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Sova S, Kelly LA. Enzyme Modification and Oxidative Cross-linking Using Carboxylate-, Phenol- and Catechol-Conjugated 1,8-Naphthalimides. Photochem Photobiol 2019; 95:1169-1178. [PMID: 30993721 DOI: 10.1111/php.13110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/10/2019] [Indexed: 11/27/2022]
Abstract
The ground- and excited-state interactions of β-alanine, tyrosine and l-dopa substituted 1,8 naphthalimides (NI-Ala, NI-Tyr and NI-Dopa) with lysozyme and mushroom tyrosinase were evaluated to understand the mechanism of oxidative modification. Photooxidative cross-linking of lysozyme was observed for all three conjugates. The yield was significantly reduced for NI-Tyr and NI-Dopa due to intramolecular electron transfer to the excited singlet state of the 1,8-naphthalimide. Incubation of NI-Tyr and NI-Dopa with mushroom tyrosinase resulted in an increased fluorescence from the naphthalimide, suggesting that the phenol and catechol portion of the conjugates are oxidized by the enzyme. This result demonstrates that the compounds bind in the active site of mushroom tyrosinase. The catalytic activity of mushroom tyrosinase to oxidize both tyrosine (monophenolase) and l-dopa (diphenolase) was modified by NI-Tyr and NI-Dopa. Monophenolase activity was inhibited, and the diphenolase activity was enhanced in the presence of these conjugates. Detailed Michaelis-Menten studies show that both Vmax and Km are modified, consistent with a mixed inhibition mechanism. Collectively, the results show that the compounds interact in the enzyme's active site, but also modify the distribution of the enzyme's oxidation states that are responsible for catalysis.
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Affiliation(s)
- Stacey Sova
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD
| | - Lisa A Kelly
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD
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2
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Zhang S, Fox DM, Urbanc B. Insights into Formation and Structure of Aβ Oligomers Cross-Linked via Tyrosines. J Phys Chem B 2017; 121:5523-5535. [DOI: 10.1021/acs.jpcb.7b02495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shuting Zhang
- Department
of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Dillion M. Fox
- Department
of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Brigita Urbanc
- Department
of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
- Faculty
of Mathematics and Physics, University of Ljubljana, 1000 Ljubljana, Slovenia
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3
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Williams TL, Serpell LC, Urbanc B. Stabilization of native amyloid β-protein oligomers by Copper and Hydrogen peroxide Induced Cross-linking of Unmodified Proteins (CHICUP). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:249-259. [PMID: 26699836 DOI: 10.1016/j.bbapap.2015.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 11/09/2015] [Accepted: 12/01/2015] [Indexed: 12/17/2022]
Abstract
Oligomeric assemblies are postulated to be proximate neurotoxic species in human diseases associated with aberrant protein aggregation. Their heterogeneous and transient nature makes their structural characterization difficult. Size distributions of oligomers of several amyloidogenic proteins, including amyloid β-protein (Aβ) relevant to Alzheimer's disease (AD), have been previously characterized in vitro by photo-induced cross-linking of unmodified proteins (PICUP) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Due to non-physiological conditions associated with the PICUP chemistry, Aβ oligomers cross-linked by PICUP may not be representative of in vivo conditions. Here, we examine an alternative Copper and Hydrogen peroxide Induced Cross-linking of Unmodified Proteins (CHICUP), which utilizes naturally occurring divalent copper ions and hydrogen peroxide and does not require photo activation. Our results demonstrate that CHICUP and PICUP applied to the two predominant Aβ alloforms, Aβ40 and Aβ42, result in similar oligomer size distributions. Thioflavin T fluorescence data and atomic force microscopy images demonstrate that both CHICUP and PICUP stabilize Aβ oligomers and attenuate fibril formation. Relative to noncross-linked peptides, CHICUP-treated Aβ40 and Aβ42 cause prolonged disruption to biomimetic lipid vesicles. CHICUP-stabilized Aβ oligomers link the amyloid cascade, metal, and oxidative stress hypotheses of AD into a more comprehensive understanding of the molecular basis of AD pathology. Because copper and hydrogen peroxide are elevated in the AD brain, CHICUP-stabilized Aβ oligomers are biologically relevant and should be further explored as a new therapeutic target.
