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Conter C, Favretto F, Dominici P, Martinez-Cruz LA, Astegno A. Key substrate recognition residues in the active site of cystathionine beta-synthase from Toxoplasma gondii. Proteins 2023; 91:1383-1393. [PMID: 37163386 DOI: 10.1002/prot.26507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/28/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
Cystathionine β-synthase (CBS) catalyzes the condensation of l-serine and l-homocysteine to give l-cystathionine in the transsulfuration pathway. Recently, a few O-acetylserine (l-OAS)-dependent CBSs (OCBSs) have been found in bacteria that can exclusively function with l-OAS. CBS from Toxoplasma gondii (TgCBS) can efficiently use both l-serine and l-OAS to form l-cystathionine. In this work, a series of site-specific variants substituting S84, Y160, and Y246 with hydrophobic residues found at the same positions in OCBSs was generated to explore the roles of the hydroxyl moieties of these residues as determinants of l-serine/l-OAS preference in TgCBS. We found that the S84A/Y160F/Y246V triple mutant behaved like an OCBS in terms of both substrate requirements, showing β-replacement activity only with l-OAS, and pH optimum, which is decreased by ~1 pH unit. Formation of a stable aminoacrylate upon reaction with l-serine is prevented by the triple mutation, indicating the importance of the H-bonds between the hydroxyl groups of Y160, Y246, and S84 with l-serine in formation of the intermediate. Analysis of the independent effect of each mutation on TgCBS activity and investigation of the protein-aminoacrylate complex structure allowed for the conclusion that the hydroxyl group of Y246 has a major, but not exclusive, role in controlling the l-serine preference by efficiently stabilizing its leaving group. These studies demonstrate that differences in substrate specificity of CBSs are controlled by natural variations in as few as three residue positions. A better understanding of substrate specificity in TgCBS will facilitate the design of new antimicrobial compounds.
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Affiliation(s)
- Carolina Conter
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Luis Alfonso Martinez-Cruz
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
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Vitvitsky V, Thomas M, Ghorpade A, Gendelman HE, Banerjee R. A functional transsulfuration pathway in the brain links to glutathione homeostasis. J Biol Chem 2006; 281:35785-93. [PMID: 17005561 DOI: 10.1074/jbc.m602799200] [Citation(s) in RCA: 170] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress and diminished glutathione pools play critical roles in the pathogenesis of neurodegenerative diseases, including Alzheimer and Parkinson disease. Synthesis of glutathione, the most abundant mammalian antioxidant, is regulated at the substrate level by cysteine, which is synthesized from homocysteine via the transsulfuration pathway. Elevated homocysteine and diminished glutathione levels, seen in Alzheimer and Parkinson disease patients suggest impairments in the transsulfuration pathway that connects these metabolites. However, the very existence of this metabolic pathway in the brain is a subject of controversy. The product of the first of two enzymes in this pathway, cystathionine, is present at higher levels in brain as compared with other organs. This, together with the reported absence of the second enzyme, gamma-cystathionase, has led to the suggestion that the transsulfuration pathway is incomplete in the brain. In this study, we incubated mouse and human neurons and astrocytes and murine brain slices in medium with [35S]methionine and detected radiolabel incorporation into glutathione. This label transfer was sensitive to inhibition of gamma-cystathionase. In adult brain slices, approximately 40% of the glutathione was depleted within 10 h following gamma-cystathionase inhibition. In cultured human astrocytes, flux through the transsulfuration pathway increased under oxidative stress conditions, and blockade of this pathway led to reduced cell viability under oxidizing conditions. This study establishes the presence of an intact transsulfuration pathway and demonstrates its contribution to glutathione-dependent redox-buffering capacity under ex vivo conditions in brain cells and slices.
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Affiliation(s)
- Victor Vitvitsky
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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3
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Aitken SM, Kirsch JF. The enzymology of cystathionine biosynthesis: strategies for the control of substrate and reaction specificity. Arch Biochem Biophys 2005; 433:166-75. [PMID: 15581575 DOI: 10.1016/j.abb.2004.08.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Indexed: 11/29/2022]
Abstract
The ability of enzymes to catalyze specific reactions, while excluding others, is central to cellular metabolism. Control of reaction specificity is of particular importance for enzymes that employ catalytically versatile cofactors, of which pyridoxal 5'-phosphate is a prime example. Cystathionine gamma-synthase and cystathionine beta-synthase are the first enzymes in the transsulfuration and reverse transsulfuration pathways, respectively. Each of them occupies branch-point positions in amino acid metabolism and as such are subject to transcriptional and post-translational regulation. Both enzymes catalyze the pyridoxal 5'-phosphate-dependent formation of l-cystathionine; however, their substrate and reaction specificities are distinct. The mechanisms whereby these enzymes control the chemistry of the cofactor are the subject of this review.
