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Garcés JL, Madurga S, Rey-Castro C, Mas F. Dealing with long-range interactions in the determination of polyelectrolyte ionization properties. Extension of the transfer matrix formalism to the full range of ionic strengths. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/polb.24269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Josep L. Garcés
- Chemistry Department; Technical School of Agricultural Engineering & AGROTECNIO of Lleida University (UdL); Lleida Catalonia Spain
| | - Sergio Madurga
- Physical Chemistry Unit; Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB); Barcelona Catalonia Spain
| | - Carlos Rey-Castro
- Chemistry Department; Technical School of Agricultural Engineering & AGROTECNIO of Lleida University (UdL); Lleida Catalonia Spain
| | - Francesc Mas
- Physical Chemistry Unit; Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB) of Barcelona University (UB); Barcelona Catalonia Spain
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Garcés JL, Madurga S, Borkovec M. Coupling of conformational and ionization equilibria in linear poly(ethylenimine): a study based on the site binding/rotational isomeric state (SBRIS) model. Phys Chem Chem Phys 2014; 16:4626-38. [DOI: 10.1039/c3cp54211d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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3
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Adhikari U, Scheiner S. Magnitude and Mechanism of Charge Enhancement of CH··O Hydrogen Bonds. J Phys Chem A 2013; 117:10551-62. [DOI: 10.1021/jp4081788] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Upendra Adhikari
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Steve Scheiner
- Department
of Chemistry and
Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
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13C longitudinal relaxation time measurements and DFT-GIAO NMR computations for two ammonium ions of a tetraazamacrocyclic scorpiand system. J INCL PHENOM MACRO 2013; 78:299-310. [PMID: 24431982 PMCID: PMC3887262 DOI: 10.1007/s10847-013-0298-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 02/13/2013] [Indexed: 11/19/2022]
Abstract
Abstract Spin–lattice relaxation times, T1s, for 13C nuclei in two cations Hn1n+ (n = 1, 5) of N-(2-aminoethyl)-cyclam (1, scorpiand) were determined by means of 13C{1H} NMR experiments in aqueous solution at pH 11.5 and 0.2. The theoretical study [modeling with OPLS-AA, B3LYP/6-31G(d) geometry optimizations, dispersion-corrected energies (DFT-D3), and DFT-GIAO predictions of the NMR chemical shifts (including an IEF-PCM simulation of hydration)] was also done for several conformers of the tautomer iso-H414+ not investigated before. The binding directions in protonated polyamino receptors necessary for efficient complexation of the nitrate anion(s) were briefly outlined, as well. All these results were discussed in terms of ‘abnormal’ 13C chemical shift changes found previously for the side-chain carbons of amine 1 in strongly acidic solution (HNO3). In conclusion, an earlier proposal of its association with NO3− at pH <1 was rejected. Instead, the participation of small amounts of a micro-species iso-H414+Dhydr under such conditions can be proposed. Graphical Abstract A small contribution of iso-H414+Dhydr (see figure) to an ionic mixture of pentamine 1 was proposed to explain the ‘abnormal’ 13C NMR shifts observed for atoms C11 and C12 in its side-chain arm, at pH <1.![]() Electronic supplementary material The online version of this article (doi:10.1007/s10847-013-0298-x) contains supplementary material, which is available to authorized users.
