Journal articles: 'Triosephosphate Isomerase Barrel'

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Carcamo-Noriega, Edson N., and Gloria Saab-Rincon. "Identification of fibrillogenic regions in human triosephosphate isomerase." PeerJ 4 (February 4, 2016): e1676. http://dx.doi.org/10.7717/peerj.1676.

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Background.Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to structural features, such is the case of TIM barrel topology.Methods.This work was aimed to study the fibrillogenic propensity of human triosephosphate isomerase (HsTPI) as a model of TIM barrels. In order to do so, aggregation of HsTPI was evaluated under native-like and destabilizing conditions. Fibrillogenic regions were identified by bioinformatics approaches, protein fragmentation and peptide aggregation.Results.We identified four fibrillogenic regions in the HsTPI corresponding to theβ3,β6,β7y α8 of the TIM barrel. From these, theβ3-strand region (residues 59–66) was highly fibrillogenic. In aggregation assays, HsTPI under native-like conditions led to amorphous assemblies while under partially denaturing conditions (urea 3.2 M) formed more structured aggregates. This slightly structured aggregates exhibited residual cross-βstructure, as demonstrated by the recognition of the WO1 antibody and ATR-FTIR analysis.Discussion.Despite the fibrillogenic regions present in HsTPI, the enzyme maintained under native-favoring conditions displayed low fibrillogenic propensity. This amyloid-resistance can be attributed to the three-dimensional arrangement of the protein, whereβ-strands, susceptible to aggregation, are protected in the core of the molecule. Destabilization of the protein structure may expose inner regions promotingβ-aggregation, as well as the formation of hydrophobic disordered aggregates. Being this last pathway kinetically favored over the thermodynamically more stable fibril aggregation pathway.

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Ravindra, Gudihal, and Padmanabhan Balaram. "Plasmodium falciparum triosephosphate isomerase: New insights into an old enzyme." Pure and Applied Chemistry 77, no. 1 (January 1, 2005): 281–89. http://dx.doi.org/10.1351/pac200577010281.

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Triosephosphate isomerase (TIM), a central enzyme in the glycolytic pathway, has been the subject of extensive structural and mechanistic investigations over the past 30 years. The TIM barrel is the prototype of the (β/α)8 barrel fold, which is one of the most extensively used structural motifs in enzymes. Mechanistic studies on TIM from a variety of sources have emphasized the importance of loop 6 dynamics for enzyme activity. Several conserved residues in TIM have been investigated by extensive site-directed mutagenesis of the enzyme from yeast, chicken, and trypanosoma. The cloning and sequencing of the TIM gene from the malarial parasite Plasmodium falciparum in 1993 revealed the unexpected mutation of a hitherto conserved residue serine (S96) to phenylalanine (F96). Subsequent results from the genome sequencing programs of Plasmodium falciparum, Plasmodium vivax, and Plasmodium yoelii confirmed the presence of the S96F mutation in malarial parasites. The crystal structure of PfTIM and several inhibitor complexes, including a high-resolution (1.1 Å) structure of the PfTIM 2-phosphoglycerate complex, revealed that loop 6 had a propensity to remain open, even in several ligand bound structures. Furthermore, both open and closed forms could be characterized for the same complex. Since glycolysis is the primary source of ATP for the malarial parasite during the intraerythrocytic stage, glycolytic enzymes present themselves as potential targets for inhibitors. Two distinct approaches have been explored. The use of dimer interface peptides, which interfere with assembly, has proved promising. Inactivation of the enzyme by modification of a cysteine (C13) residue, which lies close to the active site residue, lysine (K12) is another potential strategy. The differential reactivity, of the four-cysteine residues, at positions 13, 126, 196, and 217 in each subunit has been established using electrospray ionization mass spectrometry. Studies of single tryptophan mutants (W11F and W168F) of PfTIM provide a probe to study folding, stability, and inhibitor interactions.

