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Conformational fluctuations in deoxy hemoglobin revealed as a major contributor to anionic modulation of function through studies of the oxygenation and oxidation of hemoglobins A0 and Deer Lodge beta2(NA2)His --> Arg.

Organisms rely on regulation at the molecular level, such as the allosteric regulation of hemoglobin (Hb) function by anions, to meet challenges presented by changing environmental and physiological conditions. A comparison of the effects of anions on oxygenation, oxidation, and sulfhydryl reactivity of Hb leads us to suggest that a large and significant part of the shift in oxygen affinity brought about by anion binding occurs as a result of increased conformational rigidity of the T state of deoxy Hb. As conformational rigidity increases, it becomes increasingly difficult for subunits in the deoxygenated T-state tetramer to assume higher oxygen affinity forms (T', T", T"'...) with less steric hindrance. The oxygen affinity reflects the average of the rapidly equilibrating conformations within the T state and is correspondingly decreased when anion levels are increased. The initial stage of the oxidation of Hb is relatively insensitive to steric alterations and thus reflects, primarily, the electronic aspects of the quaternary (T, T', T", T"'...) <--> equilibrium. We show that the reactivity of the sterically obscured sulfhydryl of beta93 Cys in deoxy Hb is much greater in chloride-free buffers than in buffers with added chloride. Anion-induced decreases in the extent and frequency of conformational fluctuations of subunits within the T-quaternary state thus reduce sulfhydryl reactivity as well as oxygen affinity. This parallel in anionic control of function allowed us to test, and disprove, the possibility that uncompensated positive charges in the central cavity of Hb Deer Lodge increase the frequency and extent of conformational fluctuations in its deoxy structure. This Hb variant exhibits increased anion sensitivity, increased oxygen affinity, and increased ease of oxidation, but without increased reactivity of its sulfhydryl groups, indicating that active-site alterations in deoxy Hb Deer Lodge are primarily electronic and not associated with increased conformational fluctuations within its T state. The restoration of normal properties in Hb Deer Lodge by addition of anions reinforces our conclusion that anionic control can be exerted through both steric and electronic alterations. The anionic control of fluctuations within the T state of Hb illustrates an important principle of macromolecular structure-function relationships: that functional regulation can be achieved by alterations in conformational rigidity.

Anions↗

Structural organization of the human eukaryotic initiation factor 5A precursor and its site-directed variant Lys50-->Arg.

The molecular properties of the human eukaryotic initiation factor 5A precursor and its site directed Lys50-->Arg variant have been investigated and compared. Structure perturbation methods were used to gain information about the protein architecture in solution. Intrinsic and extrinsic spectroscopic probes strategically located in the protein matrix detected the independent unfolding of two molecular regions. Three cysteines out of four were titrated in the native protein and the peculiar presence of a tyrosinate band at neutral pH was detected. At alkaline pH only two tyrosines out of three were titratable in the native protein, with an apparent pK of about 9.9. Native protein and its Lys50-->Arg variant reacted in a similar fashion to guanidine and to pH variation, but differently to thermal stress. The complex thermal unfolding of both proteins indicated the presence of intermediates. Spectroscopic data showed that these intermediates are differently structured. Consequently, the two proteins seem to have different unfolding pathways.

Amino Acid Substitution↗

An intact Raf zinc finger is required for optimal binding to processed Ras and for ras-dependent Raf activation in situ.

The function of the c-Raf-1 zinc finger domain in the activation of the Raf kinase was examined by the creation of variant zinc finger structures. Mutation of Raf Cys 165 and Cys 168 to Ser strongly inhibits the Ras-dependent activation of c-Raf-1 by epidermal growth factor (EGF). Deletion of the Raf zinc finger and replacement with a homologous zinc finger from protein kinase C gamma (PKC gamma) (to give gamma/Raf) also abrogates EGF-induced activation but enables a vigorous phorbol myristate acetate (PMA)-induced activation. PMA activation of gamma/Raf does not require endogenous Ras or PKCs and probably occurs through a PMA-induced recruitment of gamma/Raf to the plasma membrane. The impaired ability of EGF to activate the Raf zinc finger variants in situ is attributable, at least in part, to a major decrement in their binding to Ras-GTP; both Raf zinc finger variants exhibit decreased association with Ras (V12) in situ upon coexpression in COS cells, as well as diminished binding in vitro to immobilized, processed COS recombinant Ras(V12)-GTP. In contrast, Raf binding to unprocessed COS or prokaryotic recombinant Ras-GTP is unaffected by Raf zinc finger mutation. Thus, the Raf zinc finger contributes an important component to the overall binding to Ras-GTP in situ, through an interaction between the zinc finger and an epitope on Ras, distinct from the effector loop, that is present only on prenylated Ras.

