An alpha-helical peptidomimetic inhibitor of the HIV-1 Rev-RRE interaction

The interaction between the HIV-1 Rev protein and the Rev-Responsive Element (RRE) RNA is an attractive target for anti-viral therapy. We have designed alpha-helical peptidomimetics of Rev-like peptides using side chain-side chain macrolactam formation between positions i and i+4. One peptidomimetic having an appropriate location, orientation, and length of the macrolactam exhibited both significant helical character and specific RRE binding. This molecule displays 2-fold greater RNA specificity than the wild-type Rev peptide and more than 20-fold greater specificity than an uncyclized control peptide. Thus, specific, high affinity recognition of the RRE is feasible utilizing a small, relatively rigid peptidomimetic scaffold.     

Formation of hydrogen-bridged cytosine dimers on Cu(110)

Cytosine was adsorbed onto a Cu(110) surface under UHV conditions. Annealing to 370 K resulted in the formation of a (6 x 6)gg low energy electron diffraction (LEED) pattern, even at submonolayer coverages. Examination of this structure with scanning tunneling microscopy (STM) revealed islands of zigzag chains at low coverages and large ordered domains at monolayer saturation. Further annealing to 480 K initiated a phase transition to a (6 x 2)gg structure observed both by LEED and STM. High resolution electron energy loss spectroscopy spectra for both overlayer structures exhibited mainly in-plane modes suggesting upright/tilted species on the surface. Based on the experimental data and supported by density functional theory calculations, a model is proposed for the (6 x 2)gg structure, which involves the formation of deprotonated hydrogen bridge-bonded cytosine dimers, adsorbed through the oxygen atoms.     

Hyperfine interactions in MgF2:Fe2+ and ZnF2:Fe2+ by Mössbauer spectroscopy

Measurement of the magnetic hyperfine interaction in paramagnetic Fe²⁺ in ZnF₂ and MgF₂ by Mössbauer spectroscopy is reported. The results, ?275 ± 3 kOe and ?270 ± 3 kOe for ZnF₂:Fe²⁺ and MgF₂:Fe²⁺ respectively are compared with a previous analysis of hyperfine interactions in the rutile fluorides.     

Encodamers: unnatural peptide oligomers encoded in RNA

Conventional display libraries are generally limited to the 20 naturally occurring amino acids. Here, we demonstrate that novel unnatural amide-linked oligomers can be constructed and encoded in an attached RNA for the purpose of mRNA display library design. To do this, we translated templates of various lengths in a protein synthesis system modified to promote sense codon suppression. Unnatural residues were escorted to the ribosome as chemically acylated tRNAs added to the translation mixture. Our experiments reveal that unnatural peptide oligomers ("encodamers") consisting of an N-substituted amino acid are readily generated as mRNA-peptide fusions with excellent stepwise efficiency. The N-substituted polyamides have strikingly improved proteolytic stability relative to their naturally encoded counterparts. Overall, our work indicates that the ribosome can be used as a synthesis platform to generate encoded combinatorial chemistry outside the universal genetic code.     

Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions

Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation between the computed energies and observed frequencies of the interactions. In general, interactions with charged side chains show the most favorable energies. An Asp/Glu-G interaction may be especially favorable for recognition of unpaired guanines in RNAs. Asn and Ser/Thr/Tyr side chains are calculated to make iso-energetic interactions to the Hoogsteen face of adenine, but Asn-A interactions are much more common with DNA than RNA, and Ser/Thr/Tyr-A interactions are more common with RNA than DNA. Examination of the known interactions suggests that Ser/Thr/Tyr may be accommodated in a wider variety of protein contexts at RNA-protein interfaces. With these calculated intrinsic affinities, it should be possible to better assess the contributions of bidentate hydrogen-bonding interactions to RNA- and DNA-binding specificity.     

Characterization of partially transesterified poly(beta-hydroxyalkanoate)s using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was used for the characterization of a partially transesterified poly(beta-hydroxyalkanoate), PHA, polymer produced by the bacterial strain Alcaligenes eutrophus using saponified vegetable oils as the sole carbon sources. The transesterification was carried out separately under acidic and basic conditions to obtain PHA oligomers weighing less than 10 kDa. The intact oligomers were detected in their cationized [M + Na](+) and [M + K](+) forms by MALDI-TOFMS. A composition analysis, using the MALDI-TOF spectra, indicate that the oligomers obtained via acid catalysis were terminated with a methyl 3-hydroxybutyrate end group, and those obtained by base catalysis had a methyl crotonate (olefinic) termination. In addition to HB (hydroxy butyrate), the oligomers were found to contain a small percentage of HV (hydroxy valerate). This was independently confirmed using gas chromatography/mass spectrometry (GC/MS). In comparison, the analysis of a commercial PHA polymer, transesterified under identical conditions, only showed the presence of HB, i.e. a pure PHB homopolymer. Copyright 1999 John Wiley & Sons, Ltd.     

Ueber den Kolloidzustand von Gelatinelösungen und seine Beeinflussung durch Temperaturverschiebungen

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