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Yang, Trent C., Steve Legault, Emery A. Kayiranga, Jyothi Kumaran, Kazuhiko Ishikawa, and Wing L. Sung. "The N-Terminal β-Sheet of the Hyperthermophilic Endoglucanase from Pyrococcus horikoshii Is Critical for Thermostability." Applied and Environmental Microbiology 78, no. 9 (February 17, 2012): 3059–67. http://dx.doi.org/10.1128/aem.07576-11.

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ABSTRACTThe β-1,4-endoglucanase (EC 3.2.1.4) from the hyperthermophilic archaeonPyrococcus horikoshii(EGPh) has strong hydrolyzing activity toward crystalline cellulose. When EGPh is used in combination with β-glucosidase (EC 3.2.1.21), cellulose is completely hydrolyzed to glucose at high temperature, suggesting great potential for EGPh in bioethanol industrial applications. The crystal structure of EGPh shows a triosephosphate isomerase (TIM) (β/α)8-barrel fold with an N-terminal antiparallel β-sheet at the opposite side of the active site and a very short C-terminal sequence outside of the barrel structure. We describe here the function of the peripheral sequences outside of the TIM barrel core structure. Sequential deletions were performed from both N and C termini. The activity, thermostability, and pH stability of the expressed mutants were assessed and compared to the wild-type EGPh enzyme. Our results demonstrate that the TIM barrel core is essential for enzyme activity and that the N-terminal β-sheet is critical for enzyme thermostability. Bioinformatics analyses identified potential key residues which may contribute to enzyme hyperthermostability.

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Garrido, Francisco, María Gasset, Juliana Sanz-Aparicio, Carlos Alfonso, and María A. Pajares. "Rat liver betaine–homocysteine S-methyltransferase equilibrium unfolding: insights into intermediate structure through tryptophan substitutions." Biochemical Journal 391, no. 3 (October 25, 2005): 589–99. http://dx.doi.org/10.1042/bj20050505.

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Equilibrium folding of rat liver BHMT (betaine–homocysteine methyltransferase), a TIM (triosephosphate isomerase)-barrel tetrameric protein, has been studied using urea as denaturant. A combination of activity measurements, tryptophan fluorescence, CD and sedimentation-velocity studies suggested a multiphasic process including two intermediates, a tetramer (I4) and a monomer (J). Analysis of denaturation curves for single- and six-tryptophan mutants indicated that the main changes leading to the tetrameric intermediate are related to alterations in the helix α4 of the barrel, as well as in the dimerization arm. Further dissociation to intermediate J included changes in the loop connecting the C-terminal α-helix of contact between dimers, disruption of helix α4, and initial alterations in helix α7 of the barrel, as well as in the dimerization arm. Evolution of the monomeric intermediate continued through additional perturbations in helix α7 of the barrel and the C-terminal loop. Our data highlight the essential role of the C-terminal helix in dimer–dimer binding through its contribution to the increased stability shown by BHMT as compared with other TIM barrel proteins. The results are discussed in the light of the high sequence conservation shown by betaine–homocysteine methyltransferases and the knowledge available for other TIM-barrel proteins.

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Halloran, Kevin T., Yanming Wang, Karunesh Arora, Srinivas Chakravarthy, Thomas C. Irving, Osman Bilsel, Charles L. Brooks, and C. Robert Matthews. "Frustration and folding of a TIM barrel protein." Proceedings of the National Academy of Sciences 116, no. 33 (July 25, 2019): 16378–83. http://dx.doi.org/10.1073/pnas.1900880116.

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Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecular-level understanding of the readout from sequence to structure. We have combined sequence-sensitive native centric simulations with small-angle X-ray scattering and time-resolved Förster resonance energy transfer to monitor the formation of structure in an intermediate in the Sulfolobus solfataricus indole-3-glycerol phosphate synthase TIM barrel that appears within 50 μs and must at least partially unfold to achieve productive folding. Simulations reveal the presence of a major and 2 minor folding channels not detected in experiments. Frustration in folding, i.e., backtracking in native contacts, is observed in the major channel at the initial stage of folding, as well as late in folding in a minor channel before the appearance of the native conformation. Similarities in global and pairwise dimensions of the early intermediate, the formation of structure in the central region that spreads progressively toward each terminus, and a similar rate-limiting step in the closing of the β-barrel underscore the value of combining simulation and experiment to unravel complex folding mechanisms at the molecular level.