Amino Acid Sequence↗

Structural and biochemical features distinguish the foot-and-mouth disease virus leader proteinase from other papain-like enzymes.

The structures of the two leader protease (Lpro) variants of foot-and-mouth disease virus known to date were solved using crystals in which molecules were organized as molecular fibers. Such crystals diffract to a resolution of only approximately 3 A. This singular, pseudo-polymeric organization is present in a new Lpro crystal form showing a cubic packing. As molecular fiber formation appeared unrelated to crystallization conditions, we mutated the reactive cysteine 133 residue, which makes a disulfide bridge between adjacent monomers in the fibers, to serine. None of the intermolecular contacts found in the molecular fibers was present in crystals of this variant. Analysis of this Lpro structure, refined at 1.9 A resolution, enables a detailed definition of the active center of the enzyme, including the solvent organization. Assay of Lpro activity on a fluorescent hexapeptide substrate showed that Lpro, in contrast to papain, was highly sensitive to increases in the cation concentration and was active only across a narrow pH range. Examination of the Lpro structure revealed that three aspartate residues near the active site, not present in papain-like enzymes, are probably responsible for these properties.

Amino Acid Substitution↗

Crystal structure of wild-type chaperonin GroEL.

The 2.9A resolution crystal structure of apo wild-type GroEL was determined for the first time and represents the reference structure, facilitating the study of structural and functional differences observed in GroEL variants. Until now the crystal structure of the mutant Arg13Gly, Ala126Val GroEL was used for this purpose. We show that, due to the mutations as well as to the presence of a crystallographic symmetry, the ring-ring interface was inaccurately described. Analysis of the present structure allowed the definition of structural elements at this interface, essential for understanding the inter-ring allosteric signal transmission. We also show unambiguously that there is no ATP-induced 102 degrees rotation of the apical domain helix I around its helical axis, as previously assumed in the crystal structure of the (GroEL-KMgATP)(14) complex, and analyze the apical domain movements. These results enabled us to compare our structure with other GroEL crystal structures already published, allowing us to suggest a new route through which the allosteric signal for negative cooperativity propagates within the molecule. The proposed mechanism, supported by known mutagenesis data, underlines the importance of the switching of salt bridges.

Adenosine Triphosphate↗

Lanthanoid Rhenium Aluminides with a High Content of Aluminum: LnRe(2)Al(10) (Ln = Ho-Lu) with a New Structure Type and NdRe(2)Al(10) with CaCr(2)Al(10)-Type Structure.

The title compounds were obtained by reaction of the elemental components with an excess of aluminum after dissolving the matrix in hydrochloric acid. The compounds LnRe(2)Al(10) (Ln = Ho-Lu) crystallize with a new structure type, which was determined from single-crystal X-ray data of LuRe(2)Al(10): Cmcm, a = 929.1(1) pm, b = 1027.7(2) pm, c = 2684.1(5) pm, Z = 12. The two different lutetium atoms of the structure are coordinated by four rhenium and 16 aluminum atoms, while the two rhenium positions are in distorted icosahedral coordination of two lutetium and 10 aluminum atoms. The 12 different aluminum atoms have between 12 and 14 neighbors, of which two are rhenium and one or two are lutetium atoms. The structure may be considered as a stacking variant of the recently determined structure of YbFe(2)Al(10). Both structures are related to that of ThMn(12). They contain hexagonally close-packed, puckered sheets similar to those known from the close-packed TiAl(3)-type structure. In LuRe(2)Al(10) and YbFe(2)Al(10) these sheets of the compositions Re(2)Al(6) and Fe(2)Al(6), respectively, alternate with less densely packed layers of the composition LnAl(4). The crystal structures of YbRe(2)Al(10) (LuRe(2)Al(10) type, a = 930.7(2) pm, b = 1029.3(2) pm, c = 2687.9(5) pm) and NdRe(2)Al(10) (CaCr(2)Al(10) type, a = 1293.7(1) pm, c = 517.4(1) pm) were also refined from single-crystal X-ray data. The refinements of the occupancy factors of these as well as those of 20 other intermetallic compounds with high aluminum content indicate a seemingly slightly lower (on average 2-3%) scattering power for the aluminum positions in all cases. This is ascribed to the differing electron distributions in the free and in the bonded aluminum atoms. The cell volume of YbRe(2)Al(10) indicates a mixed or intermediate +II/+III valence of the ytterbium atoms.

