@article{khan_walden_theil_goss_2017, title={Thermodynamic and Kinetic Analyses of Iron Response Element (IRE)-mRNA Binding to Iron Regulatory Protein, IRP1}, volume={7}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-017-09093-5}, abstractNote={Abstract}, journal={SCIENTIFIC REPORTS}, author={Khan, Mateen A. and Walden, William E. and Theil, Elizabeth C. and Goss, Dixie J.}, year={2017}, month={Aug} }
 @article{bernacchioni_ghini_theil_turano_2016, title={Modulating the permeability of ferritin channels}, volume={6}, ISSN={["2046-2069"]}, DOI={10.1039/c5ra25056k}, abstractNote={Electric field gradients across the C3 and C4 ferritin channels controls the directional Fe2+fluxes towards the catalytic ferroxidase center.}, number={25}, journal={RSC ADVANCES}, author={Bernacchioni, C. and Ghini, V. and Theil, E. C. and Turano, P.}, year={2016}, pages={21219–21227} }
 @misc{theil_tosha_beherat_2016, title={Solving Biology's Iron Chemistry Problem with Ferritin Protein Nanocages}, volume={49}, ISSN={["1520-4898"]}, DOI={10.1021/ar500469e}, abstractNote={Ferritins reversibly synthesize iron-oxy(ferrihydrite) biominerals inside large, hollow protein nanocages (10-12 nm, ∼480 000 g/mol); the iron biominerals are metabolic iron concentrates for iron protein biosyntheses. Protein cages of 12- or 24-folded ferritin subunits (4-α-helix polypeptide bundles) self-assemble, experimentally. Ferritin biomineral structures differ among animals and plants or bacteria. The basic ferritin mineral structure is ferrihydrite (Fe2O3·H2O) with either low phosphate in the highly ordered animal ferritin biominerals, Fe/PO4 ∼ 8:1, or Fe/PO4 ∼ 1:1 in the more amorphous ferritin biominerals of plants and bacteria. While different ferritin environments, plant bacterial-like plastid organelles and animal cytoplasm, might explain ferritin biomineral differences, investigation is required. Currently, the physiological significance of plant-specific and animal-specific ferritin iron minerals is unknown. The iron content of ferritin in living tissues ranges from zero in "apoferritin" to as high as ∼4500 iron atoms. Ferritin biomineralization begins with the reaction of Fe(2+) with O2 at ferritin enzyme (Fe(2+)/O oxidoreductase) sites. The product of ferritin enzyme activity, diferric oxy complexes, is also the precursor of ferritin biomineral. Concentrations of Fe(3+) equivalent to 2.0 × 10(-1) M are maintained in ferritin solutions, contrasting with the Fe(3+) Ks ∼ 10(-18) M. Iron ions move into, through, and out of ferritin protein cages in structural subdomains containing conserved amino acids. Cage subdomains include (1) ion channels for Fe(2+) entry/exit, (2) enzyme (oxidoreductase) site for coupling Fe(2+) and O yielding diferric oxy biomineral precursors, and (3) ferric oxy nucleation channels, where diferric oxy products from up to three enzyme sites interact while moving toward the central, biomineral growth cavity (12 nm diameter) where ferric oxy species, now 48-mers, grow in ferric oxy biomineral. High ferritin protein cage symmetry (3-fold and 4-fold axes) and amino acid conservation coincide with function, shown by amino acid substitution effects. 3-Fold symmetry axes control Fe(2+) entry (enzyme catalysis of Fe(2+)/O2 oxidoreduction) and Fe(2+) exit (reductive ferritin mineral dissolution); 3-fold symmetry axes influence Fe(2+)exit from dissolved mineral; bacterial ferritins diverge slightly in Fe/O2 reaction mechanisms and intracage paths of iron-oxy complexes. Biosynthesis rates of ferritin protein change with Fe(2+) and O2 concentrations, dependent on DNA-binding, and heme binding protein, Bach 1. Increased cellular O2 indirectly stabilizes ferritin DNA/Bach 1 interactions. Heme, Fe-protoporphyrin IX, decreases ferritin DNA-Bach 1 binding, causing increased ferritin mRNA biosynthesis (transcription). Direct Fe(2+) binding to ferritin mRNA decreases binding of an inhibitory protein, IRP, causing increased ferritin mRNA translation (protein biosynthesis). Newly synthesized ferritin protein consumes Fe(2+) in biomineral, decreasing Fe(2)(+) and creating a regulatory feedback loop. Ferritin without iron is "apoferritin". Iron removal from ferritin, experimentally, uses biological reductants, for example, NADH + FMN, or chemical reductants, for example, thioglycolic acid, with Fe(2+) chelators; physiological mechanism(s) are murky. Clear, however, is the necessity of ferritin for terrestrial life by conferring oxidant protection (plants, animals, and bacteria), virulence (bacteria), and embryonic survival (mammals). Future studies of ferritin structure/function and Fe(2+)/O2 chemistry will lead to new ferritin uses in medicine, nutrition, and nanochemistry.}, number={5}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Theil, Elizabeth C. and Tosha, Takehiko and Beherat, Rabindra K.}, year={2016}, month={May}, pages={784–791} }
 @article{behera_torres_tosha_bradley_goulding_theil_2015, title={Fe2+ substrate transport through ferritin protein cage ion channels influences enzyme activity and biomineralization}, volume={20}, ISSN={["1432-1327"]}, DOI={10.1007/s00775-015-1279-x}, abstractNote={Ferritins, complex protein nanocages, form internal iron-oxy minerals (Fe2O3·H2O), by moving cytoplasmic Fe(2+) through intracage ion channels to cage-embedded enzyme (2Fe(2+)/O2 oxidoreductase) sites where ferritin biomineralization is initiated. The products of ferritin enzyme activity are diferric oxy complexes that are mineral precursors. Conserved, carboxylate amino acid side chains of D127 from each of three cage subunits project into ferritin ion channels near the interior ion channel exits and, thus, could direct Fe(2+) movement to the internal enzyme sites. Ferritin D127E was designed and analyzed to probe properties of ion channel size and carboxylate crowding near the internal ion channel opening. Glu side chains are chemically equivalent to, but longer by one -CH2 than Asp, side chains. Ferritin D127E assembled into normal protein cages, but diferric peroxo formation (enzyme activity) was not observed, when measured at 650 nm (DFP λ max). The caged biomineral formation, measured at 350 nm in the middle of the broad, nonspecific Fe(3+)-O absorption band, was slower. Structural differences (protein X-ray crystallography), between ion channels in wild type and ferritin D127E, which correlate with the inhibition of ferritin D127E enzyme activity include: (1) narrower interior ion channel openings/pores; (2) increased numbers of ion channel protein-metal binding sites, and (3) a change in ion channel electrostatics due to carboxylate crowding. The contributions of ion channel size and structure to ferritin activity reflect metal ion transport in ion channels are precisely regulated both in ferritin protein nanocages and membranes of living cells.}, number={6}, journal={JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY}, author={Behera, Rabindra K. and Torres, Rodrigo and Tosha, Takehiko and Bradley, Justin M. and Goulding, Celia W. and Theil, Elizabeth C.}, year={2015}, month={Sep}, pages={957–969} }
 @misc{theil_2015, title={IRE mRNA riboregulators use metabolic iron (Fe2+) to control mRNA activity and iron chemistry in animals}, volume={7}, ISSN={["1756-591X"]}, DOI={10.1039/c4mt00136b}, abstractNote={A family of noncoding RNAs bind Fe2+to change protein synthesis.}, number={1}, journal={METALLOMICS}, author={Theil, Elizabeth C.}, year={2015}, pages={15–24} }