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Phosphatidylinositol-4,5-bisphosphate ionization and domain formation in the presence of lipids with hydrogen bond donor capabilities. Chem Phys Lipids 2012; 165:696-704. [DOI: 10.1016/j.chemphyslip.2012.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 07/06/2012] [Accepted: 07/07/2012] [Indexed: 01/29/2023]
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6
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Tsuzuki S, Uchimaru T, Mikami M. Magnitude of CH/O interactions between carbohydrate and water. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1192-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Kooijman EE, King KE, Gangoda M, Gericke A. Ionization Properties of Phosphatidylinositol Polyphosphates in Mixed Model Membranes. Biochemistry 2009; 48:9360-71. [DOI: 10.1021/bi9008616] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Kuad P, Schurhammer R, Maechling C, Antheaume C, Mioskowski C, Wipff G, Spiess B. Complexation of Cs+, K+ and Na+ by norbadione A triggered by the release of a strong hydrogen bond : nature and stability of the complexes. Phys Chem Chem Phys 2009; 11:10299-310. [DOI: 10.1039/b912518c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Design and synthesis of 4″,6″-unsaturated cyclic ADP-carbocyclic-ribose, a Ca2+-mobilizing agent selectively active in T cells. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.07.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Mills SJ, Dozol H, Vandeput F, Backers K, Woodman T, Erneux C, Spiess B, Potter BVL. 3-Hydroxybenzene 1,2,4-Trisphosphate, a Novel Second Messenger Mimic and unusual Substrate for Type-I myo-Inositol 1,4,5-Trisphosphate 5-Phosphatase: Synthesis and Physicochemistry. Chembiochem 2006; 7:1696-706. [PMID: 16964627 DOI: 10.1002/cbic.200600125] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
3-Hydroxybenzene 1,2,4-trisphosphate 4 is a new myo-inositol 1,4,5-trisphosphate analogue based on the core structure of benzene 1,2,4-trisphosphate 2 with an additional hydroxyl group at position-3, and is the first noninositol based compound to be a substrate for inositol 1,4,5-trisphosphate 5-phosphatase. In physicochemical studies on 2, when three equivalents of protons were added, the (31)P NMR spectrum displayed monophasic behaviour in which phosphate-1 and phosphate-2 behaved independently in most of the studied pH range. For compound 4, phosphate-2 and phosphate-4 interacted with the 3-OH group, which does not titrate at physiological pH, displaying complex biphasic behaviour which demonstrated co-operativity between these groups. Phosphate-1 and phosphate-2 strongly interacted with each other and phosphate-4 experienced repulsion because of the interaction of the 3-OH group. Benzene 1,2,4-trisphosphate 2 is resistant to inositol 1,4,5-trisphosphate type I 5-phosphatase catalysed dephosphorylation. However, surprisingly, 3-hydroxybenzene 1,2,4-trisphosphate 4 was dephosphorylated by this 5-phosphatase to give the symmetrical 2,3-dihydroxybenzene 1,4-bisphosphate 16. The extra hydroxyl group is shown to form a hydrogen bond with the vicinal phosphate groups at -15 degrees C, and (1)H NMR titration of the ring and hydroxyl protons in 4 shows the OH proton to be strongly stabilized as soon as the phosphate groups are deprotonated. The effect of the phenolic 3-OH group in compound 4 confirms a critical role for the 6-OH group of the natural messenger in the dephosphorylation mechanism that persists even in radically modified analogues.
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Affiliation(s)
- Stephen J Mills
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
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Riley AM, Trusselle M, Kuad P, Borkovec M, Cho J, Choi JH, Qian X, Shears SB, Spiess B, Potter* BVL. scyllo-inositol pentakisphosphate as an analogue of myo-inositol 1,3,4,5,6-pentakisphosphate: chemical synthesis, physicochemistry and biological applications. Chembiochem 2006; 7:1114-22. [PMID: 16755629 PMCID: PMC1892220 DOI: 10.1002/cbic.200600037] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Indexed: 01/08/2023]
Abstract
myo-Inositol 1,3,4,5,6-pentakisphosphate (Ins(1,3,4,5,6)P(5)), an inositol polyphosphate of emerging significance in cellular signalling, and its C-2 epimer scyllo-inositol pentakisphosphate (scyllo-InsP(5)) were synthesised from the same myo-inositol-based precursor. Potentiometric and NMR titrations show that both pentakisphosphates undergo a conformational ring-flip at higher pH, beginning at pH 8 for scyllo-InsP(5) and pH 9 for Ins(1,3,4,5,6)P(5). Over the physiological pH range, however, the conformation of the inositol rings and the microprotonation patterns of the phosphate groups in Ins(1,3,4,5,6)P(5) and scyllo-InsP(5) are similar. Thus, scyllo-InsP(5) should be a useful tool for identifying biologically relevant actions of Ins(1,3,4,5,6)P(5), mediated by specific binding sites, and distinguishing them from nonspecific electrostatic effects. We also demonstrate that, although scyllo-InsP(5) and Ins(1,3,4,5,6)P(5) are both hydrolysed by multiple inositol polyphosphate phosphatase (MINPP), scyllo-InsP(5) is not dephosphorylated by PTEN or phosphorylated by Ins(1,3,4,5,6)P(5) 2-kinases. This finding both reinforces the value of scyllo-InsP(5) as a biological control and shows that the axial 2-OH group of Ins(1,3,4,5,6)P(5) plays a part in substrate recognition by PTEN and the Ins(1,3,4,5,6)P(5) 2-kinases.