Journal Article↗

Familial mutations and the thermodynamic stability of the recombinant human prion protein.

Hereditary forms of human prion disease are linked to specific mutations in the PRNP gene. It has been postulated that these mutations may facilitate the pathogenic process by reducing the stability of the prion protein (PrP). To test this hypothesis, we characterized the recombinant variants of human PrP(90-231) containing point mutations corresponding to Gerstmann-Straussler-Scheinker disease (P102L), Creutzfeld-Jakob disease (E200K), and fatal familial insomnia (M129/D178N). The first two of these mutants could be recovered form from the periplasmic space of Escherichia coli in a soluble form, whereas the D178N variant aggregated into inclusion bodies. The secondary structure of the two soluble variants was essentially identical to that of the wild-type protein. The thermodynamic stability of these mutants was assessed by unfolding in guanidine hydrochloride and thermal denaturation. The stability properties of the P102L variant were indistinguishable from those of wild-type PrP, whereas the E200K mutation resulted in a very small destabilization of the protein. These data, together with the predictive analysis of other familial mutations, indicate that some hereditary forms of prion disease cannot be rationalized using the concept of mutation-induced thermodynamic destabilization of the cellular prion protein.

Creutzfeldt-Jakob Syndrome↗

Structure of very early protein folding intermediates: new insights through a variant of hydrogen exchange labelling.

BACKGROUND: Hydrogen exchange labelling has been a key method in characterizing the structure of transient folding intermediates. In studies of several proteins, however, there has been clear spectroscopic evidence for partial folding of some kind at very early times, before any protection from exchange was measurable. These results, presumably a consequence of limited stability of specific backbone interactions, have made it difficult to assess the extent of native-like folding in the very early intermediates. We have used a variant of the labelling method to investigate marginally stable structures formed within the first few milliseconds of refolding of two such proteins, hen lysozyme and ubiquitin. RESULTS: In lysozyme, population of a subset of native-like secondary structures on this timescale is revealed, thus reconciling the exchange behaviour with circular dichroism measurements and confirming the significance of the rapidly formed embryonic structure as a foundation for the subsequent folding pathway. In the case of ubiquitin, by contrast, no significantly protective structure was detectable, suggesting that here secondary structural elements can be populated only marginally ahead of the major cooperative folding event; this was also supported by stopped-flow circular dichroism measurements. CONCLUSIONS: The hydrogen exchange approach can be extended to probe the formation of native-like structure formed in very early folding intermediates, even when the stability of specific interactions is marginal. In the case of lysozyme, this has provided a new window on an early stage of organization of the alpha-helical domain.

Animals↗

Histidine-rich domain of the knob protein of the human malaria parasite Plasmodium falciparum.

Membranes of erythrocytes infected with the human malaria parasite Plasmodium falciparum develop protrusions called knobs. These structures are essential for the survival of the parasite in the host, and their induction requires the synthesis of the knob protein by the parasite. We describe the isolation of a cDNA clone encoding the amino-terminal half of the knob protein. A cDNA library was constructed from RNA prepared from ring stages of a P. falciparum isolate that has retained its ability to induce knobs (knob+ phenotype). A synthetic oligonucleotide probe encoding polyhistidine was used to isolate the cDNA clone, which encodes the amino-terminal half of a polypeptide with all the known attributes of the knob protein. The gene is not transcribed in variants that do not synthesize the knob protein and thereby cannot induce knobs (knob- phenotype). The apparent lack of transcription in knob- variants is due to different mechanisms: although the gene is present in one knob- isolate, it has been deleted in a cloned knob- variant. The primary structure of the polypeptide deduced from a partial sequence of the cDNA is distinctly different from other malarial histidine-rich polypeptides. The amino-terminal sequence shows the characteristic features of a signal peptide. This is followed by a histidine-rich domain and a subsequent region which contains one histidine. Peptide map analysis of the knob protein is consistent with the structural features deduced from the sequence analysis of the cDNA.

