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Chatterjee S, Kumari S, Rath S, Priyadarshanee M, Das S. Diversity, structure and regulation of microbial metallothionein: metal resistance and possible applications in sequestration of toxic metals. Metallomics 2020; 12:1637-1655. [PMID: 32996528 DOI: 10.1039/d0mt00140f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Metallothioneins (MTs) are a group of cysteine-rich, universal, low molecular weight proteins distributed widely in almost all major taxonomic groups ranging from tiny microbes to highly organized vertebrates. The primary function of this protein is storage, transportation and binding of metals, which enable microorganisms to detoxify heavy metals. In the microbial world, these peptides were first identified in a cyanobacterium Synechococcus as the SmtA protein which exhibits high affinity towards rising level of zinc and cadmium to preserve metal homeostasis in a cell. In yeast, MTs aid in reserving copper and confer protection against copper toxicity by chelating excess copper ions in a cell. Two MTs, CUP1 and Crs5, originating from Saccharomyces cerevisiae predominantly bind to copper though are capable of binding with zinc and cadmium ions. MT superfamily 7 is found in ciliated protozoa which show high affinity towards copper and cadmium. Several tools and techniques, such as western blot, capillary electrophoresis, inductively coupled plasma, atomic emission spectroscopy and high performance liquid chromatography, have been extensively utilized for the detection and quantification of microbial MTs which are utilized for the efficient remediation and sequestration of heavy metals from a contaminated environment.
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Affiliation(s)
- Shreosi Chatterjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769 008, Odisha, India.
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Mehta GD, Ball DA, Eriksson PR, Chereji RV, Clark DJ, McNally JG, Karpova TS. Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast. Mol Cell 2018; 72:875-887.e9. [PMID: 30318444 DOI: 10.1016/j.molcel.2018.09.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/08/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022]
Abstract
It is unknown how the dynamic binding of transcription factors (TFs) is molecularly linked to chromatin remodeling and transcription. Using single-molecule tracking (SMT), we show that the chromatin remodeler RSC speeds up the search process of the TF Ace1p for its response elements (REs) at the CUP1 promoter. We quantified smFISH mRNA data using a gene bursting model and demonstrated that RSC regulates transcription bursts of CUP1 only by modulating TF occupancy but does not affect initiation and elongation rates. We show by SMT that RSC binds to activated promoters transiently, and based on MNase-seq data, that RSC does not affect the nucleosomal occupancy at CUP1. Therefore, transient binding of Ace1p and rapid bursts of transcription at CUP1 may be dependent on short repetitive cycles of nucleosome mobilization. This type of regulation reduces the transcriptional noise and ensures a homogeneous response of the cell population to heavy metal stress.
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Affiliation(s)
- Gunjan D Mehta
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A Ball
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter R Eriksson
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Razvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - James G McNally
- Institute for Soft Matter and Functional Materials, Helmholtz Center Berlin, Berlin 12489, Germany
| | - Tatiana S Karpova
- CCR/LRBGE Optical Microscopy Core, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Gaspar‐Cordeiro A, Marques Caetano S, Amaral C, Rodrigues‐Pousada C, Pimentel C. Ace1 prevents intracellular copper accumulation by regulating Fet3 expression and thereby restricting Aft1 activity. FEBS J 2018; 285:1861-1872. [DOI: 10.1111/febs.14450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/16/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Ana Gaspar‐Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Oeiras Portugal
| | - Soraia Marques Caetano
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Oeiras Portugal
| | - Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Oeiras Portugal
| | | | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Oeiras Portugal