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Affiliation(s)
- Thomas L Williams
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA
| | - Louise C Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex, UK
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, PA 19104, USA; Faculty of Mathematics and Physics, University of Ljubljana, Slovenia.
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Koniev O, Wagner A. Developments and recent advancements in the field of endogenous amino acid selective bond forming reactions for bioconjugation. Chem Soc Rev 2015; 44:5495-551. [PMID: 26000775 DOI: 10.1039/c5cs00048c] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioconjugation methodologies have proven to play a central enabling role in the recent development of biotherapeutics and chemical biology approaches. Recent endeavours in these fields shed light on unprecedented chemical challenges to attain bioselectivity, biocompatibility, and biostability required by modern applications. In this review the current developments in various techniques of selective bond forming reactions of proteins and peptides were highlighted. The utility of each endogenous amino acid-selective conjugation methodology in the fields of biology and protein science has been surveyed with emphasis on the most relevant among reported transformations; selectivity and practical use have been discussed.
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Affiliation(s)
- Oleksandr Koniev
- Laboratory of Functional Chemo-Systems (UMR 7199), Labex Medalis, University of Strasbourg, 74 Route du Rhin, 67401 Illkirch-Graffenstaden, France.
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Tamura T, Tsukiji S, Hamachi I. Native FKBP12 Engineering by Ligand-Directed Tosyl Chemistry: Labeling Properties and Application to Photo-Cross-Linking of Protein Complexes in Vitro and in Living Cells. J Am Chem Soc 2012; 134:2216-26. [DOI: 10.1021/ja209641t] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Shinya Tsukiji
- Top Runner
Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka,
Niigata 940-2188, Japan
| | - Itaru Hamachi
- Department of Synthetic
Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
- Core Research for
Evolutional Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo
102-0075, Japan
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Endrizzi BJ, Huang G, Kiser PF, Stewart RJ. Specific covalent immobilization of proteins through dityrosine cross-links. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:11305-10. [PMID: 17154619 DOI: 10.1021/la0618216] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Dityrosine cross-links are widely observed in nature in structural proteins such as elastin and silk. Natural oxidative cross-linking between tyrosine residues is catalyzed by a diverse group of metalloenzymes. Dityrosine formation is also catalyzed in vitro by metal-peptide complexes such as Gly-Gly-His-Ni(II). On the basis of these observations, a system was developed to specifically and covalently surface immobilize proteins through dityrosine cross-links. Methacrylate monomers of the catalytic peptide Gly-Gly-His-Tyr-OH (GGHY) and the Ni(II)-chelating group nitrilotriacetic acid (NTA) were copolymerized with acrylamide into microbeads. Green fluorescent protein (GFP), as a model protein, was genetically tagged with a tyrosine-modified His6 peptide on its carboxy terminus. GFP-YGH6, specifically associated with the NTA-Ni(II) groups, was covalently coupled to the bead surface through dityrosine bond formation catalyzed by the colocalized GGHY-Ni(II) complex. After extensive washing with EDTA to disrupt metal coordination bonds, we observed that up to 75% of the initially bound GFP-YGH6 remained covalently bound to the bead while retaining its structure and activity. Dityrosine cross-linking was confirmed by quenching the reaction with free tyrosine. The method may find particular utility in the construction and optimization of protein microarrays.
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Affiliation(s)
- Betsy J Endrizzi
- Department of Bioengineering, University of Utah, 20 South 2030 East, Room 506, Salt Lake City, UT 84112, USA
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Amini F, Denison C, Lin HJ, Kuo L, Kodadek T. Using oxidative crosslinking and proximity labeling to quantitatively characterize protein-protein and protein-Peptide complexes. ACTA ACUST UNITED AC 2004; 10:1115-27. [PMID: 14652079 DOI: 10.1016/j.chembiol.2003.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The quantitative analysis of protein-protein and protein-peptide complexes is of fundamental importance in biochemistry. We report here that nickel-catalyzed proximity biotinylation and Ru(II)(bpy)(3)(2+)-mediated oxidative crosslinking can be used to measure the equilibrium dissociation constant and stoichiometry of protein complexes. Only small amounts of protein are required, neither of the binding partners must be immobilized on a surface, and no special instrumentation is necessary. This chemistry should provide a useful complement to existing methods for the analysis of protein-protein and protein-peptide interactions.