Amino Acid Sequence↗

Isolation and characterization of a trisulfide variant of recombinant human growth hormone formed during expression in Escherichia coli.

A new variant of human growth hormone was recently found [Pavlu, B. & Gellerfors, P. (1993) Bioseparation 3, 257-265]. We report here the identification and the structural determination of this variant. The variant, which is formed during the expression of human growth hormone in Escherichia coli, was found to be more hydrophobic than rhGH as judged by its prolonged elution time by hydrophobic interaction chromatography. The rhGH hydrophobic variant (rhGH-HV) was isolated and subjected to trypsin digestion and RP-HPLC analysis, resulting in an altered retention time of one single tryptic peptide as compared to the corresponding fragment of rhGH. This tryptic peptide constitutes the C-terminus (aa 179-191) of hGH and contains one of the two disulfide bridges in hGH, viz. Cys182-Cys189. Amino acid sequences and composition analyses of the tryptic peptide from rhGH-HV (Tv18-19) and the corresponding tryptic peptide from rhGH (T18+19) were identical. Electrospray mass spectrometry (ES MS) of Tv18+19 isolated from rhGH-HV revealed a monoisotopic mass increase of 32.7, as compared to T18+19 from rhGH. A synthetic Tv18+19 peptide having a trisulfide bridge between Cys182 and Cys189 showed identical fragment in ES/MS compared to Tv18+19 isolated from rhGH-HV, i.e. m/z 617.7 and 682.9. These fragments are formed through a unique cleavage in the trisulfide (Cys182-SSS-Cys189) bridge not found in the corresponding T18+19 disulfide peptide. Furthermore, the synthetic Tv18+19 co-eluted in RP-HPLC with Tv18+19 isolated from rhGH-HV. Two-dimensional NMR spectroscopy of the synthetic T18+19 and Tv18+19 peptides were performed. Using these data all protons were assigned. The major chemical shift changes (delta delta > 0.05 ppm) observed were for the beta-protons of Cys182 and Cys189 in Tv18+19 as compared to T18+19. CD spectroscopy data were also in agreement with the above results. Based on these physico-chemical data rhGH-HV has been structurally defined as a trisulfide variant of rhGH. The receptor binding properties of rhGH-HV was studied by a biosensor device, BIAcore. The binding capacity of rhGH-HV was similar to rhGH with a binding stoichiometry to the rhGHBP of 1:1.6 and 1:1.5, respectively, indicating that the trisulfide modification did not affect its receptor binding properties.

Amino Acid Sequence↗

Identification of N-linked oligosaccharides of rat insulin-like growth factor binding protein-4.

Insulin-like growth factor binding protein-4 (IGFBP-4) is, like the other five IGFBPs, a critical regulator of the activity of insulin-like growth factor (IGF)-I and IGF-II. Whereas IGFBP-1 and IGFBP-2 are not glycosylated, IGFBP-3 and IGFBP-4 are N-glycosylated and IGFBP-5 and IGFBP-6 are O-glycosylated. In this study we identified the glycosylation of IGFBP-4 using a nanoflow LC/MS/MS techniques. Although N-linked oligosaccharides are structurally diverse, their variants are well reported in the literature. Based on the molecular weight of the possible oligosaccharide moieties, we identified five different glycosylation isoforms of the protein. Identified glycans were biantennary and differ in the number of sialic acid terminal residues and/or core modification with fucose.

Amino Acid Sequence↗

Comparison of three different recombinant hepatitis B virus core particles expressed in Escherichia coli.