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Affiliation(s)
- Andrew M. Riley
- Dr. A. M. Riley, Dr. M. Trusselle, Prof. Dr. B. V. L. Potter, Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY (UK), Fax: (+44) 1225-386114, E-mail:
| | - Melanie Trusselle
- Dr. A. M. Riley, Dr. M. Trusselle, Prof. Dr. B. V. L. Potter, Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY (UK), Fax: (+44) 1225-386114, E-mail:
| | - Paul Kuad
- Dr. P. Kuad, Prof. Dr. B. Spiess, Département de Pharmacochimie de la Communication Cellulaire, UMR 7175-LC1 du CNRS-ULP, Faculté de Pharmacie, 74, route du Rhin, B. P. 24, 67401 Illkirch Cedex (France.)
| | - Michal Borkovec
- Dr. M. Borkovec, Department of Inorganic, Analytical, and Applied Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4 (Switzerland)
| | - Jaiesoon Cho
- Dr. J. Cho, Dr. J. H. Choi, Dr. X. Qian, Dr. S. B. Shears, Inositide Signaling Group, Laboratory of Signal Transduction and National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (USA)
| | - Jae H. Choi
- Dr. J. Cho, Dr. J. H. Choi, Dr. X. Qian, Dr. S. B. Shears, Inositide Signaling Group, Laboratory of Signal Transduction and National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (USA)
| | - Xun Qian
- Dr. J. Cho, Dr. J. H. Choi, Dr. X. Qian, Dr. S. B. Shears, Inositide Signaling Group, Laboratory of Signal Transduction and National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (USA)
| | - Stephen B. Shears
- Dr. J. Cho, Dr. J. H. Choi, Dr. X. Qian, Dr. S. B. Shears, Inositide Signaling Group, Laboratory of Signal Transduction and National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709 (USA)
| | - Bernard Spiess
- Dr. P. Kuad, Prof. Dr. B. Spiess, Département de Pharmacochimie de la Communication Cellulaire, UMR 7175-LC1 du CNRS-ULP, Faculté de Pharmacie, 74, route du Rhin, B. P. 24, 67401 Illkirch Cedex (France.)
| | - Barry V. L. Potter*
- Dr. A. M. Riley, Dr. M. Trusselle, Prof. Dr. B. V. L. Potter, Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY (UK), Fax: (+44) 1225-386114, E-mail:
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Garcés JL, Koper GJM, Borkovec M. Ionization Equilibria and Conformational Transitions in Polyprotic Molecules and Polyelectrolytes. J Phys Chem B 2006; 110:10937-50. [PMID: 16771347 DOI: 10.1021/jp060684i] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The coupling between proton binding and conformational degrees of freedom in polyprotic molecules and polyelectrolytes is studied theoretically. Our approach combines the classical rotational isomeric state (RIS) model developed by Flory and the site binding (SB) model used to treat proton binding equilibria. The properties of the resulting SBRIS model, which treats conformational degrees of freedom and proton binding on equal footing, are studied with statistical mechanical techniques. Quantities of interest, such as titration curves, conformational probabilities, or macroscopic binding constants, are expressed as thermal averages and are evaluated by direct enumeration of states or by transfer matrix techniques. We further demonstrate that in the SBRIS model conformational degrees of freedom can be averaged out, leading to the contracted description within the SB model. In most cases, this contraction leads to higher order interactions, which may not be present at the SBRIS level (e.g., triplet interactions). Several examples are discussed to illustrate the concepts developed. The case of succinic acid exemplifies the situation in its simplest form. The model can further rationalize the very different titration behavior of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA). In particular, the characteristic "jump" in the titration curve of PMAA is described quantitatively and is interpreted in terms of a conformational transition.
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Affiliation(s)
- José L Garcés
- Center of Theoretical Chemistry and Department of Physical Chemistry, Barcelona University, Martí i Franqués, 1, E-08028 Barcelona, Catalonia, Spain
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Klingen AR, Bombarda E, Ullmann GM. Theoretical investigation of the behavior of titratable groups in proteins. Photochem Photobiol Sci 2006; 5:588-96. [PMID: 16761087 DOI: 10.1039/b515479k] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper presents a theoretical analysis of the titration behavior of strongly interacting titratable residues in proteins. Strongly interacting titratable residues exist in many proteins such as for instance bacteriorhodopsin, cytochrome c oxidase, cytochrome bc(1), or the photosynthetic reaction center. Strong interaction between titratable groups can lead to irregular titration behavior. We analyze under which circumstances titration curves can become irregular. We demonstrate that conformational flexibility alone can not lead to irregular titration behavior. Strong interaction between titratable groups is a necessary, but not sufficient condition for irregular titration curves. In addition, the two interacting groups also need to titrate in the same pH-range. These two conditions together lead to irregular titration curves. The mutation of a single residue within a cluster of interacting titratable residues can influence the titration behavior of the other titratable residues in the cluster. We demonstrate this effect on a cluster of four interacting residues. This example underlines that mutational studies directed at identifying the role of a certain titratable residue in a cluster of interacting residues should always be accompanied by an analysis of the effect of the mutation on the titration behavior of the other residues.