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Affiliation(s)
- Susan M Aitken
- Department of Biology, Carleton University, Ottawa, Ontario, Canada K1S 5B6.
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Abstract
An O-acetylserine sulfhydrylase (OASS) from the hyperthermophilic archaeon Aeropyrum pernix K1, which shares the pyridoxal 5'-phosphate binding motif with both OASS and cystathionine beta-synthase (CBS), was cloned and expressed by using Escherichia coli Rosetta(DE3). The purified protein was a dimer and contained pyridoxal 5'-phosphate. It was shown to be an enzyme with CBS activity as well as OASS activity in vitro. The enzyme retained 90% of its activity after a 6-h incubation at 100 degrees C. In the O-acetyl-L-serine sulfhydrylation reaction, it had a pH optimum of 6.7, apparent K(m) values for O-acetyl-L-serine and sulfide of 28 and below 0.2 mM, respectively, and a rate constant of 202 s(-1). In the L-cystathionine synthetic reaction, it showed a broad pH optimum in the range of 8.1 to 8.8, apparent K(m) values for L-serine and L-homocysteine of 8 and 0.51 mM, respectively, and a rate constant of 0.7 s(-1). A. pernix OASS has a high activity in the L-cysteine desulfurization reaction, which produces sulfide and S-(2,3-hydroxy-4-thiobutyl)-L-cysteine from L-cysteine and dithiothreitol.
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Affiliation(s)
- Koshiki Mino
- Special Division for Human Life Technology, National Institute of Advanced Industrial Science and Technology (AIST, Kansai), Ikeda, Osaka 563-8577, Japan
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Aitken SM, Kirsch JF. Kinetics of the yeast cystathionine beta-synthase forward and reverse reactions: continuous assays and the equilibrium constant for the reaction. Biochemistry 2003; 42:571-8. [PMID: 12525186 DOI: 10.1021/bi026681n] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cystathionine beta-synthase (CBS) is a pyridoxal-phosphate-dependent enzyme that catalyzes a beta-replacement reaction in which the hydroxyl group of serine (L-Ser) is displaced by the thiol of homocysteine (L-Hcys) to form cystathionine (L-Cth) in the first step of the trans-sulfuration pathway. A new continuous assay for the forward reaction, employing cystathionine beta-lyase and L-lactate dehydrogenase as coupling enzymes, is described. It alleviates product inhibition by L-Cth and revealed that the values for (1.2 mM) and for substrate inhibition by L-Hcys ( = 2.0 mM) are lower than those previously reported. A continuous, 5,5'-dithio-bis-(2-nitrobenzoic acid) (DTNB)-based assay for the CBS-catalyzed hydrolysis of L-Cth to L-Ser and L-Hcys provides a tool for investigation of the reverse reaction (k(catR) = 0.56 s(-)(1), = 0.083 mM). The (catR)/ versus pH profile of ytCBS is bell-shaped with a pH optimum of 8.3, and the pK(a) values for the acidic and basic limbs are 8.05 and 8.63, respectively. The latter is assigned to the alpha-amino group of L-Cth (pK(a) = 8.54). The internal aldimine of ytCBS remains protonated at pH < 11; therefore, the acidic pK(a) is assigned to an enzyme functionality that is not associated with the internal aldimine. K(eq) was determined directly and from the kinetic parameters, and the values are 0.61 and 1.2 microM, respectively.
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Affiliation(s)
- Susan M Aitken
- Molecular and Cell Biology Department, University of California-Berkeley, Berkeley, California 94720-3206, USA
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Shiraiwa T, Nakagawa K, Kanemoto N, Kinda T, Yamamoto H. Synthesis of optically active homocysteine from methionine and its use in preparing four stereoisomers of cystathionine. Chem Pharm Bull (Tokyo) 2002; 50:1081-5. [PMID: 12192140 DOI: 10.1248/cpb.50.1081] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to synthesize four stereoisomers of cystathionine (CYT), D- and L-homocysteines (D- and L-Hcy) were synthesized from methionine (Met) by a facile procedure. L-Met was reacted with dichloroacetic acid in concentrated hydrochloric acid under reflux to give (4S)-1,3-thiazane-2,4-dicarboxylic acid hydrochloride [(4S)-TDC.HCl]. L-Hcy was obtained by treatment of (4S)-TDC.HCl with hydroxylamine. D-Hcy was also synthesized from D-Met via (4R)-TDC.HCl intermediate. The obtained D- and L-Hcy were condensed with (R)- and (S)-2-amino-3-chloropropanoic acid hydrochlorides under alkaline conditions to give four stereoisomers of CYT.