 @article{bernacchioni_ciambellotti_theil_turano_2015, title={Is His54 a gating residue for the ferritin ferroxidase site?}, volume={1854}, ISSN={["1878-1454"]}, DOI={10.1016/j.bbapap.2015.02.011}, abstractNote={Ferritin is a ubiquitous iron concentrating nanocage protein that functions through the enzymatic oxidation of ferrous iron and the reversible synthesis of a caged ferric-oxo biomineral. Among vertebrate ferritins, the bullfrog M homopolymer ferritin is a frequent model for analyzing the role of specific amino acids in the enzymatic reaction and translocation of iron species within the protein cage. X-ray crystal structures of ferritin in the presence of metal ions have revealed His54 binding to iron(II) and other divalent cations, with its imidazole ring proposed as "gate" that influences iron movement to/from the active site. To investigate its role, His54 was mutated to Ala. The H54A ferritin variant was expressed and its reactivity studied via UV-vis stopped-flow kinetics. The H54A variant exhibited a 20% increase in the initial reaction rate of formation of ferric products with 2 or 4 Fe²⁺/subunit and higher than 200% with 20 Fe²⁺/subunit. The possible meaning of the increased efficiency of the ferritin reaction induced by this mutation is proposed taking advantage of the comparative sequence analysis of other ferritins. The data here reported are consistent with a role for His54 as a metal ion trap that maintains the correct levels of access of iron to the active site. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.}, number={9}, journal={BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS}, author={Bernacchioni, Caterina and Ciambellotti, Silvia and Theil, Elizabeth C. and Turano, Paola}, year={2015}, month={Sep}, pages={1118–1122} }
 @article{schweitzer_zheng_cleland_goodwin_boatman_theil_marcus_fakra_2014, title={A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time}, volume={281}, number={1775}, journal={Proceedings of the Royal Society of London. Series B}, author={Schweitzer, M. H. and Zheng, W. X. and Cleland, T. P. and Goodwin, M. B. and Boatman, E. and Theil, E. and Marcus, M. A. and Fakra, S. C.}, year={2014} }
 @article{theil_turano_ghini_allegrozzi_bernacchioni_2014, title={Coordinating subdomains of ferritin protein cages with catalysis and biomineralization viewed from the C (4) cage axes}, volume={19}, ISSN={["1432-1327"]}, DOI={10.1007/s00775-014-1103-z}, abstractNote={Integrated ferritin protein cage function is the reversible synthesis of protein-caged, solid Fe2O3·H2O minerals from Fe2+ for metabolic iron concentrates and oxidant protection; biomineral order differs in different ferritin proteins. The conserved 432 geometric symmetry of ferritin protein cages parallels the subunit dimer, trimer, and tetramer interfaces, and coincides with function at several cage axes. Multiple subdomains distributed in the self-assembling ferritin nanocages have functional relationships to cage symmetry such as Fe2+ transport though ion channels (threefold symmetry), biomineral nucleation/order (fourfold symmetry), and mineral dissolution (threefold symmetry) studied in ferritin variants. On the basis of the effects of natural or synthetic subunit dimer cross-links, cage subunit dimers (twofold symmetry) influence iron oxidation and mineral dissolution. 2Fe2+/O2 catalysis in ferritin occurs in single subunits, but with cooperativity (n = 3) that is possibly related to the structure/function of the ion channels, which are constructed from segments of three subunits. Here, we study 2Fe2+ + O2 protein catalysis (diferric peroxo formation) and dissolution of ferritin Fe2O3·H2O biominerals in variants with altered subunit interfaces for trimers (ion channels), E130I, and external dimer surfaces (E88A) as controls, and altered tetramer subunit interfaces (L165I and H169F). The results extend observations on the functional importance of structure at ferritin protein twofold and threefold cage axes to show function at ferritin fourfold cage axes. Here, conserved amino acids facilitate dissolution of ferritin-protein-caged iron biominerals. Biological and nanotechnological uses of ferritin protein cage fourfold symmetry and solid-state mineral properties remain largely unexplored.}, number={4-5}, journal={JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY}, author={Theil, Elizabeth C. and Turano, Paola and Ghini, Veronica and Allegrozzi, Marco and Bernacchioni, Caterina}, year={2014}, month={Jun}, pages={615–622} }
 @article{bernacchioni_ghini_pozzi_di pisa_theil_turano_2014, title={Loop Electrostatics Modulates the Intersubunit Interactions in Ferritin}, volume={9}, ISSN={["1554-8937"]}, DOI={10.1021/cb500431r}, abstractNote={Functional ferritins are 24-mer nanocages that self-assemble with extended contacts between pairs of 4-helix bundle subunits coupled in an antiparallel fashion along the C2 axes. The largest intersubunit interaction surface in the ferritin nanocage involves helices, but contacts also occur between groups of three residues midway in the long, solvent-exposed L-loops of facing subunits. The anchor points between intersubunit L-loop pairs are the salt bridges between the symmetry-related, conserved residues Asp80 and Lys82. The resulting quaternary structure of the cage is highly soluble and thermostable. Substitution of negatively charged Asp80 with a positively charged Lys in homopolymeric M ferritin introduces electrostatic repulsions that inhibit the oligomerization of the ferritin subunits. D80K ferritin was present in inclusion bodies under standard overexpressing conditions in E. coli, contrasting with the wild type protein. Small amounts of fully functional D80K nanocages formed when expression was slowed. The more positively charged surface results in a different solubility profile and D80K crystallized in a crystal form with a low density packing. The 3D structure of D80K variant is the same as wild type except for the side chain orientations of Lys80 and facing Lys82. When three contiguous Lys groups are introduced in D80KI81K ferritin variant the nanocage assembly is further inhibited leading to lower solubility and reduced thermal stability. Here, we demonstrate that the electrostatic pairing at the center of the L-loops has a specific kinetic role in the self-assembly of ferritin nanocages.}, number={11}, journal={ACS CHEMICAL BIOLOGY}, author={Bernacchioni, Caterina and Ghini, Veronica and Pozzi, Cecilia and Di Pisa, Flavio and Theil, Elizabeth C. and Turano, Paola}, year={2014}, month={Nov}, pages={2517–2525} }
 @article{behera_theil_2014, title={Moving Fe2+ from ferritin ion channels to catalytic OH centers depends on conserved protein cage carboxylates}, volume={111}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1318417111}, abstractNote={Significance}, number={22}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Behera, Rabindra K. and Theil, Elizabeth C.}, year={2014}, month={Jun}, pages={7925–7930} }