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Affiliation(s)
- Astrid R Klingen
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, D-95447 Bayreuth, Germany
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Kuad P, Borkovec M, Desage-El Murr M, Le Gall T, Mioskowski C, Spiess B. Inframolecular Protonation Process of Norbadione A: Influence of the Ionic Environment and Stereochemical Consequences. J Am Chem Soc 2005; 127:1323-33. [PMID: 15669874 DOI: 10.1021/ja0483185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microscopic protonation mechanism, at an inframolecular level, of norbadione A, a pigment extracted from mushrooms and known to complex cesium cations, was determined by using 1H NMR titrations and the cluster expansion method. This study revealed a pH dependent Z to E isomer switch that occurs in both pulvinic moieties. As a consequence, norbadione A can exist in solution in four stereomeric forms (E-E, E-Z, Z-E, and Z-Z), which can be of interest in the development of molecular-level devices. In the presence of 0.15 M NaCl, the calculated microconstants showed an unusual apparent cooperativity between the enol groups, which results from the release of the sodium cations upon protonation of norbadione A.
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Affiliation(s)
- Paul Kuad
- Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR 7081 du CNRS, Université Louis Pasteur, Faculté de Pharmacie, 74, route du Rhin, 67401 Illkirch Cedex, France
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Horne G, Maechling C, Fleig A, Hirata M, Penner R, Spiess B, Potter BVL. d-6-Deoxy-myo-inositol 1,3,4,5-tetrakisphosphate, a mimic of d-myo-inositol 1,3,4,5-tetrakisphosphate: biological activity and pH-dependent conformational properties. Biochem Biophys Res Commun 2004; 320:1262-70. [PMID: 15249226 DOI: 10.1016/j.bbrc.2004.06.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Indexed: 10/26/2022]
Abstract
D-6-Deoxy-myo-inositol 1,3,4,5-tetrakisphosphate [D-6-deoxy-Ins(1,3,4,5)P(4)] 3 is a novel deoxygenated analogue of D-myo-inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P(4)] 2, a central and enigmatic molecule in the polyphosphoinositide pathway of cellular signalling. D-6-Deoxy-Ins(1,3,4,5)P(4) is a moderate inhibitor of Ins(1,4,5)P(3) 5-phosphatase [1.8microM] compared to Ins(1,3,4,5)P(4) [0.15microM] and similar to that of L-Ins(1,3,4,5)P(4) [1.8microM]. In displacement of [(3)H] Ins(1,4,5)P(3) from the rat cerebellar Ins(1,4,5)P(3) receptor, while slightly weaker [IC(50)=800nM] than that of D-Ins(1,3,4,5)P(4) [IC(50)=220nM], 3 is less markedly different and again similar to that of L-Ins(1,3,4,5)P(4) [IC(50)=660nM]. 3 is an activator of I(CRAC) when inward currents are measured in RBL-2H3-M1 cells using patch-clamp electrophysiological techniques with a facilitation curve different to that of Ins(1,3,4,5)P(4). Physicochemical properties were studied by potentiometric (31)P and (1)H NMR titrations and were similar to those of Ins(1,3,4,5)P(4) apart from the observation of a biphasic titration curve for the P1 phosphate group. A novel vicinal phosphate charge-induced conformational change of the inositol ring above pH 10 was observed for D-6-deoxy-Ins(1,3,4,5)P(4) that would normally be hindered because of the central stabilising role played by the 6-OH group in Ins(1,3,4,5)P(4). We conclude that the 6-OH group in Ins(1,3,4,5)P(4) is crucial for its physicochemical behaviour and biological properties of this key inositol phosphate.