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Affiliation(s)
- Frank Amini
- Center for Biomedical Inventions, Departments of Internal Medicine and Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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9
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Fancy DA, Denison C, Kim K, Xie Y, Holdeman T, Amini F, Kodadek T. Scope, limitations and mechanistic aspects of the photo-induced cross-linking of proteins by water-soluble metal complexes. CHEMISTRY & BIOLOGY 2000; 7:697-708. [PMID: 10980450 DOI: 10.1016/s1074-5521(00)00020-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Chemical cross-linking is a valuable tool with which to study protein-protein interactions. Recently, a new kind of cross-linking reaction was developed in which the photolysis of associated proteins with visible light in the presence of ammonium persulfate and tris(2,2'-bipyridyl)ruthenium(II) dication or palladium(II) porphyrins results in rapid and efficient covalent coupling (Fancy, D.A. & Kodadek, T. (1999). Proc. Natl. Acad. Sci. USA 96, 6020-6024 and Kim, K., Fancy, D.A. & Kodadek, T. (1999). J. Am. Chem. Soc. 121, 11896-11897). Here, mechanistic and practical aspects of the reaction of importance for its application to biochemical problems are examined. RESULTS It is shown that the photo-initiated cross-linking chemistry can be optimized for the analysis of protein-protein interactions in crude cell extracts. A number of commonly used epitope or affinity tags survive the reaction in functional form, allowing the simple visualization of the cross-linked products, or their isolation. It is shown that very little light-independent oxidation of protein residues occurs and that significant perturbation of complexes of interest prior to the brief photolysis period does not occur. Finally, evidence is presented that is consistent with a mechanistic model in which ammonium persulfate functions simply as an electron acceptor, facilitating the generation of the key high valent metal complex from the photoexcited species by electron transfer. In the absence of an electron acceptor, a much lower efficiency reaction is observed that appears to involve products resulting from reaction of the excited state metal complex with molecular oxygen. CONCLUSIONS These results provide useful practical information for chemists and biochemists who may wish to employ this new cross-linking chemistry for the analysis of protein complexes. They also shed new light on the mechanism of this interesting reaction.
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Affiliation(s)
- D A Fancy
- Department of Internal Medicine, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8573, USA
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Han Y, Kodadek T. Peptides selected to bind the Gal80 repressor are potent transcriptional activation domains in yeast. J Biol Chem 2000; 275:14979-84. [PMID: 10809742 DOI: 10.1074/jbc.275.20.14979] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The activation domain of the yeast Gal4 protein binds specifically to the Gal80 repressor and is also thought to associate with one or more coactivators in the RNA polymerase II holoenzyme and chromatin remodeling machines. This is a specific example of a common situation in biochemistry where a single protein domain can interact with multiple partners. Are these different interactions related chemically? To probe this point, phage display was employed to isolate peptides from a library based solely on their ability to bind Gal80 protein in vitro. Peptide-Gal80 protein association is shown to be highly specific and of moderate affinity. The Gal80 protein-binding peptides compete with the native activation domain for the repressor, suggesting that they bind to the same site. It was then asked if these peptides could function as activation domains in yeast when tethered to a DNA binding domain. Indeed, this is the case. Furthermore, one of the Gal80-binding peptides binds directly to a domain of the Gal11 protein, a known coactivator. The fact that Gal80-binding peptides are functional activation domains argues that repressor binding and activation/coactivator binding are intimately related properties. This peptide library-based approach should be generally useful for probing the chemical relationship of different binding interactions or functions of a given native domain.