 @article{khan_ma_walden_merrick_theil_goss_2014, title={Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions}, volume={42}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gku248}, abstractNote={Metal ion binding was previously shown to destabilize IRE-RNA/IRP1 equilibria and enhanced IRE-RNA/eIF4F equilibria. In order to understand the relative importance of kinetics and stability, we now report rapid rates of protein/RNA complex assembly and dissociation for two IRE-RNAs with IRP1, and quantitatively different metal ion response kinetics that coincide with the different iron responses in vivo. kon, for FRT IRE-RNA binding to IRP1 was eight times faster than ACO2 IRE-RNA. Mn2+ decreased kon and increased koff for IRP1 binding to both FRT and ACO2 IRE-RNA, with a larger effect for FRT IRE-RNA. In order to further understand IRE-mRNA regulation in terms of kinetics and stability, eIF4F kinetics with FRT IRE-RNA were determined. kon for eIF4F binding to FRT IRE-RNA in the absence of metal ions was 5-times slower than the IRP1 binding to FRT IRE-RNA. Mn2+ increased the association rate for eIF4F binding to FRT IRE-RNA, so that at 50 µM Mn2+ eIF4F bound more than 3-times faster than IRP1. IRP1/IRE-RNA complex has a much shorter life-time than the eIF4F/IRE-RNA complex, which suggests that both rate of assembly and stability of the complexes are important, and that allows this regulatory system to respond rapidly to change in cellular iron.}, number={10}, journal={NUCLEIC ACIDS RESEARCH}, author={Khan, Mateen A. and Ma, Jia and Walden, William E. and Merrick, William C. and Theil, Elizabeth C. and Goss, Dixie J.}, year={2014}, pages={6567–6577} }
 @article{kwak_schwartz_haldar_behera_tosha_theil_solomon_2014, title={Spectroscopic Studies of Single and Double Variants of M Ferritin: Lack of Conversion of a Biferrous Substrate Site into a Cofactor Site for O-2 Activation}, volume={53}, ISSN={["0006-2960"]}, DOI={10.1021/bi4013726}, abstractNote={Ferritin has a binuclear non-heme iron active site that functions to oxidize iron as a substrate for formation of an iron mineral core. Other enzymes of this class have tightly bound diiron cofactor sites that activate O2 to react with substrate. Ferritin has an active site ligand set with 1-His/4-carboxylate/1-Gln rather than the 2-His/4-carboxylate set of the cofactor site. This ligand variation has been thought to make a major contribution to this biferrous substrate rather than cofactor site reactivity. However, the Q137E/D140H double variant of M ferritin, has a ligand set that is equivalent to most of the diiron cofactor sites, yet did not rapidly react with O2 or generate the peroxy intermediate observed in the cofactor sites. Therefore, in this study, a combined spectroscopic methodology of circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD has been applied to evaluate the factors required for the rapid O2 activation observed in cofactor sites. This methodology defines the coordination environment of each iron and the bridging ligation of the biferrous active sites in the double and corresponding single variants of frog M ferritin. Based on spectral changes, the D140H single variant has the new His ligand binding, and the Q137E variant has the new carboxylate forming a μ-1,3 bridge. The spectra for the Q137E/D140H double variant, which has the cofactor ligand set, however, reflects a site that is more coordinately saturated than the cofactor sites in other enzymes including ribonucleotide reductase, indicating the presence of additional water ligation. Correlation of this double variant and the cofactor sites to their O2 reactivities indicates that electrostatic and steric changes in the active site and, in particular, the hydrophobic nature of a cofactor site associated with its second sphere protein environment, make important contributions to the activation of O2 by the binuclear non-heme iron enzymes.}, number={3}, journal={BIOCHEMISTRY}, author={Kwak, Yeonju and Schwartz, Jennifer K. and Haldar, Suranjana and Behera, Rabindra K. and Tosha, Takehiko and Theil, Elizabeth C. and Solomon, Edward I.}, year={2014}, month={Jan}, pages={473–482} }
 @article{theil_2013, title={Ferritin: The Protein Nanocage and Iron Biomineral in Health and in Disease}, volume={52}, ISSN={["1520-510X"]}, DOI={10.1021/ic400484n}, abstractNote={At the center of iron and oxidant metabolism is the ferritin superfamily: protein cages with Fe(2+) ion channels and two catalytic Fe/O redox centers that initiate the formation of caged Fe2O3·H2O. Ferritin nanominerals, initiated within the protein cage, grow inside the cage cavity (5 or 8 nm in diameter). Ferritins contribute to normal iron flow, maintenance of iron concentrates for iron cofactor syntheses, sequestration of iron from invading pathogens, oxidant protection, oxidative stress recovery, and, in diseases where iron accumulates excessively, iron chelation strategies. In eukaryotic ferritins, biomineral order/crystallinity is influenced by nucleation channels between active sites and the mineral growth cavity. Animal ferritin cages contain, uniquely, mixtures of catalytically active (H) and inactive (L) polypeptide subunits with varied rates of Fe(2+)/O2 catalysis and mineral crystallinity. The relatively low mineral order in liver ferritin, for example, coincides with a high percentage of L subunits and, thus, a low percentage of catalytic sites and nucleation channels. Low mineral order facilitates rapid iron turnover and the physiological role of liver ferritin as a general iron source for other tissues. Here, current concepts of ferritin structure/function/genetic regulation are discussed and related to possible therapeutic targets such as mini-ferritin/Dps protein active sites (selective pathogen inhibition in infection), nanocage pores (iron chelation in therapeutic hypertransfusion), mRNA noncoding, IRE riboregulator (normalizing the ferritin iron content after therapeutic hypertransfusion), and protein nanovessels to deliver medicinal or sensor cargo.}, number={21}, journal={INORGANIC CHEMISTRY}, author={Theil, Elizabeth C.}, year={2013}, month={Nov}, pages={12223–12233} }
 @article{theil_turano_2013, title={METALLOENZYMES Cage redesign explains assembly}, volume={9}, number={3}, journal={Nature Chemical Biology}, author={Theil, E. C. and Turano, P.}, year={2013}, pages={143–144} }
 @article{theil_westhof_2011, title={New Dimensions of RNA in Molecular Recognition and Catalysis}, volume={44}, ISSN={["0001-4842"]}, DOI={10.1021/ar200261e}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTNew Dimensions of RNA in Molecular Recognition and CatalysisElizabeth C. Theil and Eric WesthofView Author Information CHORI (Children's Hospital Oakland Research Institute), UC-Berkeley, and North Carolina State University IBMC-CNRS and University of StrasbourgCite this: Acc. Chem. Res. 2011, 44, 12, 1255–1256Publication Date (Web):December 20, 2011Publication History Published online20 December 2011Published inissue 20 December 2011https://pubs.acs.org/doi/10.1021/ar200261ehttps://doi.org/10.1021/ar200261eeditorialACS PublicationsCopyright © 2011 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views1851Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (560 KB) Get e-AlertscloseSUBJECTS:Catalysis,Genetics,Molecular structure,Monomers,Peptides and proteins Get e-Alerts}, number={12}, journal={ACCOUNTS OF CHEMICAL RESEARCH}, author={Theil, Elizabeth C. and Westhof, Eric}, year={2011}, month={Dec}, pages={1255–1256} }