The properties of three different recombinant hepatitis B virus core proteins expressed in Escherichia coli were compared: an N-terminal fusion protein, a C-terminally truncated protein and a sequence-authentic protein. All three proteins assembled into capsid-like particles with typical HBc-antigenicity, sedimentation behavior and distinctive electron microscopical images. Apart from this, however, variant HBc proteins displayed properties different from sequence-authentic HBc protein p21.4. Unlike p21.4, the particles of the N-terminal fusion protein p22.2 were sensitive to proteolytic attack by trypsin at variable sites within its arginine-rich C-terminus but not in its extended N-terminus. We therefore conclude that the C-terminal region is located on the surface of the p22.2 particle. These particles also showed increased HBe-antigenicity, as did the C-terminally truncated core particles p17.6, and to an even greater extent p18* particles which were derived from p22.2 by tryptic digestion. This might be interpreted as evidence for an--albeit minor--structural change. All variant core particles were less stable and contained less RNA. Electron microscopic indication for DNA binding of C-terminal deleted p17.6 particles was obtained using an aqueous spreading technique.

Amino Acid Sequence↗

[The principles of data formalization for building the genetic-morphological model of shoot development in flowering plants].

Shoot system of a plant can be divided into elementary molecules composed of phyllome, internode, and meristem of the lateral bud. The capacity of plants for open growth is manifested as multiple reproductions of the modules. These main principles of plant structural organization can be used to formalize and integrate the data from various disciplines studying the shoot development--genetics of development, morphology, etc. At the example of model species Arabidopsis thaliana we show that the data on genetic control of shoot development can be considered in terms of individual modules reorganization. Several variants of the modules structural reorganization are allowed: reduction or transformation of phyllome, change in the internode length, and triggering active/inactive status of the lateral shoot meristem. Each variant of the module structure corresponds to specific pattern of genes activity. Such integration of the data on genetic and structural aspects of morphogenesis can form a basis for mathematical modeling of plant development.

Arabidopsis↗

Genetic effects on chromatin accessibility reveal the molecular mechanisms of complex traits in maize.

Cis-regulatory elements (CREs) are critical for modulating gene expression and phenotypic diversity in maize. While genome-wide association study (GWAS) hits and expression quantitative trait loci (eQTLs) are often enriched in CREs, their molecular mechanisms remain poorly understood. Characterizing CREs within accessible chromatin regions (ACRs) offers a powerful approach to link noncoding variants to chromatin structure alterations and phenotypic variation. Here, we generated ATAC-seq profiles from seedling leaves of 214 maize inbred lines, identifying 82&#x2009;174 consensus ACRs. Notably, 39.55% of these ACRs exhibited significant population-wide chromatin accessibility variation. By mapping chromatin accessibility quantitative trait loci (caQTLs), we discovered 27&#x2009;004 loci, including 1398 predicted to disrupt transcription factor (TF)-binding sites. Integration with multi-omics data revealed 7405 caACR-target gene pairs and linked 56 caACRs to GWAS signals for 51 agronomic traits, with significant enrichment in flowering-related pathways. Functional candidates such as ZmZIM30 - putatively regulated by caACRs - emerged as key regulators of flowering time. At the fad7 locus associated with linolenic acid content, allelic variants overlapping a caQTL showed differential chromatin accessibility. Our study provides a high-resolution cis-elements of maize leaves, deciphers the genetic basis of chromatin accessibility variation, and bridges noncoding caQTLs to molecular mechanisms underlying GWAS hits.

Zea mays↗

Multiple molecular determinants for allosteric modulation of alternatively spliced AMPA receptors.

Positive allosteric regulation of glutamate AMPA receptors involves conformational changes that can attenuate receptor desensitization and enhance ion flux through the channel pore. Many allosteric modulators (e.g., cyclothiazide and aniracetam) preferentially affect the flip (i) or flop (o) alternatively spliced isoform of AMPA receptors, implicating residues in the flip-flop domain as critical determinants of splice variant sensitivity. Indeed, previous mutational analyses have demonstrated that the differential sensitivity to cyclothiazide and aniracetam depends on a single amino acid, Ser (flip) and Asn (flop), suggesting that this residue may be solely responsible for differences in modulation of AMPA receptor isoforms. The present studies tested this hypothesis by investigating the molecular determinants of modulation of AMPA receptor splice variants by a structurally distinct compound, LY404187, which displays strikingly different and opposing kinetics of allosteric regulation characterized by a time-dependent enhancement in potentiation of homomeric GluR1-GluR4i and a time-dependent reduction in potentiation of GluR1-GluR4o. Site-directed mutagenesis of residues in the flip-flop domain of GluR2 revealed that, although exchange of Asn775 for Ser in GluR2o was sufficient to confer the GluR2i phenotype of potentiation, the corresponding mutation, Ser775Asn, in GluR2i did not impart the GluR2o response. In fact, the GluR2o kinetics of modulation depended on a novel set of substitutions in GluR2i, including Thr765Asn, Pro766Ala, and Val779Leu in combination with Ser775Asn. Collectively, these results show that, unlike cyclothiazide and aniracetam, the residues that confer splice variant differences in modulation by LY404187 are not identical and indicate that allosteric regulation of AMPA receptors can arise from multiple molecular determinants.

