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J A Ippolito

Publications and source records attributed to J A Ippolito.

17 recordsLinked to original sources
PubMed2006

Biosolids affect soil barium in a dryland wheat agroecosystem.

In December 2003, the USEPA released an amended list of 15 "candidate pollutants for exposure and hazard screening" with regard to biosolids land application, including Ba. Therefore, we decided to monitor soil Ba concentrations from a dryland wheat (Triticum aestivum L.)-fallow agroecosystem experiment. This experiment received 10 biennial biosolids applications (1982-2003) at rates from 0 to 26.8 dry Mg ha(-1) per application year. The study was conducted on a Platner loam (Aridic Paleustoll), approximately 30 km east of Brighton, CO. Total soil Ba, as measured by 4 M HNO(3), increased with increasing biosolids application rate. In the soil-extraction data from 1988 to 2003, however, we observed significant (P < 0.10) linear or exponential declines in ammonium bicarbonate-diethylenetriaminepentaacetic acid (AB-DTPA) extractable Ba concentrations as a function of increasing biosolids application rates. This was observed in 6 of 7 and 3 of 7 yr for the 0- to 20- and 20- to 60-cm soil depths, respectively. Results suggest that while total soil Ba increased as a result of biosolids application with time, the mineral form of Ba was present in forms not extractable with AB-DTPA. Scanning electron microscopy using energy dispersive spectroscopy verified soil Ba-S compounds in the soil surface, probably BaSO(4). Wet chemistry sequential extraction suggested BaCO(3) precipitation was increasing in the soil subsurface. Our research showed that biosolids application may increase total soil Ba, but soil Ba precipitates are insoluble and should not be an environmental concern in similar soils under similar climatic and management conditions.

Agriculture↗
PubMed2005

Soil properties affecting wheat yields following drilling-fluid application.

Oil and gas drilling operations use drilling fluids (mud) to lubricate the drill bit and stem, transport formation cuttings to the surface, and seal off porous geologic formations. Following completion of the well, waste drilling fluid is often applied to cropland. We studied potential changes in soil compaction as indicated by cone penetration resistance, pH, electrical conductivity (EC(e)), sodium adsorption ratio (SAR), extractable soil and total straw and grain trace metal and nutrient concentrations, and winter wheat (Triticum aestivum L. 'TAM 107') grain yield following water-based, bentonitic drilling-fluid application (0-94 Mg ha(-1)) to field test plots. Three methods of application (normal, splash-plate, and spreader-bar) were used to study compaction effects. We measured increasing SAR, EC(e), and pH with drilling-fluid rates, but not to levels detrimental to crop production. Field measurements revealed significantly higher compaction within areas affected by truck travel, but also not enough to affect crop yield. In three of four site years, neither drilling-fluid rate nor application method affected grain yield. Extractions representing plant availability and plant analyses results indicated that drilling fluid did not significantly increase most trace elements or nutrient concentrations. These results support land application of water-based bentonitic drilling fluids as an acceptable practice on well-drained soils using controlled rates.

Agriculture↗
PubMed2001

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif.

Analysis of the 2.4-A resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.

Adenosine↗
PubMed2000

The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolution.

The crystal structure of a 28 nt RNA fragment containing the human immunodeficiency virus type 1 (HIV-1) Rev response element high affinity binding site for Rev protein has been solved at 1.6 A resolution. The overall structure of the RRE helix is greatly distorted from A-form geometry by the presence of two purine-purine base-pairs and two single nucleotide bulges. G48 and G71 form a Hoogsteen-type asymmetric base-pair with G71 adopting a syn conformation. The non-canonical regions in the unliganded Rev response element molecule narrow the major groove width with respect to standard A-RNA. The Rev response element structure observed here represents a closed form of the Rev binding site and differs from conformations of the RNA observed previously by solution NMR studies.

Base Sequence↗
PubMed1999

SELEX and missing phosphate contact analyses reveal flexibility within the AP-2[alpha] protein: DNA binding complex.