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Affiliation(s)
- Graeme Horne
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, UK
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Synthesis and structure of and DFT-studies on 1,3,5-[P(O)(i-PrO)2]3C6H3 and its CHCl3 adduct: analysis of the Cl3C–H⋯OP hydrogen bond. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Riley AM, Dozol H, Spiess B, Potter BVL. 2-O-(2-Aminoethyl)-myo-inositol 1,4,5-trisphosphate as a novel ligand for conjugation: physicochemical properties and synthesis of a new Ins(1,4,5)P(3) affinity matrix. Biochem Biophys Res Commun 2004; 318:444-52. [PMID: 15120621 DOI: 10.1016/j.bbrc.2004.04.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2004] [Indexed: 11/22/2022]
Abstract
2-O-(2-Aminoethyl)-Ins(1,4,5)P(3), (5), a novel derivative of the Ca(2+)-mobilising second messenger d-myo-inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)], was synthesised from myo-inositol. 5 was found to be a potent mobiliser of intracellular Ca(2+), and an Ins(1,4,5)P(3) affinity matrix synthesised from 5 was effective at selectively binding N-terminal fragments of the Ins(1,4,5)P(3) receptor containing the intact Ins(1,4,5)P(3) binding site. The microprotonation scheme for 5 was resolved and the related constants were determined in comparison with Ins(1,4,5)P(3) and another reactive Ins(1,4,5)P(3) analogue 1-O-(2-aminoethyl-1-phospho)-Ins(4,5)P(2), (2a), by potentiometric and NMR titration methods. The (31)P and (1)H NMR titration curves for compound 5 and Ins(1,4,5)P(3) are remarkably close, indicating analogous acid-base properties and intramolecular interactions for the two compounds. The 1-phosphate-modified Ins(1,4,5)P(3) derivative 2a, on the contrary, behaves as a bisphosphorylated rather than a trisphosphorylated inositol. Thus, 5 is a new reactive Ins(1,4,5)P(3) analogue of considerable potential for investigation of the chemical biology of Ins(1,4,5)P(3)-mediated cellular signalling.
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Affiliation(s)
- Andrew M Riley
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, UK
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Dozol H, Maechling C, Graff R, Matsuda A, Shuto S, Spiess B. Conformational and inframolecular studies of the protonation of adenophostin analogues lacking the adenine moiety. Biochim Biophys Acta Gen Subj 2004; 1671:1-8. [PMID: 15026139 DOI: 10.1016/j.bbagen.2003.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2003] [Revised: 12/10/2003] [Accepted: 12/10/2003] [Indexed: 10/26/2022]
Abstract
Four adenophostin analogues lacking the adenine moiety were subjected to 31P- and 1H-NMR titrations in order to determine the acid-base behaviour of the individual ionisable groups of the molecules and the complex interplay of intramolecular interactions resulting from the protonation process. For the two trisphosphorylated compounds, the curve pattern of the phosphorus nuclei corresponds to the superimposition of the titration curves of a monophosphorylated polyol and a polyol carrying two vicinal phosphates, suggesting that the two phosphate moieties behave independently. Also, the general shape of 1H-NMR titration curves of the studied compounds is very close to that of adenophostin A, indicating that the adenine moiety does not specifically interact with the phosphorylated sugar moieties. The curves show, however, that both trisphosphorylated compounds adopt slightly different preferential conformations which could contribute to explain the difference in their affinity for Ins(1,4,5)P3 receptor. Their macroscopic as well as the microscopic protonation constants are higher than those of adenophostin A, indicating that the adenine moiety plays a base-weakening effect on the phosphate groups. Further analysis of the microscopic protonation constants confirms that the compound whose conformation is the closest to that of adenophostin A also shows the highest biological activity. The two bisphosphorylated analogues studied behave very similarly, suggesting that the deletion of the hydroxymethyl group on the pentafuranosyl ring only weakly influences the protonation process of the phosphate groups that bear the glucopyranose moiety.
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Affiliation(s)
- Hélène Dozol
- Laboratoire de Pharmacochimie Moléculaire, UMR 7081 du CNRS, Faculté de Pharmacie, ULP, 74, route du Rhin, B.P. 24, 67401 Illkirch, France
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Felemez M, Spiess B. 1H NMR titrations of hydroxy protons in aqueous solution as a method of investigation of intramolecular hydrogen-bonding in phosphorylated compounds: examples of myo-inositol 2-phosphate and myo-inositol 1,2,6-tris(phosphates). J Am Chem Soc 2003; 125:7768-9. [PMID: 12822972 DOI: 10.1021/ja021265b] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1H NMR hydroxy proton titration experiments for myo-inositol 2-phosphate and myo-inositol 1,2,6-tris(phosphates) in aqueous solution are presented to demonstrate that by following OH signals versus pH, evidence can be brought for HB interaction between the hydroxyl and phosphate groups. The chemical shifts of the OH protons vicinal to phosphate groups appear deshielded by ca. 2.5 ppm with regard to those two centers removed from the phosphates. Remarkably, the deshielded protons are only present when their neighboring phosphate groups are fully deprotonated but persist until high pHs. From these results, C-OH...2-O3P-O type I, C-HO...-HO3P-O type II and C-OH...-HO3P-O type III hydrogen bonds are evidenced and discussed.