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Kumar, Jay Prakash, Harshvardhan Rao, Vinod Nayak, and S. Ramaswamy. "Crystal structures and kinetics ofN-acetylneuraminate lyase fromFusobacterium nucleatum." Acta Crystallographica Section F Structural Biology Communications 74, no. 11 (October 17, 2018): 725–32. http://dx.doi.org/10.1107/s2053230x18012992.

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N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) toN-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host–pathogen interactions. In this study, atomic resolution structures of NanA fromFusobacterium nucleatum(FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatumis a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterialN-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure–function relationship, the steady-state kinetic parameters of the enzyme are also reported.

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Shi, Rong, Marco Pineda, Eunice Ajamian, Qizhi Cui, Allan Matte, and Miroslaw Cygler. "Structure of l-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic l-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold." Journal of Bacteriology 190, no. 24 (October 10, 2008): 8137–44. http://dx.doi.org/10.1128/jb.01049-08.

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ABSTRACT Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a β-keto acid decarboxylation reaction to produce l-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (l-xylulose-5-phosphate 3-epimerase) and UlaF (l-ribulose-5-phosphate 4-epimerase), yielding d-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel β-strands. The enzyme binds Zn2+, which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the β1/α1 loop and α3′ helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands β7 and β8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the l-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.

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Mahanta, Pranjal, Amit Bhardwaj, Krishan Kumar, Vanga S. Reddy, and Suryanarayanarao Ramakumar. "Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (β/α)8-triosephosphate isomerase barrel enzyme." FEBS Journal 282, no. 18 (July 15, 2015): 3543–55. http://dx.doi.org/10.1111/febs.13355.

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Yadav, Malti, Kamalendu Pal, and Udayaditya Sen. "Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication." Biochemical Journal 476, no. 21 (November 15, 2019): 3333–53. http://dx.doi.org/10.1042/bcj20190399.

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Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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Dinis, Pedro, Daniel L. M. Suess, Stephen J. Fox, Jenny E. Harmer, Rebecca C. Driesener, Liliana De La Paz, James R. Swartz, Jonathan W. Essex, R. David Britt, and Peter L. Roach. "X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly." Proceedings of the National Academy of Sciences 112, no. 5 (January 20, 2015): 1362–67. http://dx.doi.org/10.1073/pnas.1417252112.

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Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN− ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR analysis of HydG. At one end of the HydG (βα)8 triosephosphate isomerase (TIM) barrel, a canonical [4Fe-4S] cluster binds SAM in close proximity to the proposed tyrosine binding site. At the opposite end of the active-site cavity, the structure reveals the auxiliary Fe-S cluster in two states: one monomer contains a [4Fe-5S] cluster, and the other monomer contains a [5Fe-5S] cluster consisting of a [4Fe-4S] cubane bridged by a μ2-sulfide ion to a mononuclear Fe2+ center. This fifth iron is held in place by a single highly conserved protein-derived ligand: histidine 265. EPR analysis confirms the presence of the [5Fe-5S] cluster, which on incubation with cyanide, undergoes loss of the labile iron to yield a [4Fe-4S] cluster. We hypothesize that the labile iron of the [5Fe-5S] cluster is the site of Fe(CO)x(CN)y synthon formation and that the limited bonding between this iron and HydG may facilitate transfer of the intact synthon to its cognate acceptor for subsequent H-cluster assembly.

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Shukla, Anshuman, and Purnananda Guptasarma. "Folding of β/α-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (β/α)8-barrel." Proteins: Structure, Function, and Bioinformatics 55, no. 3 (April 1, 2004): 548–57. http://dx.doi.org/10.1002/prot.20066.

