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  • tRNA  (2)
  • Follicle-stimulating hormone  (1)
  • Phage peptide display library  (1)
  • 1
    ISSN: 1572-8773
    Keywords: tRNA ; tDNA ; anticodon domain ; transition metal ion effects ; spectroscopic characterization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Biologically active DNA analogs of tRNAPhe (tDNAPhe) were used to investigate metal ion interaction with tRNA-like structures lacking the 2′OH. Binding of Mg2+ to the 76 oligonucleotide tDNAPhe, monitored by circular dichroism spectroscopy, increased base stacking and thus the conformational stability of the molecule. Mg2+ binding was dependent on a d(m5C) in the anticodon region. In contrast to Mg2+, Cd2+ decreased base stacking interactions, thereby destabilizing the molecule. Since alterations in the anticodon region contributed to most of the spectral changes observed, detailed studies were conducted with anticodon hairpin heptadecamers (tDNAAC Phe). The conformation of tDNAAC Phe-d(m5C) in the presence of 1 mm Cd2+, Co2+, Cr2+, Cu2+, Ni2+, Pb2+, VO2+ or Zn2+ differed significantly from that of the biologically active structure resulting from interaction with Mg2+, Mn2+ or Ca2+. Nanomolar concentrations of the transition metals were sufficient to denature the tDNAAC Phe-d(m5C) structure without catalyzing cleavage of the oligonucleotide. In the absence of Mg2+ and at [Cd2+] to [tDNAAc Phe-d(m5C)] ratios of approximately 0.2–1.0, tDNAAC Phe-d(m5C40) formed a stable conformation with one Cd2+ bound with a K d = 3.7 × 10-7. In contrast to Mg2+, Cd2+ altered the DNA analogs without discriminating between modified and unmodified tDNAAC Phe. This ability of transition metals to disrupt higher order DNA structures, and possibly RNA, at μM concentrations, in vitro, demonstrates that these structures are potential targets in chronic metal exposure, in vivo.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-4943
    Keywords: Follicle-stimulating hormone ; FSH peptide ; NMR ; peptide structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The receptor binding surface of human follicle-stimulating hormone (hFSH) is mimicked by synthetic peptides corresponding to the hFSH-β chain amino acid sequences 33–53 [Santa-Coloma, T. A., Dattatreyamurty, D., and Reichert, L. E., Jr. (1990),Biochemistry 29, 1194–1200], 81–95 [Santa-Coloma, T. A., and Reichert, L. E., Jr. (1990),J. Biol. Chem. 265, 5037–5042], and the combined sequence (33–53)–(81–95) [Santa-Coloma, T. A., Crabb, J. W., and Reichert, L. E., Jr. (1991),Mol. Cell. Endocrinol. 78, 197–204]. These peptides have been shown to inhibit binding of hFSH to its receptor. Circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy were used to determine the structure of the first peptide in this series, the 21 amino acid peptide hFSH-β-(33–53), H2N-YTRDLVYKDPARPKIQKTCTF-COOH. Analysis of CD data indicated the presence of approximately equal amounts of antiparallel β-pleated sheet, turns including a β-turn, “other” structures, and a small amount ofa-helix. The major characteristics of the structure were found to be relatively stable at acidicpH and the predominant effect of increased solvent polarity was a small increase ina-helical content. One- and two-dimensional NMR techniques were used to obtain full proton and carbon signal assignments in aqueous solution atpH 3.1. Analysis of NMR results confirmed the presence of the structural features revealed by CD analysis and provided a detailed picture of the secondary structural elements and global folding pattern in hFSH-β-(33–53). These features included an antiparallel β-sheet (residues 38–51 and 46–48), turns within residues 41–46, and 50–52 (a β-turn) and a small N-terminal helical region comprised of amino acids 34–36. One of the turns is facilitated by prolines 42 and 45. Proline-45 was constrained to thetrans conformation, whereas proline-42 favored thetrans conformer (∼70%) over thecis (∼30%). Two resonances were observed for the single alanine residue (A-43) sequentially proximal to P-42, but the rest of the structure was minimally affected by the isomerization at proline-42. The major population of molecules, containingtrans-42 andtrans-45 prolines, presented 120 NOEs. Distance geometry calculations with 140 distance constraints and energy minimization refinements were used to derive a moderately well-defined model of the peptide's structure. The hFSH-β-(33–53) structure has a highly polar surface composed of six cationic amino acid (arginie-35, lysine-40, arginine-44, lysine-46, glutamine-48, and lysine-49) and two anionic residues (aspartate-36 and aspartic acid-41). A hydrophobic region in the structure is composed of residues in the antiparallel β-sheet and β-turn which fold to produce a distorted “hairpin.” The structure of this domain, together with the protruding and positively charged region in the vicinity of residues 42–45, may mimic the surface of hFSH that binds to the receptor.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1573-4943
    Keywords: Phage peptide display library ; peptide–RNA binding ; tRNA ; U1 snRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNAPhe (tRNA AC Phe ) were selected from a random-sequence, 15-amino acid bacteriophage display library. An experimental system, including an affinity selection method, was designed to identify primary RNA-binding peptide sequences without bias to known amino acid sequences and without incorporating nonspecific binding of the anionic RNA backbone. Nitrocellulose binding assays were used to evaluate the binding of RNA by peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bacteriophage were determined from the foreign insert DNA sequences, and peptides corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs (K d ≍ 0.1–5.0 μM) were analyzed successfully using fluorescence and circular dichroism spectroscopies. These methodologies demonstrate the feasibility of rapidly identifying, isolating, and initiating the analyses of small peptides that bind to RNAs in an effort to define better the chemistry, structure, and function of protein–RNA complexes.
    Type of Medium: Electronic Resource
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