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Affiliation(s)
- Marc Felemez
- Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR 7081 du CNRS, Université Louis Pasteur, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch Cedex, France
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Ullmann GM. Relations between Protonation Constants and Titration Curves in Polyprotic Acids: A Critical View. J Phys Chem B 2003. [DOI: 10.1021/jp026454v] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Matthias Ullmann
- IWR - Biocomputing, University Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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21
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Dozol H, Blum-Held C, Guédat P, Maechling C, Lanners S, Schlewer G, Spiess B. Inframolecular acid–base studies of the tris and tetrakis myo-inositol phosphates including the 1,2,3-trisphosphate motif. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(02)00440-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Acharya S, Acharya P, Földesi A, Chattopadhyaya J. Cross-modulation of physicochemical character of aglycones in dinucleoside (3'-->5') monophosphates by the nearest neighbor interaction in the stacked state. J Am Chem Soc 2002; 124:13722-30. [PMID: 12431102 DOI: 10.1021/ja026831h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Each nucleobase in a series of stacked dinucleoside (3'-->5') monophosphates, in both acidic and alkaline pH, shows ((1)H NMR) not only its own pK(a) but also the pK(a) of the neighboring nucleobase as a result of cross-modulation of two-coupled pi systems of neighboring aglycones. This means that the electronic character of two nearest neighbors are not like the monomeric counterparts anymore; they have simultaneously changed, almost quantitatively, to something that is a hybrid of the two due to two-way transmission of charge (i.e. 3'-->5' as well as 5'-->3'). This change is permanent due to total modulation of each others pseudoaromatic character by intramolecular stacking, which can be tuned by the nature of the medium across the whole pH range. The small difference observed in the pK(a) of the dimer compared to the monomer is a result of the change in microenvironment in the former. The charge transfer takes place between two stacked nucleobases from the negatively charged end because of the attempt to minimize the charge difference between the two neighboring pseudoaromatic aglycones. Experimental evidence points that the charge transmission in the stacked state takes place by atom-pisigma interaction between nearest neighbor nucleobases in 1-6. The net result of this cross-talk between two neighboring aglycones is a unique set of aglycones in an oligo- or polynucleotide, whose physicochemical property and the pseudoaromatic character are completely dependent both upon the sequence makeup, and whether they are stacked or unstacked. Thus, the physicochemical property of individual nucleobases in an oligonucleotide is determined in a tunable manner, depending upon who the nearest neighbors are, which may have considerable implication in the specific ligand binding ability of an aptamer, the pK(a) and the hydrogen bonding ability in a microenvironment, in the use of codon triplets in the protein biosynthesis or in the triplet usage by the anticodon-codon interaction.