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Affiliation(s)
- Tadashi Shiraiwa
- Unit of Chemistry, Faculty of Engineering and High Technology Research Center, Kansai University, Osaka, Japan.
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Abstract
Cystathionine beta-synthase found in yeast catalyzes a pyridoxal phosphate-dependent condensation of homocysteine and serine to form cystathionine. Unlike the homologous mammalian enzymes, yeast cystathionine beta-synthase lacks a second cofactor, heme, which facilitates detailed kinetic studies of the enzyme because the different pyridoxal phosphate-bound intermediates can be followed by their characteristic absorption spectra. We conducted a rapid reaction kinetic analysis of the full-length yeast enzyme in the forward and reverse directions. In the forward direction, we observed formation of the external aldimine of serine (14 mm(-1) s(-1)) and the aminoacrylate intermediate (15 s(-1)). Homocysteine binds to the aminoacrylate with a bimolecular rate constant of 35 mm(-1) s(-1) and rapidly converts to cystathionine (180 s(-1)), leading to the accumulation of a 420 nm absorbing species, which has been assigned as the external aldimine of cystathionine. Release of cystathionine is slow (k = 2.3 s(-1)), which is similar to k(cat) (1.7 s(-1)) at 15 degrees C, consistent with this being a rate-determining step. In the reverse direction, cystathionine binds to the enzyme with a bimolecular rate constant of 1.5 mm(-1) s(-1) and is rapidly converted to the aminoacrylate without accumulation of the external aldimine. The kinetic behavior of the full-length enzyme shows notable differences from that reported for a truncated form of the enzyme lacking the C-terminal third of the protein (Jhee, K. H., Niks, D., McPhie, P., Dunn, M. F., and Miles, E. W. (2001) Biochemistry 40, 10873-10880).
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Affiliation(s)
- Shinichi Taoka
- Biochemistry Department, University of Nebraska, Lincoln, Nebraska 68588-0664, USA
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Abstract
CBS1 from Magnaporthe grisea is a structural and functional homolog of the cystathionine beta-synthase (CBS) gene from Saccharomyces cerevisiae. Our studies indicated that M. grisea can utilize homocysteine and methionine through a CBS-independent pathway. The results also revealed responses of M. grisea to homocysteine that are reminiscent of human homocystinuria.
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Affiliation(s)
- Sze Chung Clive Lo
- Microbial Research, Paradigm Genetics, Inc., Research Triangle Park, North Carolina 27709, USA.
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Jhee KH, Niks D, McPhie P, Dunn MF, Miles EW. Yeast cystathionine beta-synthase reacts with L-allothreonine, a non-natural substrate, and L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine. Biochemistry 2002; 41:1828-35. [PMID: 11827527 DOI: 10.1021/bi011756t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our studies of the reaction mechanism of cystathionine beta-synthase from yeast (Saccharomyces cerevisiae) are facilitated by the spectroscopic properties of the pyridoxal phosphate coenzyme. The enzyme catalyzes the reaction of L-serine with L-homocysteine to form L-cystathionine through a series of pyridoxal phosphate intermediates. In this work, we explore the substrate specificity of the enzyme by use of substrate analogues combined with kinetic measurements under pre-steady-state conditions and with circular dichroism and fluorescence spectroscopy under steady-state conditions. Our results show that L-allothreonine, but not L-threonine, serves as an effective substrate. L-Allothreonine reacts with the pyridoxal phosphate cofactor to form a stable 3-methyl aminoacrylate intermediate that absorbs maximally at 446 nm. The rapid-scanning stopped-flow results show that the binding of L-allothreonine as the external aldimine is faster than formation of the 3-methyl aminoacrylate intermediate. The 3-methyl aminoacrylate intermediate reacts with L-homocysteine to form a new amino acid, 3-methyl-L-cystathionine, which was characterized by nuclear magnetic resonance spectroscopy. This new amino acid may be a useful analogue of L-cystathionine.
