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Wu Z, Duan H, Cheng Y, Guo D, Peng L, Hu Y, Hu J, Luo T. A novel ligand swing-mediated active site coordination change of human apurinic/apyrimidinic endonuclease 1: A potential cytotoxic mechanism of nickel ion in the base excision repair. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Aboelnga MM, Wetmore SD. Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme. J Am Chem Soc 2019; 141:8646-8656. [PMID: 31046259 DOI: 10.1021/jacs.9b03986] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mohamed M. Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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3
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Abstract
Before a deleterious DNA lesion can be replaced with its undamaged counterpart, the lesion must first be removed from the genome. This process of removing and replacing DNA lesions is accomplished by the careful coordination of several protein factors during DNA repair. One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). APE1 preforms AP site incision with surgical precision and skill, by sculpting the DNA to place the cleavage site in an optimal position for nucleophilic attack within its compact protein active site. APE1, however, has demonstrated broad surgical expertise, and applies its DNA cleavage activity to a wide variety of DNA and RNA substrates. Here, we discuss what is known and unknown about APE1 cleavage mechanisms, focusing on structural and mechanistic considerations. Importantly, disruptions in the biological functions associated with APE1 are linked to numerous human maladies, including cancer and neurodegenerative diseases. The continued elucidation of APE1 mechanisms is required for rational drug design towards novel and strategic ways to target its associated repair pathways.
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Affiliation(s)
- Amy M Whitaker
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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4
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Batebi H, Dragelj J, Imhof P. Role of AP-endonuclease (Ape1) active site residues in stabilization of the reactant enzyme-DNA complex. Proteins 2018; 86:439-453. [PMID: 29344998 DOI: 10.1002/prot.25460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 11/11/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1 (Ape1) is an important metal-dependent enzyme in the base excision repair mechanism, responsible for the backbone cleavage of abasic DNA through a phosphate hydrolysis reaction. Molecular dynamics simulations of Ape1 complexed to its substrate DNA performed for models containing 1 or 2 Mg2+ -ions as cofactor located at different positions show a complex with 1 metal ion bound on the leaving group site of the scissile phosphate to be the most likely reaction-competent conformation. Active-site residue His309 is found to be protonated based on pKa calculations and the higher conformational stability of the Ape1-DNA substrate complex compared to scenarios with neutral His309. Simulations of the D210N mutant further support the prevalence of protonated His309 and strongly suggest Asp210 as the general base for proton acceptance by a nucleophilic water molecule.
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Affiliation(s)
- Hossein Batebi
- Department of Physics, Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany
| | - Jovan Dragelj
- Department of Biology, Chemistry, and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36A, Berlin, 14195, Germany
| | - Petra Imhof
- Department of Physics, Institute of Theoretical Physics, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany
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5
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Batebi H, Imhof P. Phosphodiester hydrolysis computed for cluster models of enzymatic active sites. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-2020-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Capturing snapshots of APE1 processing DNA damage. Nat Struct Mol Biol 2015; 22:924-31. [PMID: 26458045 PMCID: PMC4654669 DOI: 10.1038/nsmb.3105] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/06/2015] [Indexed: 12/22/2022]
Abstract
DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. We report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylated CpG dinucleotides. These structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. These snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.
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Braun W, Schein CH. Membrane interaction and functional plasticity of inositol polyphosphate 5-phosphatases. Structure 2015; 22:664-6. [PMID: 24807076 DOI: 10.1016/j.str.2014.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In this issue of Structure, Trésaugues and colleagues determined the interaction of membrane-bound phosphoinositides with three clinically significant human inositol polyphosphate 5-phosphatases (I5Ps). A comparison to the structures determined with soluble substrates revealed differences in the binding mode and suggested how the I5Ps and apurinic endonuclease (APE1) activities evolved from the same metal-binding active center.
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Affiliation(s)
- Werner Braun
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Catherine H Schein
- Foundation for Applied Molecular Evolution, 720 SW 2nd Avenue Suite 201, Gainesville, FL 32601, USA
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Kaur G, Cholia RP, Mantha AK, Kumar R. DNA repair and redox activities and inhibitors of apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1): a comparative analysis and their scope and limitations toward anticancer drug development. J Med Chem 2014; 57:10241-56. [PMID: 25280182 DOI: 10.1021/jm500865u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional enzyme involved in DNA repair and activation of transcription factors through its redox function. The evolutionarily conserved C- and N-termini are involved in these functions independently. It is also reported that the activity of APE1/Ref-1 abruptly increases several-fold in various human cancers. The control over the outcomes of these two functions is emerging as a new strategy to combine enhanced DNA damage and chemotherapy in order to tackle the major hurdle of increased cancer cell growth and proliferation. Studies have targeted these two domains individually for the design and development of inhibitors for APE1/Ref-1. Here, we have made, for the first time, an attempt at a comparative analysis of APE1/Ref-1 inhibitors that target both DNA repair and redox activities simultaneously. We further discuss their scope and limitations with respect to the development of potential anticancer agents.
