁺ altered the inherent structure of PS-CPLX and markedly reduced its ability to induce and propagate mineral formation. Incorporated Zn²⁺ caused significantly less effect, low (<20 μM) levels causing almost no inhibition. Levels of Zn²⁺ present in MVs do not appear to inhibit their nucleational activity.     

Steric effects of isoleucine 107 on heme reorientation reaction in human myoglobin

Structural factors to regulate the heme reorientation reaction in myoglobin were examined and we found that the side chain at position 107 (Ile107), which is located between the 2-vinyl and 3-methyl groups of heme, forms a kinetic barrier for the heme rotation about the alpha-gamma axis. The phenylalanine-substituted mutant showed an extremely slow heme reorientation rate, compared to that of the wild-type protein, while replacement by the decreased side chain, valine, at position 107 accelerated the reorientation reaction. Considering that the spectroscopic data show only minor structural changes in the heme environments of the Ile107 mutants, the side chain at position 107 sterically interacts with the heme peripheral groups in the activation state for the heme reorientation, which supports the intramolecular mechanism that the heme rotates about the alpha-gamma axis without leaving the "protein cage."     

Synthesis and structural diversity of 2-pyridylmethylideneamine complexes of zinc(II) chloride

The addition reactions of zinc(II) chloride to N-substituted pyridine-2-carbaldimines [Py-CHNR, R = Me (1a), Ph (1b), Bz (1c), allyl (1d)] lead to different complexes dependent on the N-bound substituent R. The 1:1 complexes show molecular structures of the type [(Py-CHNR)ZnCl₂] for R = methyl (2a), phenyl (2b), and allyl (2d) with a distorted tetrahedral environment for the zinc atom. The zinc complex with the N-methylated pyridine-2-carbaldimine also forms a dimer of the type [(Py-CHNR)ZnCl₂]₂ (2a)₂ with a square pyramidal coordination sphere of zinc. A 3:2 stoichiometry is observed for R = benzyl and an ion pair of the type [Zn(Py-CHNR)₃]²⁺ [ZnCl₄]²⁻ (2c) is found in the solid state.     

Clastogenic effects of zinc in mammals

The eventual clastogenic properties of zinc chloride have been assessed as well in vitro as in vivo studies on mammalian somatic cells. For this purpose, human peripheral lymphocytes were treated in 48 or 72 hours cultures with 0, 20 or 200 micrograms zinc chloride, whereas C57Bl mice have received during one month a normal or poor calcium diet in combination or not with 0.5 g % of zinc. Chromosome analysis of treated human lymphocytes and of bone marrow cells of mice fed a poor dietary calcium supplemented with zinc has shown a significant increase in structural chromosome aberrations.     

Steric stabilization of poly-L-Lysine/DNA complexes by the covalent attachment of semitelechelic poly[N-(2-hydroxypropyl)methacrylamide

The concept of steric stabilization was utilized for self-assembling polyelectrolyte poly-L-lysine/DNA (pLL/DNA) complexes using covalent attachment of semitelechelic poly[N-(2-hydroxypropyl)methacrylamide] (pHPMA). We have examined the effect of coating of the complexes with pHPMA on their physicochemical stability, phagocytic uptake in vitro, and biodistribution in vivo. The coated complexes showed stability against aggregation in 0.15 M NaCl and reduced binding of albumin, chosen as a model for the study of the interactions of the complexes with plasma proteins. The presence of coating pHPMA had no effect on the morphology of the complexes as shown by transmission electron microscopy. However, results of the study of polyelectrolyte exchange reactions with heparin and pLL suggested decreased stability of the coated complexes in these types of reactions compared to uncoated pLL/DNA complexes. Coated complexes showed decreased phagocytic capture by mouse peritoneal macrophages in vitro. Decreased phagocytosis in vitro, however, did not correlate with results of in vivo study in mice showing no reduction in the liver uptake and no increase in the circulation times in the blood. We propose that the rapid plasma elimination of coated pLL/DNA complexes is a result of binding serum proteins and also of their low stability toward polyelectrolyte exchange reactions as a consequence of their equilibrium nature.     

Steric and hydrophobic effects in alkyl isocyanide binding to Rhodospirillum molischianum cytochrome c'

Equilibrium constants for the binding of a series of alkyl isocyanides to ferrous cytochrome c' from Rhodospirillum molischianum have been measured spectrophotometrically. The equilibrium constants range from 3.3 M-1 to 2.6 x 10(2) M-1 and follow the order methyl greater than ethyl less than n-propyl less than tert-butyl less than n-butyl less than amyl less than cyclohexyl less than n-hexyl. The decrease in equilibrium constant from methyl to ethyl isocyanide provides evidence for a steric interaction between the ligand and the protein. The increase in equilibrium constant from ethyl to n-hexyl isocyanide is accounted for by a favorable partitioning of the ligand into a hydrophobic heme coordination site. The effect of steric interactions on the differences in the binding constants has been further evaluated by comparing the alkyl isocyanide and CO binding constants for the ferrous cytochrome c' to those of a sterically unconstrained model heme complex in a detergent micelle. The results indicate that the heme coordination site of the ferrous cytochrome c' is severely sterically hindered, similar to that of the reported crystal structure of Rs. molischianum ferric cytochrome c'.     

Steric effects on penicillin-sensitive peptidoglycan synthesis in a membrane-wall system Gaffkya homari.

Residues 4 and 5 of the pentapeptide moiety, R-Ala1-DGlu2-Lys3-DAla4-DAla5, of peptidoglycan play an important role in the donor phase of cross-linked glycan synthesis. To assess the role of these residues in this phase, a series of UDP-MurNAc-peptides were biosynthesized with residues 4 and 5 replaced singly by either D-alpha-amino-n-butyric acid, D-norvaline, or D-valine. The six nucleotides were compared with UDP-MurNAc-Ala-DGlu-Lys-DAla-DAla (reference) in nascent (penicillin-insensitive) peptidoglycan synthesis and in penicillin-sensitive peptidoglycan synthesis. The synthesis of penicillin-sensitive peptidoglycan is catalyzed by membrane-walls isolated from Gaffkya homari and would appear to require the concerted action of transglycosylase and transpeptidase. The membrane-wall system shows a high degree of discrimination for the steric substituents, -CH3 and -CH2CH3, in residue 4. For example, for UDP-MurNAc-Ala-DGly-Lys-DAbu-DAla and -Ala-DGlu-Lys-DAla-DAbu, Vmax/km is 0.19 and 0.95 and Vmax is 0.03 and 0.52, respectively, of the value for the reference nucleotide. In contrast, for the synthesis of nascent peptidoglycan with these nucleotides Vmax/Km is 0.75 and 0.80, and Vmax is 0.71 and 1.0, respectively, of the value for the reference nucleotide. This trend was also illustrated with the other nucleotides in the time course experiments. These results indicate that the penicillin-sensitive enzyme(s), presumably the transpeptidase, has a higher degree of specificity in the donor phase for D-alanine in residue 4 than for D-alanine in residue 5 in the cross-linking stage of peptidoglycan synthesis.