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    Ribozyme-catalyzed dipeptide synthesis in monovalent metal ions alone

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    Authors
    Sun, Lele
    Cui, Zhiyong
    Li, Chunfang
    Huang, Shufang
    Zhang, Biliang
    UMass Chan Affiliations
    Program in Molecular Medicine
    Department of Molecular Genetics and Microbiology
    Graduate School of Biomedical Sciences
    Document Type
    Journal Article
    Publication Date
    2007-03-03
    Keywords
    Catalysis; Cations, Divalent; Cations, Monovalent; Dipeptides; Hydrogen-Ion Concentration; Metals; Peptide Biosynthesis, Nucleic Acid-Independent; RNA, Catalytic
    Life Sciences
    Medicine and Health Sciences
    
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    Link to Full Text
    http://dx.doi.org/10.1021/bi061995m
    Abstract
    Previously we have identified a highly active ribozyme (R180, cis ribozyme) that can catalyze dipeptide synthesis using N-biotinylcaproyl-aminoacyl-adenylate anhydride (Bio-aa-5'-AMP) as its substrate. In this work, we re-engineered the cis R180 ribozyme into a 158-nt trans ribozyme (TR158) and designed a new substrate (5'-Phe-linker-20-mer). First, the metal ion requirements were examined and compared between the two ribozymes. Both R180 and TR158 ribozymes were active in Mg2+ and Ca2+ but inert with Zn2+, Cu2+, Mn2+, and Co2+. It is intriguing that both ribozymes were highly active in Li+, Na+, or K+ alone but showed very low activity with NH4+. The two ribozymes showed similar linear concentration dependence on Li+ and K+, while they displayed different dependency behavior on Mg2+. Moreover, by using the trans system, the detailed kinetic studies and pH dependent experiments were performed in either 10 mM Mg2+ or 1.0 M Li+. Analysis of kcat and Km values obtained at different pHs (6.0 to 9.0) indicated that it is the catalytic activity of the ribozyme but not the substrate binding affinity that changes significantly with pH. The slopes of the linear parts of the pH-rate plots were close to 1.0 in both Mg2+- and Li+-mediated reactions, suggesting that one proton transfer is involved in the rate-limiting step of catalysis. Overall, our results suggest that Mg2+ and Li+ function similarly in the ribozyme-catalyzed dipeptide synthesis.
    Source
    Biochemistry. 2007 Mar 27;46(12):3714-23. Epub 2007 Mar 2. Link to article on publisher's site
    DOI
    10.1021/bi061995m
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/32656
    PubMed ID
    17330961
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1021/bi061995m
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