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Affiliation(s)
- Gagandeep Kaur
- Laboratory for Drug Design and Synthesis, Centre for Chemical and Pharmaceutical Sciences, School of Basic and Applied Sciences, Central University of Punjab , Bathinda, 151001, Punjab, India
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He H, Chen Q, Georgiadis MM. High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I. Biochemistry 2014; 53:6520-9. [PMID: 25251148 PMCID: PMC4204877 DOI: 10.1021/bi500676p] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Apurinic/apyrimidinic
endonuclease I (APE1) is an essential base
excision repair enzyme that catalyzes a Mg2+-dependent
reaction in which the phosphodiester backbone is cleaved 5′
of an abasic site in duplex DNA. This reaction has been proposed to
involve either one or two metal ions bound to the active site. In
the present study, we report crystal structures of Mg2+, Mn2+, and apo-APE1 determined at 1.4, 2.2, and 1.65
Å, respectively, representing two of the highest resolution structures
yet reported for APE1. In our structures, a single well-ordered Mn2+ ion was observed coordinated by D70 and E96; the Mg2+ site exhibited disorder modeled as two closely positioned
sites coordinated by D70 and E96 or E96 alone. Direct metal binding
analysis of wild-type, D70A, and E96A APE1, as assessed by differential
scanning fluorimetry, indicated a role for D70 and E96 in binding
of Mg2+ or Mn2+ to APE1. Consistent with the
disorder exhibited by Mg2+ bound to the active site, two
different conformations of E96 were observed coordinated to Mg2+. A third conformation for E96 in the apo structure is similar
to that observed in the APE1–DNA–Mg2+ complex
structure. Thus, binding of Mg2+ in three different positions
within the active site of APE1 in these crystal structures corresponds
directly with three different conformations of E96. Taken together,
our results are consistent with the initial capture of metal by D70
and E96 and repositioning of Mg2+ facilitated by the structural
plasticity of E96 in the active site.
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Affiliation(s)
- Hongzhen He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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Trésaugues L, Silvander C, Flodin S, Welin M, Nyman T, Gräslund S, Hammarström M, Berglund H, Nordlund P. Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases. Structure 2014; 22:744-55. [PMID: 24704254 DOI: 10.1016/j.str.2014.01.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 11/15/2022]
Abstract
SHIP2, OCRL, and INPP5B belong to inositol polyphosphate 5-phophatase subfamilies involved in insulin regulation and Lowes syndrome. The structural basis for membrane recognition, substrate specificity, and regulation of inositol polyphosphate 5-phophatases is still poorly understood. We determined the crystal structures of human SHIP2, OCRL, and INPP5B, the latter in complex with phosphoinositide substrate analogs, which revealed a membrane interaction patch likely to assist in sequestering substrates from the lipid bilayer. Residues recognizing the 1-phosphate of the substrates are highly conserved among human family members, suggesting similar substrate binding modes. However, 3- and 4-phosphate recognition varies and determines individual substrate specificity profiles. The high conservation of the environment of the scissile 5-phosphate suggests a common reaction geometry for all members of the human 5-phosphatase family.
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Affiliation(s)
- Lionel Trésaugues
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Camilla Silvander
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden.
| | - Susanne Flodin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Welin
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Tomas Nyman
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Martin Hammarström
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Helena Berglund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Pär Nordlund
- Structural Genomics Consortium, Karolinska Institutet, 17177 Stockholm, Sweden; Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden; Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, 637551, Singapore.
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11
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Abstract
SIGNIFICANCE Human apurinic/apyrimidinic endonuclease 1 (APE1, also known as REF-1) was isolated based on its ability to cleave at AP sites in DNA or activate the DNA binding activity of certain transcription factors. We review herein topics related to this multi-functional DNA repair and stress-response protein. RECENT ADVANCES APE1 displays homology to Escherichia coli exonuclease III and is a member of the divalent metal-dependent α/β fold-containing phosphoesterase superfamily of enzymes. APE1 has acquired distinct active site and loop elements that dictate substrate selectivity, and a unique N-terminus which at minimum imparts nuclear targeting and interaction specificity. Additional activities ascribed to APE1 include 3'-5' exonuclease, 3'-repair diesterase, nucleotide incision repair, damaged or site-specific RNA cleavage, and multiple transcription regulatory roles. CRITICAL ISSUES APE1 is essential for mouse embryogenesis and contributes to cell viability in a genetic background-dependent manner. Haploinsufficient APE1(+/-) mice exhibit reduced survival, increased cancer formation, and cellular/tissue hyper-sensitivity to oxidative stress, supporting the notion that impaired APE1 function associates with disease susceptibility. Although abnormal APE1 expression/localization has been seen in cancer and neuropathologies, and impaired-function variants have been described, a causal link between an APE1 defect and human disease remains elusive. FUTURE DIRECTIONS Ongoing efforts aim at delineating the biological role(s) of the different APE1 activities, as well as the regulatory mechanisms for its intra-cellular distribution and participation in diverse molecular pathways. The determination of whether APE1 defects contribute to human disease, particularly pathologies that involve oxidative stress, and whether APE1 small-molecule regulators have clinical utility, is central to future investigations.