The AP-2 family of transcription factors are defined by the presence of a novel DNA binding domain, termed a 'basic helix-span-helix' motif. The AP-2 genes regulate important aspects of vertebrate embryogenesis and have also been linked to the control of cell proliferation and tumorigenesis, but the cellular targets that the AP-2 proteins control are largely undefined. In particular, since only a limited number of sequences have previously been utilized to define the nature of the AP-2 binding site, the range of DNA sequences recognized by the AP-2 proteins remains unknown. We have therefore utilized a SELEX analysis to identify multiple new AP-2[alpha] binding sites. Moreover, we have devised a novel missing phosphate and nucleotide competition analysis to characterize the residues in the binding site required for AP-2[alpha] protein:DNA contact. These studies suggest that the AP-2[alpha] protein:DNA complex is flexible and indicate that AP-2[alpha] can bind three related sequence motifs: GCC N3 GGC, GCC N4 GGC and GCC N3/4 GGG. The availability of these more refined consensus sequences should assist in the identification of target genes for this critical transcription factor.

Base Sequence↗
PubMed1998

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.

The crystal structure of an HIV-1 trans-activation response region (TAR) RNA fragment containing the binding site for the trans-activation protein Tat has been determined to 1.3-A resolution. In this crystal structure, the characteristic UCU bulge of TAR adopts a conformation that is stabilized by three divalent calcium ions and differs from those determined previously by solution NMR. One metal ion, crucial to the loop conformation, binds directly to three phosphates in the loop region. The structure emphasizes the influence of metal ion binding on RNA structure and, given the abundance of divalent metal ion in the cell, raises the question of whether metal ions play a role in the conformation of TAR RNA and the interaction of TAR with Tat and cyclin T in vivo.

Base Sequence↗
PubMed1995

Structure-assisted redesign of a protein-zinc-binding site with femtomolar affinity.

We have inserted a fourth protein ligand into the zinc coordination polyhedron of carbonic anhydrase II (CAII) that increases metal affinity 200-fold (Kd = 20 fM). The three-dimensional structures of threonine-199-->aspartate (T199D) and threonine-199-->glutamate (T199E) CAIIs, determined by x-ray crystallographic methods to resolutions of 2.35 Angstrum and 2.2 Angstrum, respectively, reveal a tetrahedral metal-binding site consisting of H94, H96, H119, and the engineered carboxylate side chain, which displaces zinc-bound hydroxide. Although the stereochemistry of neither engineered carboxylate-zinc interaction is comparable to that found in naturally occurring protein zinc-binding sites, protein-zinc affinity is enhanced in T199E CAII demonstrating that ligand-metal separation is a significant determinant of carboxylate-zinc affinity. In contrast, the three-dimensional structure of threonine-199-->histidine (T199H) CAII, determined to 2.25-Angstrum resolution, indicates that the engineered imidazole side chain rotates away from the metal and does not coordinate to zinc; this results in a weaker zinc-binding site. All three of these substitutions nearly obliterate CO2 hydrase activity, consistent with the role of zinc-bound hydroxide as catalytic nucleophile. The engineering of an additional protein ligand represents a general approach for increasing protein-metal affinity if the side chain can adopt a reasonable conformation and achieve inner-sphere zinc coordination. Moreover, this structure-assisted design approach may be effective in the development of high-sensitivity metal ion biosensors.

Binding Sites↗
PubMed1995

Structure of His94-->Asp carbonic anhydrase II in a new crystalline form reveals a partially occupied zinc binding site.