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Saab-Rincón, Gloria, Leticia Olvera, Maricela Olvera, Enrique Rudiño-Piñera, Eleuterio Benites, Xavier Soberón, and Enrique Morett. "Evolutionary Walk between (β/α)8 Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase." Journal of Molecular Biology 416, no. 2 (February 2012): 255–70. http://dx.doi.org/10.1016/j.jmb.2011.12.042.

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NÁJERA, Hugo, Miguel COSTAS, and D. Alejandro FERNÁNDEZ-VELASCO. "Thermodynamic characterization of yeast triosephosphate isomerase refolding: insights into the interplay between function and stability as reasons for the oligomeric nature of the enzyme." Biochemical Journal 370, no. 3 (March 15, 2003): 785–92. http://dx.doi.org/10.1042/bj20021439.

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The reasons underlying the oligomeric nature of some proteins such as triosephosphate isomerase (TIM) are unclear. It has been proposed that this enzyme is an oligomer, mainly because of its stability rather than for functional reasons. To address this issue, the reversible denaturation and renaturation of the homodimeric TIM from baker's yeast (Saccharomyces cerevisiae) induced by guanidinium chloride and urea have been characterized by spectroscopic, functional and hydrodynamic techniques. The unfolding and refolding of this enzyme are not coincident after ‘conventional’ equilibrium times. Unfolding experiments did not reach equilibrium, owing to a very slow dissociation and/or unfolding process. By contrast, equilibrium was reached in the refolding direction. The simplest equilibrium pathway compatible with the obtained data was found to be a three-state process involving an inactive and expanded monomer. The Gibbs energy changes for monomer folding (ΔGfold0 = −16.6±0.7kJ·mol-1) and monomer association (ΔGassoc0 = −70.3±1.1kJ·mol-1) were calculated from data obtained in the two denaturants. From an analysis of the present data and data from the literature on the stability of TIM from different species and for other β/α barrels, and model simulations on the effect of stability in the catalytic activity of the enzyme, it is concluded that the low stability of the monomers is neither the only, nor the main, cause for the dimeric nature of TIM. There is interplay between function and stability.

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Matsui, Motomu, and Wataru Iwasaki. "Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction." Systematic Biology, August 17, 2019. http://dx.doi.org/10.1093/sysbio/syz049.

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Abstract A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.

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Borisenko, Ilya, Maria Daugavet, Alexander Ereskovsky, Andrey Lavrov, and Olga Podgornaya. "Novel protein from larval sponge cells, ilborin, is related to energy turnover and calcium binding and is conserved among marine invertebrates." Open Biology 12, no. 2 (February 2022). http://dx.doi.org/10.1098/rsob.210336.

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Sponges (phylum Porifera) are early-branching animals, whose outwardly simple body plan is underlain by a complex genetic repertoire. The transition from a mobile larva to an attached filter-feeding organism occurs by metamorphosis, a process accompanied by a radical change of the body plan and cell transdifferentiation. The continuity between larval cells and adult tissues is still obscure. In a previous study, we have produced polyclonal antibodies against the major protein of the flagellated cells covering the larva of the sponge Halisarca dujardini , used them to trace the fate of these cells and shown that the larval flagellated cells transdifferentiate into the choanocytes. In the present work, we identified the sequence of this novel protein, which we named ilborin. A search in the open databases showed that multiple orthologues of the newly identified protein are present in sponges, cnidarians, flatworms, ctenophores and echinoderms, but none of them has been described yet. Ilborin has two conserved domains: triosephosphate isomerase-barrel, which has enzymatic activity against macroergic compounds, and canonical EF-hand, which binds calcium. mRNA of ilborin is expressed in the larval flagellated cells. We suggest that the new protein is involved in the calcium-mediated regulation of energy metabolism, whose activation precedes metamorphosis.

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Journal articles on the topic 'Triosephosphate Isomerase Barrel'

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