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The copper-dependent ACE1 transcription factor activates the transcription of the mco1 gene from the basidiomycete Phanerochaete chrysosporium. Microbiology (Reading) 2008; 154:491-499. [DOI: 10.1099/mic.0.2007/013128-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Affiliation(s)
- Dennis R Winge
- University of Utah Health Sciences Center, Salt Lake City, Utah 84132, USA
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Gross C, Kelleher M, Iyer VR, Brown PO, Winge DR. Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J Biol Chem 2000; 275:32310-6. [PMID: 10922376 DOI: 10.1074/jbc.m005946200] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In Saccharomyces cerevisiae, copper ions regulate gene expression through the two transcriptional activators, Ace1 and Mac1. Ace1 mediates copper-induced gene expression in cells exposed to stressful levels of copper salts, whereas Mac1 activates a subset of genes under copper-deficient conditions. DNA microarray hybridization experiments revealed a limited set of yeast genes differentially expressed under growth conditions of excess copper or copper deficiency. Mac1 activates the expression of six S. cerevisiae genes, including CTR1, CTR3, FRE1, FRE7, YFR055w, and YJL217w. Two of the last three newly identified Mac1 target genes have no known function; the third, YFR055w, is homologous to cystathionine gamma-lyase encoded by CYS3. Several genes that are differentially expressed in cells containing a constitutively active Mac1, designated Mac1(up1), are not direct targets of Mac1. Induction or repression of these genes is likely a secondary effect of cells because of constitutive Mac1 activity. Elevated copper levels induced the expression of the metallothioneins CUP1 and CRS5 and two genes, FET3 and FTR1, in the iron uptake system. Copper-induced FET3 and FTR1 expression arises from an indirect copper effect on cellular iron pools.
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Affiliation(s)
- C Gross
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry, Salt Lake City, Utah 84132, USA
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8
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Winge DR. Copper-regulatory domain involved in gene expression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 448:237-46. [PMID: 10079831 DOI: 10.1007/978-1-4615-4859-1_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- D R Winge
- University of Utah Health Sciences Center, Department of Medicine, Salt Lake City 84132, USA
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9
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Joshi A, Serpe M, Kosman DJ. Evidence for (Mac1p)2.DNA ternary complex formation in Mac1p-dependent transactivation at the CTR1 promoter. J Biol Chem 1999; 274:218-26. [PMID: 9867833 DOI: 10.1074/jbc.274.1.218] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mac1 protein in Saccharomyces cerevisiae is required for the expression CTR1 and FRE1, which, respectively, encode the copper permease and metal reductase that participate in copper uptake. Mac1p binds to a core GCTC sequence present as a repeated unit in the promoters of both genes. We show here that Mac1p DNA binding required an intact N-terminal protein domain that includes a likely zinc finger motif. This binding was enhanced by the presence of a TATTT sequence immediately 5' to the core GCTC, in contrast to a TTTTT one. This increased binding was demonstrated clearly in vitro in electrophoretic mobility shift assays that showed Mac1p.DNA complex formation to a single TATTTGCTC element but not to a TTTTTGCTC one. Furthermore, the fraction of Mac1p in a ternary (Mac1p)2.DNA complex in comparison to a binary Mac1p.DNA complex increased when the DNA included two TATTTGCTC elements. A similar increase in ternary complex formation was demonstrated upon homologous mutation of the FRE1 Mac1p-dependent promoter element. The in vivo importance of this ternary complex formation at the CTR1 promoter was indicated by the stronger trans-activity of this promoter mutated to contain two TATTT elements and the attenuated activity of a mutant promoter containing two TTTTT elements that in vitro supported only a weak ternary complex signal in the shift assay. The stronger binding to TATTT appeared due to a more favorable protein contact with adenine in comparison to thymine at this position. An in vivo two-hybrid analysis demonstrated a Mac1p-Mac1p protein-protein interaction. This Mac1p-Mac1p interaction may promote (Mac1p)2.DNA ternary complex formation at Mac1p-responsive upstream activating sequences.