The structure of histidine 94-->aspartate (H94D) carbonic anhydrase II (CAII) crystallized in an orthorhombic space group has been determined to 2.5 A resolution. This crystal form is not isomorphous with monoclinic wild-type enzyme crystals or with the monoclinic crystal form of H94D CAII reported earlier [Kiefer,L.L., Ippolito, J.A., Fierke, C.A. and Christianson, D.W. (1993) J. Am. Chem. Soc., 115, 12581-12582]. In monoclinic H94D CAII, a fully occupied zinc ion is tetrahedrally coordinated by D94, H96, H119 and a water molecule. In orthorhombic H94D CAII, a partially occupied zinc ion is coordinated by H96 and H119 and only weakly coordinated by a disordered D94 side chain. These differences are particularly surprising given that the two crystal forms co-precipitate in the same drop in the same experiment. Re-refinement of the orthorhombic crystal form of H94C CAII and comparison with its corresponding monoclinic crystal form yield similar results. It appears that partial-but not full-zinc dissociation accompanies the crystallization of CAII variants in the orthorhombic crystal form, and significant differences on the protein surface presumably affect the relative stability of each crystal lattice. These results underscore an unexpected ambiguity in this protein engineering experiment: which crystal structure of H94D CAII should be correlated with functional measurements made in solution?

Binding Sites↗
PubMed1994

Structural consequences of redesigning a protein-zinc binding site.

In order to probe the structural importance of zinc ligands in the active site of human carbonic anhydrase II (CAII), we have determined the three-dimensional structures of H94C (in metal-bound form), H94C-BME (i.e., disulfide-linked with beta-mercaptoethanol), H94A, H96C, H119C, and H119D variants of CAII by X-ray crystallographic methods at resolutions of 2.2, 2.35, 2.25, 2.3, 2.2, and 2.25 A, respectively. Each variant crystallizes isomorphously with the wild-type enzyme, in which zinc is tetrahedrally coordinated by H94, H96, H119, and hydroxide ion. The structure of H94C CAII reveals the successful substitution of the naturally occurring histidine zinc ligand by a cysteine thiolate, and metal coordination by C94 is facilitated by the plastic structural response of the beta-sheet superstructure. Importantly, the resulting structure represents the catalytically active form of the enzyme reported previously [Alexander, R. S., Kiefer, L. L., Fierke, C. A., & Christianson, D. W. (1993) Biochemistry 32, 1510-1518]. Contrastingly, the structure of H96C CAII reveals that the engineered side chain does not coordinate to zinc; instead, zinc is tetrahedrally liganded by H94, H119, and two solvent molecules. Thus, the beta-sheet superstructure is not sufficiently plastic in this location to allow C96 to coordinate to the metal ion. Substitution of the thiolate or carboxylate group for wild-type histidine in H119C and H119D CAIIs reveals that tetrahedral metal coordination is maintained in each variant; however, since there is no plastic structural response of the corresponding beta-strand, a longer metal-ligand separation results.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding Sites↗
PubMed1993

Structural and functional importance of a conserved hydrogen bond network in human carbonic anhydrase II.

Amino acid substitutions at Thr199 of human carbonic anhydrase II (CAII) (Thr199-->Ser, Ala, Val, and Pro) were characterized to investigate the importance of a conserved hydrogen bonding network. The three-dimensional structures of azide-bound and sulfate-bound T199V CAIIs were determined by x-ray crystallographic methods at 2.25 and 2.4 A, respectively (final crystallographic R factors are 0.173 and 0.174, respectively). The CO2 hydrase activities of T199S and T199P variants suggest that the side chain methyl and backbone amino functionalities stabilize the transition state by approximately 0.4 and 0.8 kcal/mol, respectively. The side chain hydroxyl group causes: stabilization of zinc-hydroxide relative to zinc-water (pKa increases approximately 2 units); stabilization of the transition state for bicarbonate dehydration relative to the CAII.HCO3- complex (approximately 5 kcal/mol); and destabilization of the CAII.HCO3- complex (approximately 0.8 kcal/mol). An inverse correlation between log(kcatCO2/KM) and the pKa of zinc-water (r = 0.95, slope = -1) indicates that the hydrogen bonding network stabilizes the chemical transition state and zinc-hydroxide similarly. These data are consistent with the hydroxyl group of Thr199 forming a hydrogen bond with the transition state and a non-hydrogen-bonded van der Waals contact with CAII.HCO3-.