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Affiliation(s)
- Mengxia Li
- Intramural Research Program, Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health , Baltimore, Maryland
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12
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Manvilla BA, Pozharski E, Toth EA, Drohat AC. Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2555-62. [PMID: 24311596 PMCID: PMC3852660 DOI: 10.1107/s0907444913027042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 10/01/2013] [Indexed: 11/10/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) mediates the repair of abasic sites and other DNA lesions and is essential for base-excision repair and strand-break repair pathways. APE1 hydrolyzes the phosphodiester bond at abasic sites, producing 5'-deoxyribose phosphate and the 3'-OH primer needed for repair synthesis. It also has additional repair activities, including the removal of 3'-blocking groups. APE1 is a powerful enzyme that absolutely requires Mg2+, but the stoichiometry and catalytic function of the divalent cation remain unresolved for APE1 and for other enzymes in the DNase I superfamily. Previously reported structures of DNA-free APE1 contained either Sm3+ or Pb2+ in the active site. However, these are poor surrogates for Mg2+ because Sm3+ is not a cofactor and Pb2+ inhibits APE1, and their coordination geometry is expected to differ from that of Mg2+. A crystal structure of human APE1 was solved at 1.92 Å resolution with a single Mg2+ ion in the active site. The structure reveals ideal octahedral coordination of Mg2+ via two carboxylate groups and four water molecules. One residue that coordinates Mg2+ directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily. This structure, together with a recent structure of the enzyme-product complex, inform on the stoichiometry and the role of Mg2+ in APE1-catalyzed reactions.
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Affiliation(s)
- Brittney A. Manvilla
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Edwin Pozharski
- Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, USA
| | - Eric A. Toth
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
| | - Alexander C. Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 North Greene Street, Baltimore, MD 21201, USA
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Tsutakawa SE, Shin DS, Mol CD, Izumi T, Arvai AS, Mantha AK, Szczesny B, Ivanov IN, Hosfield DJ, Maiti B, Pique ME, Frankel KA, Hitomi K, Cunningham RP, Mitra S, Tainer JA. Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem 2013; 288:8445-8455. [PMID: 23355472 DOI: 10.1074/jbc.m112.422774] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Non-coding apurinic/apyrimidinic (AP) sites in DNA form spontaneously and as DNA base excision repair intermediates are the most common toxic and mutagenic in vivo DNA lesion. For repair, AP sites must be processed by 5' AP endonucleases in initial stages of base repair. Human APE1 and bacterial Nfo represent the two conserved 5' AP endonuclease families in the biosphere; they both recognize AP sites and incise the phosphodiester backbone 5' to the lesion, yet they lack similar structures and metal ion requirements. Here, we determined and analyzed crystal structures of a 2.4 Å resolution APE1-DNA product complex with Mg(2+) and a 0.92 Å Nfo with three metal ions. Structural and biochemical comparisons of these two evolutionarily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally similar to Nfo active site components, as further tested and supported by computational analyses. We observe a magnesium-water cluster in the APE1 active site, with only Glu-96 forming the direct protein coordination to the Mg(2+). Despite differences in structure and metal requirements of APE1 and Nfo, comparison of their active site structures surprisingly reveals strong geometric conservation of the catalytic reaction, with APE1 catalytic side chains positioned analogously to Nfo metal positions, suggesting surprising functional equivalence between Nfo metal ions and APE1 residues. The finding that APE1 residues are positioned to substitute for Nfo metal ions is supported by the impact of mutations on activity. Collectively, the results illuminate the activities of residues, metal ions, and active site features for abasic site endonucleases.
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Affiliation(s)
| | - David S Shin
- Scripps Research Institute, La Jolla, California 92037
| | | | - Tadahide Izumi
- University of Kentucky, Lexington, Kentucky 40536; University of Texas Medical Branch, Galveston, Texas 77555
| | | | - Anil K Mantha
- University of Texas Medical Branch, Galveston, Texas 77555
| | | | | | | | | | - Mike E Pique
- Scripps Research Institute, La Jolla, California 92037
| | | | - Kenichi Hitomi
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037; Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | | | - Sankar Mitra
- University of Texas Medical Branch, Galveston, Texas 77555
| | - John A Tainer
- Lawrence Berkeley National Laboratory, Berkeley, California 94720; Scripps Research Institute, La Jolla, California 92037.
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