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Affiliation(s)
- S Acharya
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, Uppsala University, S-751 23 Uppsala, Sweden
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23
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Raboisson P, Baurand A, Cazenave JP, Gachet C, Retat M, Spiess B, Bourguignon JJ. Novel antagonists acting at the P2Y(1) purinergic receptor: synthesis and conformational analysis using potentiometric and nuclear magnetic resonance titration techniques. J Med Chem 2002; 45:962-72. [PMID: 11831909 DOI: 10.1021/jm0104062] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human P2Y(1) receptor is widely distributed in many tissues and has a classical structure of a G protein-coupled receptor. Activated by adenosine-5'-diphosphate (ADP), this receptor is essential for platelet aggregation. In the present paper, we describe the synthesis of novel P2Y(1) antagonists that could be of interest at least as tools to define the physiological roles of the P2Y(1) receptor, at best as new antithrombotic agents. Thus, we prepared the 2,N(6)-dimethyl-2'-deoxyadenosine-3',5'-bisphosphate derivative, 1e. The biological activity was demonstrated by the ability of compound 1e to inhibit ADP-induced platelet aggregation, shape change, and intracellular calcium rise. This compound was a full antagonist at the P2Y(1) receptor with a pA(2) value of 7.11 +/- 0.11 and was found to be 4-fold more potent than the reference N(6)-methyl-2'-deoxyadenosine-3',5'-bisphosphate (1a, pA(2) = 6.55 +/- 0.05), revealing the potency-enhancing effects of the 2-methyl group. The better activity of 1e as compared to 1a was analyzed using both potentiometric and nuclear magnetic resonance titration techniques, which highlighted specific conformational features of this compound. These results clearly indicate the preference for both compounds for an anti conformation at the N-glycosyl linkage. Furthermore, the percentage of S conformer of 1e is close to that of 1a, which is nearly 70% at pH = 2.8 and increases dramatically when pH increases. From the macroprotonation constants, it can be noted that compound 1e is significantly more basic than 1a. This is indeed expected for the N1 adenine nitrogen due to the electron-donating character of the methyl moiety. By considering the microconstants of the phosphate groups, the higher basicity of P3 and P5 for 1e may be due to the decrease in the local dielectric constant induced by the substitution of the hydrogen atom by a more lipophilic methyl group. Thus, it may be suggested that the gain in activity of 1e when compared to the reference compound 1a would result from its gain in basicity rather than steric and conformational modifications. The synthesis of the first selective radioligand acting at the P2Y(1) receptor ([(33)P]-N(6)-methyl-2'-deoxyadenosine-3',5'-bisphosphate, 17) is also reported and will be used in the future for efficient screening needed for drug optimization.
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Affiliation(s)
- Pierre Raboisson
- Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR 7081 du CNRS, Faculté de Pharmacie, Université Louis Pasteur, 74, Route du Rhin, 67401 Illkirch Cedex, France
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24
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Raymo FM, Bartberger MD, Houk KN, Stoddart JF. The magnitude of [C-H...O] hydrogen bonding in molecular and supramolecular assemblies. J Am Chem Soc 2001; 123:9264-7. [PMID: 11562207 DOI: 10.1021/ja010443i] [Citation(s) in RCA: 169] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ab initio calculations at the MP2/6-311++G** level on model systems (N-methylpyridinium complexes of dimethyl ether and dimethyl phosphate anion) provide quantitative measures of the large stabilization energies that arise from [C-H...O] contacts in charged systems. These attractive interactions control (i) the self-assembly of bipyridinium-based catenanes and rotaxanes in solution, (ii) the self-organization of left-handed Z-DNA with alternating [dC-dG] sequences in the solid state, and (iii) the binding of pyridinium derivatives with single- and double-stranded DNA. Slightly attractive interactions occur between the donor ether and phosphate moieties and a neutral pyridine molecule in the gas phase. Electrostatic potential and solvation calculations demonstrate that [C-H...O] interactions which involve a cationic [C-H] donor are dominated by electrostatic terms.
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Affiliation(s)
- F M Raymo
- Center for Supramolecular Science, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, USA
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25
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Bombarda E, Morellet N, Cherradi H, Spiess B, Bouaziz S, Grell E, Roques BP, Mély Y. Determination of the pK(a) of the four Zn2+-coordinating residues of the distal finger motif of the HIV-1 nucleocapsid protein: consequences on the binding of Zn2+. J Mol Biol 2001; 310:659-72. [PMID: 11439030 DOI: 10.1006/jmbi.2001.4770] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The nucleocapsid protein NCp7 of human immunodeficiency virus type 1 is characterized by two highly conserved CCHC motifs that bind Zn2+ strongly. To elucidate the striking pH-dependence of the apparent Zn2+-binding constants of these motifs further, we investigated, using 1H NMR, potentiometry and fluorescence spectroscopy, the acid-base properties of the four Zn2+-coordinating residues of (35-50)NCp7, a peptide corresponding to the distal finger motif of NCp7. With the exception of the H(beta2) proton of Cys39, the pH-dependence of the H(beta) proton resonances of the three Cys residues and, the H(delta) and H(epsilon) resonances of His44 in the apopeptide could be fitted adequately with a single pK(a). This suggests that the protonating groups are non-interacting, a feature that was confirmed by a potentiometric titration. The pK(a) of His44, Cys36, Cys39, and Cys49 in the apopeptide were found to be 6.4, 8.0, 8.8 and 9.3, respectively. Accordingly, the deprotonation is almost sequential and may thus induce a sequential binding of Zn2+ to the four coordinating residues. The high pK(a) of Cys49 is probably related to the negative charge of the neighboring Asp48. Such a high pK(a) may be a general feature in nucleocapsid proteins (NCs), since an acidic residue generally occupies the (i-1) position of the C-terminal Cys residue of single-finger NCs and distal finger motifs in two-finger NCs. Molecular dynamics simulation suggested the formation of a hydrogen bonded network that weakly structured the Cys36-Cys39 segment in the apopeptide. This network depends on the protonation state of Cys36 and may thus explain the biphasic behavior of the pH-dependence of the Cys39 H(beta2) resonance. Finally, the pK(a) values were used to build up a model describing the coordination of Zn2+ to (35-50)NCp7 at equilibrium. It appears that each protonation step of the coordination complex decreases the Zn2+-binding constant by about four orders of magnitude and that a significant dissociation of Zn2+ from the holopeptide can be achieved in acidic cell compartments.