Amino Acids↗
PubMed1993

Structure of an engineered His3Cys zinc binding site in human carbonic anhydrase II.

X-ray crystallographic analysis of the Thr-199-->Cys (T199C) variant of human carbonic anhydrase II reveals the first high-resolution structure of an engineered zinc coordination polyhedron in a metalloenzyme. In the wild-type enzyme, Thr-199 accepts a hydrogen bond from zinc-bound hydroxide; in the variant, the polypeptide backbone is sufficiently plastic to permit Cys-199 to displace hydroxide ion and coordinate to zinc with nearly perfect coordination stereochemistry. Importantly, the resulting His3-Cys-Zn2+ motif binds zinc more tightly than the wild-type enzyme [Kiefer, L. L., Krebs, J. F., Paterno, S. A., & Fierke C. A. (1993) Biochemistry (preceding paper in this issue)]. This novel zinc coordination polyhedron is analogous to that postulated for matrix metalloproteinase zymogens such as prostromelysin, where a cysteine-zinc interaction is responsible for the inactivity of the zymogen. Intriguingly, Cys-199 of T199C CAII is displaced from zinc coordination by soaking crystals in high concentrations of acetazolamide. Hence, residual catalytic activity measured for this variant probably arises from an alternate conformer of Cys-199 which allows the catalytic nucleophile, hydroxide ion, to be activated by zinc coordination.

Amino Acid Sequence↗
PubMed1993

Purification and characterization of Klebsiella aerogenes UreE protein: a nickel-binding protein that functions in urease metallocenter assembly.

The Klebsiella aerogenes ureE gene product was previously shown to facilitate assembly of the urease metallocenter (Lee, M.H., et al., 1992, J. Bacteriol. 174, 4324-4330). UreE protein has now been purified and characterized. Although it behaves as a soluble protein, UreE is predicted to possess an amphipathic beta-strand and exhibits unusually tight binding to phenyl-Sepharose resin. Immunogold electron microscopic studies confirm that UreE is a cytoplasmic protein. Each dimeric UreE molecule (M(r) = 35,000) binds 6.05 + 0.25 nickel ions (Kd of 9.6 +/- 1.3 microM) with high specificity according to equilibrium dialysis measurements. The nickel site in UreE was probed by X-ray absorption and variable-temperature magnetic circular dichroism spectroscopies. The data are most consistent with the presence of Ni(II) in pseudo-octahedral geometry with 3-5 histidyl imidazole ligands. The remaining ligands are nitrogen or oxygen donors. UreE apoprotein has been crystallized and analyzed by X-ray diffraction methods. Addition of nickel ion to apoprotein crystals leads to the development of fractures, consistent with a conformational change upon binding nickel ion. We hypothesize that UreE binds intracellular nickel ion and functions as a nickel donor during metallocenter assembly into the urease apoprotein.

Amino Acid Sequence↗
PubMed1993

Bronchiolitis obliterans organizing pneumonia and rheumatoid arthritis.

The case of a 68-year-old woman who presented with dyspnea and upper lobe pulmonary infiltrates and shortly thereafter developed seropositive, erosive polyarticular rheumatoid arthritis (RA) is presented. An open-lung biopsy to evaluate progression of infiltrates showed bronchiolitis obliterans-organizing pneumonia (BOOP). Both lung and articular disease responded rapidly to corticosteroid therapy. Interrelationships between BOOP, bronchiolitis obliterans, and interstitial fibrosis with connective tissue disease are discussed.

Aged↗
PubMed1992

The contribution of halogen atoms to protein-ligand interactions.