 @article{wei_theil_2000, title={Identification and characterization of the iron regulatory element in the ferritin gene of a plant (soybean)}, volume={275}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M910334199}, abstractNote={Iron increases ferritin synthesis, targeting plant DNA and animal mRNA. The ferritin promoter in plants has not been identified, in contrast to the ferritin promoter and mRNA iron-responsive element (IRE) in animals. The soybean leaf, a natural tissue for ferritin expression, and DNA, with promoter deletions and luciferase or glucuronidase reporters, delivered with particle bombardment, were used to show that an 86-base pair fragment (iron regulatory element (FRE)) controlled iron-mediated derepression of the ferritin gene. Mutagenesis with linkers of random sequence detected two subdomains separated by 21 base pairs. FRE has no detectable homology to the animal IRE or to known promoters in DNA and bound atrans-acting factor in leaf cell extracts. FRE/factor binding was abrogated by increased tissue iron, in analogy to mRNA (IRE)/iron regulatory protein in animals. Maximum ferritin derepression was obtained with 50 μm iron citrate (1:10) or 500 μm iron citrate (1:1) but Fe-EDTA was ineffective, although the leaf iron concentration was increased; manganese, zinc, and copper had no effect. The basis for different responses in ferritin expression to different iron complexes, as well as the significance of using DNA but not mRNA as an iron regulatory target in plants, remain unknown.}, number={23}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Wei, JZ and Theil, EC}, year={2000}, month={Jun}, pages={17488–17493} }
 @article{ke_sierzputowska-gracz_gdaniec_theil_2000, title={Internal loop/bulge and hairpin loop of the iron-responsive element of ferritin mRNA contribute to maximal iron regulatory protein 2 binding and translational regulation in the iso-iron-responsive element/iso-iron regulatory protein family}, volume={39}, ISSN={["0006-2960"]}, DOI={10.1021/bi9924765}, abstractNote={Iron-responsive elements (IREs), a natural group of mRNA-specific sequences, bind iron regulatory proteins (IRPs) differentially and fold into hairpins [with a hexaloop (HL) CAGUGX] with helical distortions: an internal loop/bulge (IL/B) (UGC/C) or C-bulge. C-bulge iso-IREs bind IRP2 more poorly, as oligomers (n = 28-30), and have a weaker signal response in vivo. Two trans-loop GC base pairs occur in the ferritin IRE (IL/B and HL) but only one in C-bulge iso-IREs (HL); metal ions and protons perturb the IL/B [Gdaniec et al. (1998) Biochemistry 37, 1505-1512]. IRE function (translation) and physical properties (T(m) and accessibility to nucleases) are now compared for IL/B and C-bulge IREs and for HL mutants. Conversion of the IL/B into a C-bulge by a single deletion in the IL/B or by substituting the HL CG base pair with UA both derepressed ferritin synthesis 4-fold in rabbit reticulocyte lysates (IRP1 + IRP2), confirming differences in IRP2 binding observed for the oligomers. Since the engineered C-bulge IRE was more helical near the IL/B [Cu(phen)(2) resistant] and more stable (T(m) increased) and the HL mutant was less helical near the IL/B (ribonuclease T1 sensitive) and less stable (T(m) decreased), both CG trans-loop base pairs contribute to maximum IRP2 binding and translational regulation. The (1)H NMR spectrum of the Mg-IRE complex revealed, in contrast to the localized IL/B effects of Co(III) hexaammine observed previously, perturbation of the IL/B plus HL and interloop helix. The lower stability and greater helix distortion in the ferritin IL/B-IRE compared to the C-bulge iso-IREs create a combinatorial set of RNA/protein interactions that control protein synthesis rates with a range of signal sensitivities.}, number={20}, journal={BIOCHEMISTRY}, author={Ke, YH and Sierzputowska-Gracz, H and Gdaniec, Z and Theil, EC}, year={2000}, month={May}, pages={6235–6242} }
 @article{theil_takagi_small_he_tipton_danger_2000, title={The ferritin iron entry and exit problem}, volume={297}, ISSN={["1873-3255"]}, DOI={10.1016/S0020-1693(99)00375-8}, abstractNote={The entry and exit of Fe(II) ions in ferritin are endpoints in the process which concentrates iron as a solid (hydrated ferric oxide) to be used by living cells. Ferritin is a response to the trillion fold mismatch between the solubility of iron in neutral, aqueous, aerated solutions and the requirements for protein biosynthesis. The supramolecular structure of 24 polypeptides (subunits) joined by non-covalent bonds in a highly symmetrical (4, 3, 2), large (12 nm diameter) protein with a cavity (8 nm diameter) is found in plants, animals and microorganisms. Of the five types of iron sites which can be defined, iron entry (site 1) is likely at the junction of three subunits. A ferroxidase site (site 2), present in H-type ferritins, binds Fe(II) which reacts with dioxygen to form an initial, μ-1,2 diferric peroxo complex. The peroxo complex decays into hydrogen peroxide and the multiple diferric oxo complexes that are mineral precursors (sites 3a, 3b, 3x) in transit across the protein to the cavity; the ferroxidase site is sensitive to both natural and engineered variations in Fe ligands and 'second shell amino' acids such as tyrosine 30 and leucine 134. Studies of ferritin with subunits which lack the ferroxidase site (L-type) show that the mineral anchor sites of clustered R-COOH (site 4) are sensitive to RCH3 and RSH replacements. Iron exit (site 5), studied by adding NADH/FMN as a trigger, is at or near the entry site. Iron exit can be enhanced by localized unfolding of the polypeptide at the junction of three subunits, suggesting a regulation-sensitive biological signal for iron exit. The entry and exit of iron to and from the mineral, unique to ferritin has steps which parallel those in channel ion transport, and ion transport to and from biomineral such as tooth and bone. Iron entry involves oxidation at non-heme iron catalytic centers, similar to ribonucleotide reductase and methane monoxygenase, but diverging in the role of iron as a substrate rather than a cofactor. Sorting out the evolutionary and mechanistic relationships of ferritin and other proteins which use metal ions, as well as fully characterizing all five types of the functional iron sites are challenges which will keep biological inorganic chemists occupied for some time to come.}, number={1-2}, journal={INORGANICA CHIMICA ACTA}, author={Theil, EC and Takagi, H and Small, GW and He, L and Tipton, AR and Danger, D}, year={2000}, month={Jan}, pages={242–251} }