Allosteric Regulation↗

Molybdenum chalcogenobenzimidato complexes: radical synthesis and nitrile extrusion via beta-EPh (E = S, Se, and Te) elimination.

Molybdenum chalcogenobenzimidates of formula (Ph[PhE]C=N)Mo(N[t-Bu]Ar)(3) (Ar = 3,5-C(6)H(3)Me(2)) have been obtained by treatment of Mo(N[t-Bu]Ar)(3) sequentially with benzonitrile and 0.5 equiv of PhEEPh (E = S, Se, and Te). Molecular structure determinations have been carried out for the S and Se variants. The Te variant extrudes PhCN forming structurally characterized (PhTe)Mo(N[t-Bu]Ar)(3) with facility assessed via stopped-flow kinetic measurements, while the Se and S analogues exhibit increasing stability. Quantum chemical calculations and solution calorimetry have been employed as an aid to interpretation of the PhCN extrusion reaction.

Journal Article↗

Phase stability in the systems AeAl(2-x)Mgx (Ae = Ca, Sr, Ba): electron concentration and size controlled variations on the laves phase structural theme.

The systems AeAl(2-x)Mgx (Ae = Ca, Sr, Ba) display electron concentration induced Laves phase structural changes. However, the complete sequence MgCu2 --> MgNi2 --> MgZn2 with increasing x (decreasing electron count) is only observed for Ae = Ca. Compounds SrAl(2-x)Mgx (0 < x < or = 2) and BaAl(2-x)Mgx (x = 0.85 and 2.0) were synthesized and structurally characterized by X-ray diffraction experiments. For the Sr system the structural sequence CeCu2 --> MgNi2 --> MgZn2 occurs with increasing Mg content x. Thus, larger Sr does not allow the realization of the MgCu2 structure at low x. For Ae = Ba a binary compound BaAl2 does not exist, but more Ba-rich Ba7Al13 forms. The reinvestigation of the crystal structure of Ba7Al13 by selected area and convergent beam electron diffraction in a transmission electron microscope revealed a superstructure, which subsequently could be refined from single X-ray diffraction data. The formula unit of the superstructure is Ba21Al40 (space group P31m, Z = 1, a = 10.568(1) angstroms, c = 17.205(6) angstroms). In Ba21Al40 a size match problem between Ba and Al present in Ba7Al13 is resolved. The structure of Ba7Al13 (Ba21Al40) can be considered as a Ba excess variant of the hexagonal MgNi2 Laves phase type structure. An incommensurately modulated variant of the MgNi2 structure is obtained for phases BaAl(2-x)Mgx with x = 0.8-1. At even higher Mg concentrations a structural change to the proper MgZn2 type structure takes place.

Journal Article↗

[Impact of the heterogenicity of amino acid sequence on the immunoreactivity of an antigenic epitopic complex localized within amino acids 1192-1456 of protein NS3 protein of hepatitis C virus].

Recombinant proteins were used to study the effect of heterogenicity of the primary structure of NS3 protein of hepatitis C (HCV) on the immunoreactivity of a complex of antigenic epitopes located within the amino acid sequences 1192-1456. Six genes encoding for the above fragment NS3 from different genotypes were collected from synthetic oligonucleotides and expressed in E. coli cells, by using the polymerase chain reaction. The homology of amino acid sequences of antigens ranged from 78.4 to 92.2%. All the antigens showed a higher coefficient of their reactivity with antibodies in the sera samples from patients infected by HCV of a respective genotype; however, there was no strong genotype-specific immunoreactivity. The findings lead to the conclusion that the primary structure of antigens has an impact on their immunoreactivity. Selection of variants of the primary structures of antigens is essential in developing a diagnostic test.

Antibody Specificity↗

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