The three-dimensional structure of para-fluoro-D-phenylalanine (PFF) in its complex with the zinc protease carboxypeptidase A (CPA) has been determined at 2.0 A resolution by X-ray crystallographic methods. The structure reveals that the para-fluorobenzyl side chain of the inhibitor is buried in the S'1 hydrophobic pocket of the enzyme. Intriguingly, this ligand molecule inhibits CPA better than its amino acid analogues D-phenylalanine (D-Phe) and D-tyrosine (D-Tyr) by factors of 4 and 5, respectively. Moreover, the para-fluoro derivative is a better inhibitor than para-chloro- or para-bromo-D-phenylalanine by nearly a factor of 50. This result is consistent with binding enhancements realized in other protein complexes involving halogenated ligand molecules, regardless of whether the carbon-halogen group of the ligand makes specific polar interactions or non-specific hydrophobic interactions with its protein host. In the CPA-PFF complex, the fluorine atom of PFF does not make any direct polar contact with the enzyme, and the contact surface area of the protein-ligand interface is only slightly greater, although more hydrophobic, than that of D-Phe and D-Tyr. Therefore, we conclude that the slight binding enhancement measured for PFF relative to D-Phe and D-Tyr arises predominantly from increasing the hydrophobic character of the protein-ligand interface, and not solely from increasing the degree of protein-ligand contact.

Carboxypeptidases↗
PubMed1990

Hydrogen bond stereochemistry in protein structure and function.

Fifty high resolution protein structures from the Brookhaven Protein Data Bank have been analyzed for recurring motifs in hydrogen bond stereochemistry. Although an exhaustive analysis of hydrogen bond statistics has been presented by Baker & Hubbard, a detailed stereochemical analysis of classical donor (N-H, O-H, or S-H) and acceptor (N:, O:, or S:) structure within proteins is lacking. Here, we describe the preferential hydrogen bond stereochemistry for the side-chains of glutamate and aspartate (carboxylate), glutamine and asparagine (carboxamide), arginine (guanidinium), histidine (imidazole/imidazolium), tryptophan (indole), tyrosine (phenolic hydroxyl), lysine (ammonium), serine and threonine (alkyl hydroxyl), cysteine (thiol), methionine (thioether) and cystine (disulfide). Preferential hydrogen bond stereochemistry is governed by (1) the electronic configuration of acceptor atoms, (2) the steric accessibility of donor atoms and (3) the conformation of amino acid side-chains. Applications of hydrogen bond stereochemistry are useful in the interpretation of protein structure, function and stability. Additionally, this stereochemistry is a prerequisite to the interpretation of protein-other molecule recognition and biological catalysis.

Amino Acids↗
PubMedDate not supplied

Phosphorus retention mechanisms of a water treatment residual.

Water treatment residuals (WTRs) are a by-product of municipal drinking water treatment plants and can have the capacity to adsorb tremendous amounts of P. Understanding the WTR phosphorus adsorption process is important for discerning the mechanism and tenacity of P retention. We studied P adsorbing mechanism(s) of an aluminum-based [Al2(SO4)3 x 14H2O] WTR from Englewood, CO. In a laboratory study, we shook mixtures of P-loaded WTR for 1 to 211 d followed by solution pH analysis, and solution Ca, Al, and P analysis via inductively coupled plasma atomic emission spectroscopy. After shaking periods, we also examined the solids fraction by X-ray diffraction (XRD) and electron microprobe analysis using wavelength dispersive spectroscopy (EMPA-WDS). The shaking results indicated an increase in pH from 7.2 to 8.2, an increase in desorbed Ca and Al concentrations, and a decrease in desorbed P concentration. The pH and desorbed Ca concentration increases suggested that CaCO3 controlled Ca solubility. Increased desorbed Al concentration may have been due to Al(OH)4 formation. Decreased P content, in conjunction with the pH increase, was consistent with calcium phosphate formation or precipitation. The system appeared to be undersaturated with respect to dicalcium phosphate (DCP; CaHPO4) and supersaturated with respect to octacalcium phosphate [OCP; Ca4H(PO4)3 x 2.5H2O]. The Ca and Al increases, as well as OCP formation, were supported by MINTEQA2 modeling. The XRD and EMPA-WDS results for all shaking times, however, suggested surface P chemisorption as an amorphous Al-P mineral phase.

Adsorption↗