 @article{ha_shi_small_theil_allewell_1999, title={Crystal structure of bullfrog M ferritin at 2.8 angstrom resolution: analysis of subunit interactions and the binuclear metal center}, volume={4}, ISSN={["1432-1327"]}, DOI={10.1007/s007750050310}, abstractNote={Ferritins concentrate and store iron as a mineral in all bacterial, plant, and animal cells. The two ferritin subunit types, H or M (fast) and L (slow), differ in rates of iron uptake and mineralization and assemble in vivo to form heteropolymeric protein shells made up of 24 subunits; H/L subunit ratios reflect cell specificity of H and L subunit gene expression. A diferric peroxo species that is the initial reaction product of Fe(II) in H-type ferritins, as well as in ribonucleotide reductase (R2) and methane monooxygenase hydroxylase (MMOH), has recently been characterized, exploiting the relatively high accumulation of the peroxo intermediate in frog H-subunit type recombinant ferritin with the M sequence. The stability of the diferric reaction centers in R2 and MMOH contrasts with the instability of diferric centers in ferritin, which are precursors of the ferric mineral. We have determined the crystal structure of the homopolymer of recombinant frog M ferritin in two crystal forms: P4(1)2(1)2, a = b = 170.0 A and c = 481.5 A; and P3(1)21, a = b = 210.8 A and c = 328.1 A. The structural model for the trigonal form was refined to a crystallographic R value of 19.0% (Rfree = 19.4%); the two structures have an r.m.s.d. of approximately 0.22 A for all C alpha atoms. Comparison with the previously determined crystal structure of frog L ferritin indicates that the subunit interface at the molecular twofold axes is most variable, which may relate to the presence of the ferroxidase site in H-type ferritin subunits. Two metal ions (Mg) from the crystallization buffer were found in the ferroxidase site of the M ferritin crystals and interact with Glu23, Glu58, His61, Glu103, Gln137 and, unique to the M subunit, Asp140. The data suggest that Gln137 and Asp140 are a vestige of the second GluxxHis site, resulting from single nucleotide mutations of Glu and His codons and giving rise to Ala140 or Ser140 present in other eukaryotic H-type ferritins, by additional single nucleotide mutations. The observation of the Gln137xxAsp140 site in the frog M ferritin accounts for both the instability of the diferric oxy complexes in ferritin compared to MMOH and R2 and the observed kinetic variability of the diferric peroxo species in different H-type ferritin sequences.}, number={3}, journal={JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY}, author={Ha, Y and Shi, DS and Small, GW and Theil, EC and Allewell, NM}, year={1999}, month={Jun}, pages={243–256} }
 @article{gdaniec_sierzputowska-gracz_theil_1999, title={Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy (vol 37, pg 1505, 1998)}, volume={38}, ISSN={["0006-2960"]}, DOI={10.1021/bi9950746}, abstractNote={The ferritin IRE, a highly conserved (96 -99% in vertebrates) mRNA translation regulatory element in animal mRNA, was studied by molecular modeling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg 2+. IRE isoforms in other mRNAs regulate mRNA translation or stability; all IREs bind IRPs (iron regulatory proteins). A G ‚C base pair, conserved in ferritin IREs, spans an internal loop/bulge in the middle of an A-helix and, combined with a dynamic G‚U base pair, formed a pocket suitable for Co(III) hexammine binding. On the basis of the effects of Co(III) hexammine on the 1H NMR spectrum and results of automatic docking into the IRE model, the IRE bound Co(III) hexammine at the pocket in the major groove; Mg 2+ may bind to the IRE at the same site on the basis of an analogy to Co(III) hexammine and on the Mg 2+ inhibition of Cu(phen)2 cleavage at the site. Distortion of the IRE helix by the internal loop/bulge near a conserved unpaired C required for IRP binding and adjacent to an IRP cross-linking site suggests a role for the pocket in ferritin IRE/IRP interactions. RNA sequences in the noncoding region of mRNAs can regulate mRNA function. The predicted secondary structure is a hairpin distorted by a bulge, bulge loop, or internal loop. Specificity of the three-dimensional structure of RNA regulatory elements is recognized by proteins as in the Tat/ TAR and Rev/RRE interactions of the HIV virus ( 1-3). Bulge loops and internal loops in RNA induce bends or distortions in helixes, creating specific three-dimensional structures and, often, metal binding sites ( 4). Little is known about the three-dimensional structure of natural regulatory elements in eukaryotic mRNAs. The IRE (iron responsive element) family of isoelements is a particularly well characterized control element in normal animal mRNAs encoding proteins of iron metabolism. IREs are hairpins of 9 or 10 base pairs, interrupted by a bulge loop of 1-4 nucleotides with a conserved C residue and with a terminal hexaloop, CAGUGX (reviewed most recently in refs 5-8). The metal complex Cu(phen) 2 binds at the internal bulge/loop ( 9, 10). All IREs recognize a family of RNA binding proteins, the IRPs (iron regulatory proteins); some IREs recognize other proteins as well, such as initiation factors (11, 12, 14). Single-copy IREs in the 5 ′-untranslated regions of mRNAs regulate ribosome binding, while pentuple-copy IREs in the 3 ′-untranslated regions are part of a rapid turnover element regulating mRNA stability; each type of IRE is highly conserved (96 -99%) which contrasts with the lower sequence conservation (35 -45%) between translation and rapid turnover IREs ( 8). The ferritin IRE is the best characterized IRE in terms of structure and function. Assurance of the biological relevance of IRE studies with synthetic RNA, used here and in other types of experiments, has been uniquely provided by earlier investigations using natural ferritin mRNA [poly(A +) RNA]1 to study IRE structure, the IRP binding site and IRE function in regulating protein synthesis ( 9-11, 14-16); ferritin poly(A+) RNA showed function and/or chemical and enzymatic reactivity similar to those of the synthetic RNAs. The ferritin IRE is the most efficient of the translational regulatory IREs (13), possibly because of a conserved internal loop/bulge involving UGC/C rather than the bulge C of other IREs. Previous NMR studies have focused on the role of the ferritin IRE terminal hexaloop ( 17, 18). In this study, a model of the complete IRE 30-mer is developed, assisted by NMR data from15Nand13C-labeled RNA and cobalt(III) hexammine/RNA complexes; the model is consistent with previous chemical and enzymatic studies. Co(III) hexammine significantly shifted proton NMR resonances of G7 and G27 in the internal loop/bulge region and docked in a pocket caused by distortion of the major groove in the middle of the IRE. The same region is also hypersensitive to cleavage by hydroxyl radical ( 16) and displays Mg† The work was supported in part by NIH Grant DK-20251. * Corresponding author at Department of Biochemistry, North Carolina State University, Raleigh, NC 27695-7622. Phone: 919-5155805. Fax: 919-515-5805. E-mail: Theil@bchserver.bch.ncsu.edu. ‡ Polish Academy of Sciences. § Department of Biochemistry, North Carolina State University. | Department of Chemistry, North Carolina State University. 1 Poly(A+) RNA from a natural cell rich in ferritin mRNA [the embryonic red cell in which∼10% of the mRNA is ferritin mRNA (11)] was used with immunoprecipitation to examine control of ferritin synthesis ( 11, 14, 15) or with specific primers to examine IRE structure in the RNA after reaction with structure probes or IRP binding ( 9, 16). 