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Affiliation(s)
- Kwang-Hwan Jhee
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA
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Gebhardt K, Shokraei A, Babaie E, Lindqvist BH. RNA aptamers to S-adenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody. Biochemistry 2000; 39:7255-65. [PMID: 10852725 DOI: 10.1021/bi000295t] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To explore the potential of RNA aptamers as small-molecule discriminating devices, we have characterized the properties of aptamers selected from a library of approximately 10(14) variants through their interaction with S-adenosylhomocysteine (SAH, AdoHcy). Competition studies with SAH and azaSAM analogues revealed that the Hoogsteen face of adenine is the main contributor to binding, whereas specificity for SAH is conferred by a secondary contact point at or near the sulfur/thioether of homocysteine (Hcy). Binding specificities were determined by both affinity chromatography and a novel method designed for the biosensor. The kinetic properties of individual aptamers, including the "classic" ATP aptamer that also emerged in our selection, were studied by biosensor analysis. Association rates were slow, but the complexes were stable, suggesting micro- to submicromolar affinities. A solution affinity of approximately 0.1 microM was found for the strongest binding variant under the conditions used for selection (5 mM Mg(2+)). Systematic studies of the effect of Mg(2+) and Mn(2+) on binding, however, revealed that the affinity of the aptamers could be substantially improved, and at optimized conditions of Mn(2+) the affinity of one of the aptamers approached that of an anti-SAH antibody with similar/identical binding specificity. Comparisons with the MAb suggest that the on rate is the limiting factor for high-affinity binding by these aptamers, and comparison with a truncated aptamer shows that shortening of RNA constructs may alter binding kinetics as well as sensitivity to ions.
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Affiliation(s)
- K Gebhardt
- Biotechnology Centre of Oslo, University of Oslo, Blindern, Norway.
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Shimazaki Y, Zhang J, Wakiguchi H, Kurashige T, Sagara Y, Masuoka N, Ohta J, Ubuka T, Kodama H. Different effect of diastereoisomers of L-cystathionine sulfoxide on the stimulus coupled responses of human neutrophils. Biochem Biophys Res Commun 1998; 247:387-91. [PMID: 9642137 DOI: 10.1006/bbrc.1998.8796] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The priming effect of L-cystathionine sulfoxide, which is one of the unusual cystathionine metabolites found in the urine of patients with cystathioninuria, on the stimulus-induced superoxide generation by human neutrophils was examined. The synthetic L-cystathionine sulfoxide significantly enhanced the superoxide generations induced by N-formyl-methionyl-leucyl-phenylalanine [fMLP], opsonized zymosan [OZ], arachidonic acid [AA], and phorbol 12-myristate 13-acetate [PMA]. Then the synthetic L-cystathionine sulfoxide was separated into two diastereoisomers, CS-I and CS-II, which showed a peak at 76 and 83 min on chromatogram by amino acid analyzer, respectively. CS-I enhanced the superoxide generations induced by AA and PMA but not those induced by fMLP and OZ. On the contrary, CS-II enhanced the superoxide generations induced by fMLP and OZ but not those induced by AA and PMA. The superoxide generation induced by PMA with CS-I was suppressed by H-7 and was enhanced by genistein, while that by fMLP with CS-II was suppressed by genistein and was enhanced by H-7.
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Affiliation(s)
- Y Shimazaki
- Department of Pediatrics, Department of Chemistry, Department of Medical Biology, Kochi Medical School, Oko-cho, Kochi, Nankoku, 783-8505, Japan
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Clausen T, Laber B, Messerschmidt A. Mode of action of cystathionine beta-lyase. Biol Chem 1997; 378:321-6. [PMID: 9165088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cystathionine beta-lyase (CBL) is a member of the gamma-family of pyridoxal-5'-phosphate (PLP)-dependent enzymes (Alexander et al., 1994) that cleave C(beta,gamma)-S bonds of a broad variety of substrates. Recently, we reported the X-ray crystal structures of CBL and the CBL-trifluoroalanine inactivation complex at 1.83 A and 2.3 A resolution, respectively. The structures explicitly reveal the cofactor and substrate binding pockets. Spectral analysis of substrate turnover indicates a change of hydrophobicity in the microenvironment of the aldimine bond. In combination with further spectroscopic data, crystallographic evidence permits the formulation of a likely reaction mechanism.
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Affiliation(s)
- T Clausen
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany
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Beaty JA, Jones MM, Ma L. The reactions of cis-[Pt(NH3)2(H2O)2]2+ with L-(+)-cystathionine and seleno-L-methionine: potential relevance to the molecular basis of cisplatin toxicity. Chem Res Toxicol 1992; 5:647-53. [PMID: 1446004 DOI: 10.1021/tx00029a009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NMR spectroscopic studies indicate that the hydrolysis product of cisplatin, cis-[Pt(NH3)2-(H2O)2]2+, reacts readily with the important intracellular thiol L-(+)-cystathionine and the amino acid derivative seleno-L-methionine. In both cases, the formation of six-membered mononuclear S,N- or Se, N-chelate rings was established on the basis of [1H], [13C], [77Se], [195Pt], and [13C]-(1H) DEPT (distortionless enhancement by polarization transfer), COSY (correlation spectroscopy), heterocorrelation, and NOE (nuclear Overhauser effect) difference NMR experiments. The formation of these products suggests that related in vivo processes may play a significant role in the toxicity of cisplatin. The potential loss of NH3 in such platinum complexes may lead to additional products over time.
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Affiliation(s)
- J A Beaty
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235
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