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Affiliation(s)
- E Bombarda
- Laboratoire de Pharmacologie et Physico-Chimie des Interactions Cellulaires et Moléculaires, UMR 7034 CNRS, Faculté de Pharmacie, Université Louis Pasteur, Strasbourg 1, 74, Route du Rhin, Illkirch Cedex, 67401, France
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26
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Rosenberg HJ, Riley AM, Marwood RD, Correa V, Taylor CW. Xylopyranoside-based agonists of D-myo-inositol 1,4,5-trisphosphate receptors: synthesis and effect of stereochemistry on biological activity. Carbohydr Res 2001; 332:53-66. [PMID: 11403088 DOI: 10.1016/s0008-6215(01)00067-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The synthesis of a series of tetrahydrofuranyl alpha- and beta-xylopyranoside trisphosphates, designed by excision of three motifs of adenophostin A is reported. The synthetic route features improved preparations of allyl alpha-D-xylopyranoside and its 2-O-benzyl ether, and gives access to four diastereoisomeric trisphosphates, which show a range of abilities to mobilise Ca2+ from the intracellular stores of hepatocytes. A comparison of the potencies of the four trisphosphates provides useful information relating to the effects of stereochemical variation on the recognition of carbohydrate-based trisphosphates by D-myo-inositol 1,4,5-trisphosphate receptors. 1-O-[(3'S,4'R)-3-hydroxytetrahydrofuran-4-yl] alpha-D-xylopyranoside 3,4,3'-trisphosphate (8) is the most active member of the series with a potency close to Ins(1,4,5)P3; a beta-linked analogue, 1-O-[(3'R,4'S)-3-hydroxytetrahydrofuran-4-yl] beta-D-xylopyranoside 3,4,3'-trisphosphate, is ca. 20-fold weaker than Ins(1,4,5)P3, and the other compounds are much less active. While no compound attained a potency close to that of adenophostin A, we believe that 8 represents the minimal structure for potent Ca2+-releasing activity in this type of carbohydrate-based analogue.
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Affiliation(s)
- H J Rosenberg
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, UK
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27
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Blum-Held C, Bernard P, Schlewer G, Spiess B. myo-Inositol 1,4,5,6-tetrakisphosphate and myo-inositol 3,4,5,6-tetrakisphosphate, two second messengers that may act as pH-dependent molecular switches. J Am Chem Soc 2001; 123:3399-400. [PMID: 11457089 DOI: 10.1021/ja015616i] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C Blum-Held
- Laboratoire de Pharmacologie Moléculaire UMR 7081 du CNRS-ULP, Faculté de Pharmacie 74, Route du Rhin, B.P. 24, 67401 Illkirch Cedex, France
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28
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Felemez M, Spiess B. Investigation of the ternary D-myo-inositol 1,2,6-tris(phosphate)-spermine-Zn2+ system in solution. J Inorg Biochem 2001; 84:107-11. [PMID: 11330468 DOI: 10.1016/s0162-0134(00)00220-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Interactions of Ins(1,2,6)P3 (IP), with spermine (Spm) and zinc cations have been studied by potentiometric and 31P NMR titrations. In the 4-11 pH range, two IPSpmZn2H3 and IPSpmZn2H mixed complexes are formed which are largely predominant with respect to the binary species. According to 31P NMR titration it is likely that one of the zinc cations preferably binds phosphates P1 and P6. The adduct formation between Ins(1,2,6)P3 and spermine seems also favourable to the formation of the mixed complexes. The occurrence of ternary complexes involving inositol-phosphates, biogenic amines, and metallic cations may be of relevance in the regulation of biological processes.
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Affiliation(s)
- M Felemez
- Laboratoire de Pharmacochimie Moléculaire, UMR 7081 du CNRS, Faculté de Pharmacie, Illkirch, France
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