1505 Biochemistry1998,37, 1505-1512 S0006-2960(97)01981-8 CCC: $15.00 © 1998 American Chemical Society Published on Web 01/23/1998 sensitive changes in cleavage by Cu(phen) 2 (9 , indicating solvent accessibility and suggesting that hydrated Mg 2+ binds at the site. In the IRE model, G7/U6 in the internal loop/ bulge and G18/U19 which cross-link to the IRP ( 21) are 22 Å apart, in contrast to only 18 Å in an IRE model without the interhelical pocket, which may relate to correct positioning in the IRP binding site. MATERIALS AND METHODS RNA Synthesis . The 30-mer representing the frog ferritin IRE (Figure 1) was synthesized using the double-stranded T7 polymerase site and the complement of the 30-mer as a template, as previously described ( 17); vertebrate ferritin IREs are highly conserved ( 5-8) (96-99%), but the frog ferritin IRE is the only one which has been studied in natural [poly(A+)] mRNA as well as in synthetic mRNAs and RNA oligomers. The use of full-length double-stranded template increased the yield∼1.5-2-fold; reaction volumes were 24 90 mL. Cloned T7 polymerase was isolated as described by Studier et al. ( 22). RNA was purified by electrophoresis in urea/acrylamide gels as before ( 17), electroreluted, and concentrated by alcohol precipitation. To study the effect of pH on the detection of the G ‚U base pair (Figure 2C), commercially prepared (Cybersyn) RNA was used, but was purified by gel electrophoresis and dialyzed extensively against water before use. RNA enriched in13C and15N was prepared using 13C/15N nucleotide triphosphates (NTPs) as described for the synthesis of RNA with natural abundance levels of the isotopes ( 19, 20). The13Cand15N-enriched NTPs were prepared using crude rRNA fromMethylophilus methyltrophus provided by the NIH Research Resource for Heavy Atoms at Los Alamos National Laboratory. The crude rRNA was digested with DNAse, extracted with phenol and chloroform/isoamyl alcohol (24:1), and precipitated with alcohol followed by digestion to nucleotides with nuclease P1 ( 23) and conversion to NTPs using nucleoside monophosphate kinase, guanylate kinase, pyruvate kinase, myokinase, phosphoenolpyruvate, and ATP as described by Nikonowicz et al. ( 24). After concentration, lyophilization, and alcohol precipitation, the crude NTPs were dissolved in col d 1 M triethylamine/borate buffer (TEAB) at pH 9.5 and desalted on an Affigel 601 (Biorad) column equilibrated i n 1 M TEAB buffer at 5°C (25); the NTPs were eluted with cold distilled water acidified to pH 4-5 with CO2, lyophilized, dissolved in water, filtered through a washed Centricon 10 filter, and stored at pH 8.1 and-20 °C until use. NMR Spectroscopy.RNA (0.5-1.0 mM in 10 mM sodium phosphate buffer and 0.1 mM EDTA at pH 6.8) was heated at 85°C and slowly cooled in the NMR tube. Spectra were acquired on a Bruker DRX 500 MHz spectrometer. Spectra in H2O were obtained either by the Watergate method (26) or by presaturation of the HDO signal fo r 2 s prior to applying an observation pulse or by using the jump -return water suppression and excitation maximum set to the imino resonances ( 27). Data for the two-dimensional (2D) NOESY experiment in 10% D2O/90% H2O were acquired at 12 °C using Watergate-water suppression [a 3 -9-19 pulse sequence with the gradients for water suppression with excitation maximum set to the imino resonances ( 26)]. The spectrum was 2048 × 256 complex data points with a sweep width of 12 000 Hz, a mixing time of 250 ms, a recycle delay of 1.7 s, and 256 scans per slice. Spectra were processed with FELIX 95.0 software (Biosym/Molecular Simulations, Inc.) using an exponential weighing function or shifted sinebell function to resolve overlapped imino protons. NOESY, DQF-COSY, and TOCSY experiments were recorded in 99.996% D 2O on a 500 MHz GE Omega spectrometer or a Bruker 500 MHz spectrometer. Data sets with 2048 complex points int2 and 512 complex points in t1 were acquired with 5000 Hz sweep widths in both dimensions and 128 scans per slice. NOESY spectra were acquired with mixing times of 120, 200, and 400 ms and a recycle delay o f 2 s at 12 and 20°C. The TOCSY spectrum was recorded with a 75 ms MLEV spin lock pulse and a recycle delay of 1.5 s. The DQF-COSY spectra were recorded with WALTZ decoupling of 31P during acquisition and a recycle delay of 1.6 s. The diagonal and cross-peaks of DQF-COSY spectra were phased with antiphase absorption line shape in both directions. All spectra were processed with combinations of exponential and sine-skewed functions and zero-filled to 2K× 2K data points using XWINNMR Bruker or Felix 95.0 software. Spectra with Co(III) hexammine and with varyious pHs were acquired on a Bruker DRX 500 MHz system. Imino proton spectra were obtained by the Watergate method ( 26). Typically, 2048 scans were collected. 1H spectra in 10% D2O/90% H2O were collected at 12°C in 16K point data sets consisting of 1024 scans each. Spectra of double-labeled RNA were obtained on a Varian Unity Plus 600 MHz NMR spectrometer at the University of Chicago, Biological Sciences Division NMR Facility, used in consultation with Dr. Klaas Hallenga. The 2D ( 1H-15N) HSQC experiments were carried out using gradie}, number={17}, journal={BIOCHEMISTRY}, author={Gdaniec, Z and Sierzputowska-Gracz, H and Theil, EC}, year={1999}, month={Apr}, pages={5676–5676} }
 @article{pereira_small_krebs_tavares_edmondson_theil_huynh_1998, title={Direct spectroscopic and kinetic evidence for the involvement of a peroxodiferric intermediate during the ferroxidase reaction in fast ferritin mineralization}, volume={37}, ISSN={["0006-2960"]}, DOI={10.1021/bi980847w}, abstractNote={Rapid freeze-quench (RFQ) Mössbauer and stopped-flow absorption spectroscopy were used to monitor the ferritin ferroxidase reaction using recombinant (apo) frog M ferritin; the initial transient ferric species could be trapped by the RFQ method using low iron loading (36 Fe2+/ferritin molecule). Biphasic kinetics of ferroxidation were observed and measured directly by the Mössbauer method; a majority (85%) of the ferrous ions was oxidized at a fast rate of approximately 80 s-1 and the remainder at a much slower rate of approximately 1.7 s-1. In parallel with the fast phase oxidation of the Fe2+ ions, a single transient iron species is formed which exhibits magnetic properties (diamagnetic ground state) and Mössbauer parameters (DeltaEQ = 1.08 +/- 0.03 mm/s and delta = 0.62 +/- 0.02 mm/s) indicative of an antiferromagnetically coupled peroxodiferric complex. The formation and decay rates of this transient diiron species measured by the RFQ Mössbauer method match those of a transient blue species (lambdamax = 650 nm) determined by the stopped-flow absorbance measurement. Thus, the transient colored species is assigned to the same peroxodiferric intermediate. Similar transient colored species have been detected by other investigators in several other fast ferritins (H and M subunit types), such as the human H ferritin and the Escherichia coli ferritin, suggesting a similar mechanism for the ferritin ferroxidase step in all fast ferritins. Peroxodiferric complexes are also formed as early intermediates in the reaction of O2 with the catalytic diiron centers in the hydroxylase component of soluble methane monooxygenase (MMOH) and in the D84E mutant of the R2 subunit of E. coli ribonucleotide reductase. The proposal that a single protein site, with a structure homologous to the diiron centers in MMOH and R2, is involved in the ferritin ferroxidation step is confirmed by the observed kinetics, spectroscopic properties, and purity of the initial peroxodiferric species formed in the frog M ferritin.}, number={28}, journal={BIOCHEMISTRY}, author={Pereira, AS and Small, W and Krebs, C and Tavares, P and Edmondson, DE and Theil, EC and Huynh, BH}, year={1998}, month={Jul}, pages={9871–9876} }