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Affiliation(s)
- A Joshi
- Department of Biochemistry, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214, USA
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Jensen LT, Posewitz MC, Srinivasan C, Winge DR. Mapping of the DNA binding domain of the copper-responsive transcription factor Mac1 from Saccharomyces cerevisiae. J Biol Chem 1998; 273:23805-11. [PMID: 9726991 DOI: 10.1074/jbc.273.37.23805] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mac1 from Saccharomyces cerevisiae activates transcription of genes, including CTR1 in copper-deficient cells. N-terminal fusions of Mac1 with the herpes simplex VP16 activation domain were used to show that residues 1-159 in Mac1 constitute the minimal DNA binding domain. Mac1-(1-159) purified from Escherichia coli contains two bound Zn(II) ions. Electrophoretic mobility shift assays showed direct and specific binding by Mac1-(1-159) to a DNA duplex containing the copper-responsive element TTTGCTCA. The DNA binding affinity of Mac1-(1-159) for a duplex containing a single promoter element or an inverted repeat was 5 nM for the 1:1 complex. The N-terminal 40-residue segment of Mac1 is homologous to the DNA binding zinc module found in the copper-activated transcription factors Ace1 and Amt1. A MAC1 mutation yielding a Cys11 --> Tyr substitution at the first candidate zinc ligand position relative to Ace1 resulted in a loss of in vivo function. Two TTTGCTCA promoter elements are necessary for efficient Mac1-mediated transcriptional activation. The elements appear to function synergistically. Increasing the number of elements yields more than additive enhancements in CTR1 expression.
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Affiliation(s)
- L T Jensen
- Departments of Medicine and Biochemistry, University of Utah Health Science Center, Salt Lake City, Utah 84132, USA
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Turner RB, Smith DL, Zawrotny ME, Summers MF, Posewitz MC, Winge DR. Solution structure of a zinc domain conserved in yeast copper-regulated transcription factors. NATURE STRUCTURAL BIOLOGY 1998; 5:551-5. [PMID: 9665167 DOI: 10.1038/805] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The three dimensional structure of the N-terminal domain (residues 1-42) of the copper-responsive transcription factor Amtl from Candida glabrata has been determined by two-dimensional 1H-correlated nuclear magnetic resonance (NMR) methods. The domain contains an array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) that is conserved among a family of Cu-responsive transcription factors. The structure is unlike those of previously characterized zinc finger motifs, and consists of a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues at positions 16, 18 and 19 form a basic patch that may be important for DNA binding.
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Affiliation(s)
- R B Turner
- Howard HUghes Medical Institute, University of Maryland Baltimore County 21250, USA
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Winge DR. Copper-regulatory domain involved in gene expression. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 58:165-95. [PMID: 9308366 DOI: 10.1016/s0079-6603(08)60036-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Copper ion homeostasis in yeast is maintained through regulated expression of genes involved in copper ion uptake, Cu(I) sequestration, and defense against reactive oxygen intermediates. Positive and negative copper ion regulation is observed, and both effects are mediated by Cu(I)-sensing transcription factors. The mechanism of Cu(I) regulation is distinct for transcriptional activation versus transcriptional repression. Cu(I) activation of gene expression in S. cerevisiae and C. glabrata occurs through Cu-regulated DNA binding. The activation process involves Cu(I) cluster formation within the regulatory domain in Ace1 and Amt1. Cu(I) binding stabilizes a specific conformation capable of high-affinity interaction with specific DNA promoter sequences. Cu(I)-activated transcription factors are modular proteins in which the DNA-binding domain is distinct from the domain that mediates transcriptional activation. The all-or-nothing formation of the polycopper cluster permits a graded response of the cell to environmental copper. Cu(I) triggering may involve a metal exchange reaction converting Ace1 from a Zn(II)-specific conformer to a clustered Cu(I) conformer. The Cu(I) regulatory domain occurs in transcription factors from S. cerevisiae and C. glabrata. Sequence homologs are also known in Y. lipolytica and S. pombe, although no functional information is available for these candidate regulatory molecules. The presence of the Cu(I) regulatory domain in four distinct yeast strains suggests that this Cu-responsive domain may occur in other eukaryotes. Cu-mediated repression of gene expression in S. cerevisiae occurs through Cu(I) regulation of Mac1. Cu(I) binding to Mac1 appears to inhibit the transactivation domain. The Cu(I) specificity of this repression is likely to arise from formation of a polycopper thiolate cluster.