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Affiliation(s)
- Y Han
- Departments of Internal Medicine and Biochemistry, Center for Biomedical Inventions, Ryburn Center for Molecular Cardiology, University of Texas Southwestern Medical Center, Dallas, Texas 75235-8573, USA
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11
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Kim K, Fancy DA, Carney D, Kodadek T. Photoinduced Protein Cross-Linking Mediated by Palladium Porphyrins. J Am Chem Soc 1999. [DOI: 10.1021/ja9916355] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyonghee Kim
- Departments of Internal Medicine and Biochemistry Center for Biomedical Inventions University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-8573
| | - David A. Fancy
- Departments of Internal Medicine and Biochemistry Center for Biomedical Inventions University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-8573
| | - Darren Carney
- Departments of Internal Medicine and Biochemistry Center for Biomedical Inventions University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-8573
| | - Thomas Kodadek
- Departments of Internal Medicine and Biochemistry Center for Biomedical Inventions University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-8573
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12
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Fancy DA, Kodadek T. Chemistry for the analysis of protein-protein interactions: rapid and efficient cross-linking triggered by long wavelength light. Proc Natl Acad Sci U S A 1999; 96:6020-4. [PMID: 10339534 PMCID: PMC26828 DOI: 10.1073/pnas.96.11.6020] [Citation(s) in RCA: 385] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical cross-linking is a potentially useful technique for probing the architecture of multiprotein complexes. However, analyses using typical bifunctional cross-linkers often suffer from poor yields, and large-scale modification of nucleophilic side chains can result in artifactual results attributable to structural destabilization. We report here the de novo design and development of a type of protein cross-linking reaction that uses a photogenerated oxidant to mediate rapid and efficient cross-linking of associated proteins. The process involves brief photolysis of tris-bipyridylruthenium(II) dication with visible light in the presence of the electron acceptor ammonium persulfate and the proteins of interest. Very high yields of cross-linked products can be obtained with irradiation times of <1 second. This chemistry obviates many of the problems associated with standard cross-linking reagents.
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Affiliation(s)
- D A Fancy
- Departments of Internal Medicine and Biochemistry, Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-8573, USA
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Abstract
A biomimetic protein cross-linking reaction is described which employs oxidatively-activated manganese and iron porphyrins as the reactive species. A wide range of proteins cross-link under these conditions, but only if they are intimately associated in solution. The reaction is rapid, efficient, and will be useful for the suprastructural analysis of multiprotein complexes.
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Affiliation(s)
- L A Campbell
- Department of Chemistry and Biochemistry, University of Texas, Austin 78712, USA
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14
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Fancy DA, Kodadek T. A critical role for tyrosine residues in His6Ni-mediated protein cross-linking. Biochem Biophys Res Commun 1998; 247:420-6. [PMID: 9642143 DOI: 10.1006/bbrc.1998.8558] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new type of affinity cross-linking strategy has been developed in which His6-tagged proteins can be cross-linked to their binding partners in the presence of unmodified proteins (D. Fancy, K. Melcher, S. A. Johnston, and T. Kodadek, 1996, Chem. Biol. 3, 551-559). The chemistry involves the addition of Ni(II) to the His6 tag, followed by oxidation of the metal with a peracid. It is shown here that, in addition to the His6 tag, a tyrosine residue placed in close proximity to the metal-binding site can strongly stimulate the yield of cross-linked product. This finding has important practical implications in the use of the His6-Ni-based cross-linking reaction for the analysis of multiprotein complexes.
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Affiliation(s)
- D A Fancy
- Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75235-8573, USA
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Levine J, Weickert M, Pagratis M, Etter J, Mathews A, Fattor T, Lippincott J, Apostol I. Identification of a nickel(II) binding site on hemoglobin which confers susceptibility to oxidative deamination and intramolecular cross-linking. J Biol Chem 1998; 273:13037-46. [PMID: 9582340 DOI: 10.1074/jbc.273.21.13037] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Complexation of Ni(II) with native state recombinant hemoglobin is shown to produce NH2-terminal deamination and globin cross-linking in the presence of the oxidant potassium peroxymonosulfate (OxoneTM). Both the oxidative deamination and cross-linking are exclusive to the beta chains. Recombinant hemoglobin mutants have been created to identify protein sequence requirements for these reactions. It was found that His-2 of the beta globin is required for redox active Ni(II) complexation, oxidative deamination, and cross-linking. The oxidative deamination results in the formation of a free carbonyl in place of the NH2-terminal amine of the beta chain. Most cross-linking of the beta globin occurs intramolecularly, forming beta globin dimers. Structural characterization of the beta globin dimers indicates the presence of heterogeneous cross-links within the central hemoglobin cavity between the NH2 terminus of one beta chain and the COOH-terminal region of the other.
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Affiliation(s)
- J Levine
- Somatogen Inc., Boulder, Colorado 80301, USA
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