 @article{burton_harlow_theil_1998, title={Evidence for reutilization of nodule iron in soybean seed development}, volume={21}, ISSN={["1532-4087"]}, DOI={10.1080/01904169809365453}, abstractNote={Abstract Iron (Fe) is required in plants for the function of the important processes of photosynthesis, respiration, DNA synthesis, and nitrogen (N) fixation. Concentrations of Fe show tissue specific changes during development. In soybean seeds, Fe accumulates through the linear phase of seed development, but the source of seed Fe, whether remobilized from other tissues or taken from the root environment, is not known. Root nodules of legumes have higher concentrations of Fe than other vegetative organs. To examine whether nodules could provide Fe to the seeds, two cultivars (Tokyo and Arksoy), differing in seed ferritin and Fe content were grown in a phytotron and given a single dose of 59Fe‐EDTA early in development [15 days after inoculation with Bradyrhizobium (DAI)]. The 59Fe distribution as well as immunoreactive ferritin were examined throughout development in nodule, leaf, and seed tissue. Leaves, nodules, and seeds accounted for 75 to 87% of the total plant 59Fe throughout the reproductive perio...}, number={5}, journal={JOURNAL OF PLANT NUTRITION}, author={Burton, JW and Harlow, C and Theil, EC}, year={1998}, pages={913–927} }
 @article{gdaniec_sierzputowska-gracz_theil_1998, title={Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy}, volume={37}, ISSN={["0006-2960"]}, DOI={10.1021/bi9719814}, abstractNote={The ferritin IRE, a highly conserved (96-99% in vertebrates) mRNA translation regulatory element in animal mRNA, was studied by molecular modeling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg2+. IRE isoforms in other mRNAs regulate mRNA translation or stability; all IREs bind IRPs (iron regulatory proteins). A G.C base pair, conserved in ferritin IREs, spans an internal loop/bulge in the middle of an A-helix and, combined with a dynamic G.U base pair, formed a pocket suitable for Co(III) hexammine binding. On the basis of the effects of Co(III) hexammine on the 1H NMR spectrum and results of automatic docking into the IRE model, the IRE bound Co(III) hexammine at the pocket in the major groove; Mg2+ may bind to the IRE at the same site on the basis of an analogy to Co(III) hexammine and on the Mg2+ inhibition of Cu-(phen)2 cleavage at the site. Distortion of the IRE helix by the internal loop/bulge near a conserved unpaired C required for IRP binding and adjacent to an IRP cross-linking site suggests a role for the pocket in ferritin IRE/IRP interactions.}, number={6}, journal={BIOCHEMISTRY}, author={Gdaniec, Z and Sierzputowska-Gracz, H and Theil, EC}, year={1998}, month={Feb}, pages={1505–1512} }
 @article{takagi_shi_ha_allewell_theil_1998, title={Localized unfolding at the junction of three ferritin subunits - A mechanism for iron release?}, volume={273}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.273.30.18685}, abstractNote={How and where iron exits from ferritin for cellular use is unknown. Twenty-four protein subunits create a cavity in ferritin where iron is concentrated >1011-fold as a mineral. Proline substitution for conserved leucine 134 (L134P) allowed normal assembly but increased iron exit rates. X-ray crystallography of H-L134P ferritin revealed localized unfolding at the 3-fold axis, also iron entry sites, consistent with shared use sites for iron exit and entry. The junction of three ferritin subunits appears to be a dynamic aperture with a “shutter” that cytoplasmic factors might open or close to regulate iron release in vivo.}, number={30}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Takagi, H and Shi, DS and Ha, Y and Allewell, NM and Theil, EC}, year={1998}, month={Jul}, pages={18685–18688} }
 @article{ke_wu_leibold_walden_theil_1998, title={Loops and bulge/loops in iron-responsive element isoforms influence iron regulatory protein binding - Fine-tuning of mRNA regulation?}, volume={273}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.273.37.23637}, abstractNote={A family of noncoding mRNA sequences, iron-responsive elements (IREs), coordinately regulate several mRNAs through binding a family of mRNA-specific proteins, iron regulatory proteins (IRPs). IREs are hairpins with a constant terminal loop and base-paired stems interrupted by an internal loop/bulge (in ferritin mRNA) or a C-bulge (in m-aconitase, erythroid aminolevulinate synthase, and transferrin receptor mRNAs). IRP2 binding requires the conserved C-G base pair in the terminal loop, whereas IRP1 binding occurs with the C-G or engineered U-A. Here we show the contribution of the IRE internal loop/bulge to IRP2 binding by comparing natural and engineered IRE variants. Conversion of the internal loop/bulge in the ferritin-IRE to a C-bulge, by deletion of U, decreased IRP2 binding by >95%, whereas IRP1 binding changed only 13%. Moreover, IRP2 binding to natural IREs with the C-bulge was similar to the ΔU6 ferritin-IRE: >90% lower than the ferritin-IRE. The results predict mRNA-specific variation in IRE-dependent regulation in vivo and may relate to previously observed differences in iron-induced ferritin and m-aconitase synthesis in liver and cultured cells. Variations in IRE structure and cellular IRP1/IRP2 ratios can provide a range of finely tuned, mRNA-specific responses to the same (iron) signal.}, number={37}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Ke, YH and Wu, JY and Leibold, EA and Walden, WE and Theil, EC}, year={1998}, month={Sep}, pages={23637–23640} }
 @misc{theil_1998, title={Methods of identifying transition metal complexes that selectively cleave regulatory elements of mRNA and uses thereof}, volume={5,834,199}, number={1998 Nov. 10}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Theil, E. C.}, year={1998} }
 @book{principles of chemistry in biology: a teaching companion_1998, ISBN={0841235066}, publisher={Washington, DC: American Chemical Society; Distributed by Oxford University Press}, year={1998} }
 @article{theil_1998, title={The iron responsive element (IRE) family of mRNA regulators: Regulation of iron transport and uptake compared in animals, plants, and microorganisms}, volume={35}, number={1998}, journal={Iron transport and storage in microorganisms, plants and animals}, author={Theil, E. C.}, year={1998}, pages={403–434} }