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Affiliation(s)
- D R Winge
- Department of Medicine, University of Utah Health Sciences Center, Salt Lake City 84132, USA
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Johnson JA, Dixon WJ, Tulliusa TD. Affinity of CUP2, a copper-dependent transcription factor, for DNA sequences upstream of the yeast metallothionein gene. Inorganica Chim Acta 1996. [DOI: 10.1016/0020-1693(95)04872-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Metals play a dual role in biological systems, serving as essential co-factors for a wide range of biochemical reactions yet these same metals may be extremely toxic to cells. To cope with the stress of increases in environmental metal concentrations, eukaryotic cells have developed sophisticated toxic metal sensing proteins which respond to elevations in metal concentrations. This signal is transmitted to stimulate the cellular transcriptional machinery to activate expression of metal detoxification and homeostasis genes. This review summarizes our current understanding of the biochemical and genetic mechanisms which underlie cellular responses to toxic metals via metalloregulatory transcription factors.
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Affiliation(s)
- Z Zhu
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor 48109-0606, USA
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Thorvaldsen JL, Mehra RK, Yu W, Sewell AK, Winge DR. Analysis of copper-induced metallothionein expression using autonomously replicating plasmids in Candida glabrata. Yeast 1995; 11:1501-11. [PMID: 8750238 DOI: 10.1002/yea.320111505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Candida glabrata strains and a stable plasmid were developed that were suitable for analysis of copper-inducible expression from promoters of the three metallothionein (MT) genes. The two homologous MTII genes, MTIIa and MTIIb, encode the same polypeptide but are differentially induced by copper salts. MTIIb is more highly inducible than MTIIa and cells harboring a single MTIIb exhibit a greater resistance to copper salts compared to cells harboring a single MTIIa. The differential copper inducibility was mapped to sequences between -03 and -292 upstream of the MT coding sequences. Expression of MTI is highly Cu-regulated, but this MT gene confers much less resistance than MTII genes.
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Affiliation(s)
- J L Thorvaldsen
- University of Utah Health Sciences Center, Salt Lake City 84132, USA
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Dobi A, Dameron CT, Hu S, Hamer D, Winge DR. Distinct regions of Cu(I).ACE1 contact two spatially resolved DNA major groove sites. J Biol Chem 1995; 270:10171-8. [PMID: 7730320 DOI: 10.1074/jbc.270.17.10171] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The interaction between the Cu(I).ACE1 (CuACE1) transcription factor and its DNA binding site in the yeast metallothionein gene was studied by systematically altering the DNA sequence through base substitution, modification, and deletions as well as by altering the protein structure through chemical modification. We show here that CuACE1 is comprised of two distinct domains that contact DNA through minor groove interactions located between two major groove interaction sites. The minor groove interactions are shown to be critical for formation of a stable CuACE1.DNA complex. The NH2-terminal segment of ACE1 is shown to contact the 5'-most distal major groove site.
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Affiliation(s)
- A Dobi
- Laboratory of Biochemistry, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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Culotta VC, Howard WR, Liu XF. CRS5 encodes a metallothionein-like protein in Saccharomyces cerevisiae. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)47246-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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18
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Khachigian L, Chesterman C. Synthetic peptides representing the alternatively spliced exon of the platelet-derived growth factor A-chain modulate mitogenesis stimulated by normal human serum and several growth factors. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42542-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Gralla EB, Kosman DJ. Molecular genetics of superoxide dismutases in yeasts and related fungi. ADVANCES IN GENETICS 1992; 30:251-319. [PMID: 1456112 DOI: 10.1016/s0065-2660(08)60322-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- E B Gralla
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
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Dixon WJ, Hayes JJ, Levin JR, Weidner MF, Dombroski BA, Tullius TD. Hydroxyl radical footprinting. Methods Enzymol 1991; 208:380-413. [PMID: 1664026 DOI: 10.1016/0076-6879(91)08021-9] [Citation(s) in RCA: 176] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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