 @article{ha_theil_allewell_1997, title={Preliminary analysis of amphibian red cell M ferritin in a novel tetragonal unit cell}, volume={53}, ISSN={["2059-7983"]}, DOI={10.1107/S0907444997003983}, abstractNote={The ferritins are a multigene family of proteins that concentrate and store iron in all prokaryotic and eukaryotic cells. 24 monomeric subunits which fold as four-helix bundles assemble to form a protein shell with 432 cubic symmetry and an external diameter of approximately 130 A. The iron is stored inside the protein shell as a mineralized core approximately 80 A in diameter. Recombinant amphibian red cell M ferritin crystallizes in approximately 2 M (NH(4))(2)SO(4) at pH 4.6 in a space group that has not been reported previously. Electron microscopy, precession photography, Patterson and Fourier maps of the native protein and a UO(2)(2+) derivative, and simulations were used to determine that the unit-cell dimensions are a = b = 169.6, c = 481.2 A, alpha = beta = gamma = 90 degrees and the space group is P4(1)2(1)2 or P4(3)2(1)2. A preliminary model of the structure was obtained by molecular replacement, with amphibian red cell L ferritin as the model. In contrast to previously determined ferritin crystal structures which have intermolecular contacts at the twofold and threefold molecular axes, M ferritin crystals have a novel intermolecular interaction mediated by interdigitation of the DE loops of two molecules at the fourfold molecular axes.}, journal={ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY}, author={Ha, Y and Theil, EC and Allewell, NM}, year={1997}, month={Sep}, pages={513–523} }
 @article{pereira_tavares_lloyd_danger_edmondson_theil_huynh_1997, title={Rapid and parallel formation of Fe3+ multimers, including a trimer, during H-type subunit ferritin mineralization}, volume={36}, ISSN={["0006-2960"]}, DOI={10.1021/bi970348f}, abstractNote={Conversion of Fe ions in solution to the solid phase in ferritin concentrates iron required for cell function. The rate of the Fe phase transition in ferritin is tissue specific and reflects the differential expression of two classes of ferritin subunits (H and L). Early stages of mineralization were probed by rapid freeze-quench Mossbauer, at strong fields (up to 8 T), and EPR spectroscopy in an H-type subunit, recombinant frog ferritin; small numbers of Fe (36 moles/mol of protein) were used to increase Fe3+ in mineral precursor forms. At 25 ms, four Fe3+-oxy species (three Fe dimers and one Fe trimer) were identified. These Fe3+-oxy species were found to form at similar rates and decay subsequently to a distinctive superparamagentic species designated the "young core." The rate of oxidation of Fe2+ (1026 s(-1)) corresponded well to the formation constant for the Fe3+-tyrosinate complex (920 s(-1)) observed previously [Waldo, G. S., & Theil, E. C. (1993) Biochemistry 32, 13261] and, coupled with EPR data, indicates that several or possibly all of the Fe3+-oxy species involve tyrosine. The results, combined with previous Mossbauer studies of Y30F human H-type ferritin which showed decreases in several Fe3+ intermediates and stabilization of Fe2+ [Bauminger, E. R., et al. (1993) Biochem. J. 296, 709], emphasize the involvement of tyrosyl residues in the mineralization of H-type ferritins. The subsequent decay of these multiple Fe3+-oxy species to the superparamagnetic mineral suggests that Fe3+ species in different environments may be translocated as intact units from the protein shell into the ferritin cavity where the conversion to a solid mineral occurs.}, number={25}, journal={BIOCHEMISTRY}, author={Pereira, AS and Tavares, P and Lloyd, SG and Danger, D and Edmondson, DE and Theil, EC and Huynh, BH}, year={1997}, month={Jun}, pages={7917–7927} }
 @article{theil_burton_beard_1997, title={Sustainable solution for dietary iron deficiency through plant biotechnology and breeding to increase seed ferritin control}, volume={51}, number={Suppl. 4}, journal={European Journal of Clinical Nutrition}, author={Theil, E. C. and Burton, J. W. and Beard, J. L.}, year={1997}, pages={S28–31} }
 @article{fetter_cohen_danger_sanders_theil_1997, title={The influence of conserved tyrosine 30 and tissue-dependent differences in sequence on ferritin function: use of blue and purple Fe(III) species as reporters of ferroxidation}, volume={2}, DOI={10.1007/s007750050180}, abstractNote={Ferritins uniquely direct the vectorial transfer of hydrated Fe(II)/Fe(III) ions to a condensed ferric phase in the central cavity of the soluble protein. Secondary, tertiary and quaternary structure are conserved in ferritin, but only five amino acid residues are conserved among all known ferritins. The sensitivity of ferroxidation rates to small differences in primary sequence between ferritin subunits that are cell-specifically expressed or to the conservative replacement of the conserved tyrosine 30 residue was demonstrated by examining recombinant (frog) H-type (red blood cell predominant) and M-type subunit (liver predominant) proteins which are both fast ferritins; the proteins form two differently colored Fe(III)-protein complexes absorbing at 550 nm or 650 nm, respectively. The complexes are convenient reporters of Fe(III)-protein interaction because they are transient in contrast to the Fe(III)-oxy complexes measured in the past at 310–420 nm, which are stable because of contributions from the mineral itself. The A650-nm species formed 18-fold faster in the M-subunit protein than did the 550-nm species in H-subunit ferritin, even though all the ferroxidase residues are the same; the Vmax was fivefold faster but the Hill coefficents were identical (1.6), suggesting similar mechanisms. In H-subunit ferritin, substitution of phenylalanine for conserved tyrosine 30 (located in the core of the subunit four-helix bundle) slowed ferroxidation tenfold, whereas changing surface tyrosine 25 or tyrosine 28 had no effect. The Fe(III)-tyrosinate was fortunately not changed by the mutation, based on the resonance Raman spectrum, and remained a suitable reporter for Fe(III)-protein interactions. Thus, the A550/650 nm can also report on post-oxidation events such as transport through the protein. The impact of Y30F on rates of formation of Fe(III)-protein complexes in ferritin, combined with Mössbauer spectroscopic studies that showed the parallel formation of multiple Fe(III) postoxidation species (three dinuclear oxy and one trinuclear oxy species) (A. S. Periera et al., Biochemistry 36 : 7917–7927, 1997) and the loss of several of the multimeric Fe(III) post-oxidation species in a Y30F alteration of human recombinant H-ferritin (E. R. Bauminger et al., Biochem J. 296 : 709–719, 1993), indicate that at least one of the pathways for Fe oxidation/transfer in ferritin is through the center of the four-helix bundle and is influenced by structural features dependent on tyrosine 30.}, number={5}, journal={Journal of Biological Inorganic Chemistry}, author={Fetter, J. and Cohen, J. and Danger, D. P. and Sanders, Loehr J. and Theil, E. C.}, year={1997}, pages={652–661} }
 @inbook{theil_1997, title={Translational regulation of bioiron}, DOI={10.1007/978-1-4615-5993-1_6}, booktitle={Metal ions in gene regulation}, publisher={New York: Chapman & Hall}, author={Theil, E. C.}, editor={S. Silver and Walden, W.Editors}, year={1997}, pages={131–156} }
 @article{theil_1990, title={Regulation of ferritin and transferrin receptor messenger-rnas}, volume={265}, number={9}, journal={Journal of Biological Chemistry}, author={Theil, E. C.}, year={1990}, pages={4771–4774} }
 @misc{theil_1987, title={FERRITIN - STRUCTURE, GENE-REGULATION, AND CELLULAR FUNCTION IN ANIMALS, PLANTS, AND MICROORGANISMS}, volume={56}, ISSN={["0066-4154"]}, DOI={10.1146/annurev.biochem.56.1.289}, abstractNote={The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More}, journal={ANNUAL REVIEW OF BIOCHEMISTRY}, author={THEIL, EC}, year={1987}, pages={289–315} }