NMR Structure Determination of a 28-Nucleotide Signal Recognition Particle RNA with Complete Relaxation Matrix Methods Using Corrected Nuclear Overhauser Effect Intensities
ACS Symposium Series, 1997
Chemical Function Based Alignment Generation for 3D QSAR of Highly Flexible Platelet Aggregation Inhibitors
Molecular Modeling and Prediction of Bioactivity, 2000
Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10
Journal of Biomolecular NMR, 2014
A procedure is presented for automated sequence-specific assignment of NMR resonances of uniforml... more A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80 % of the resonances of the (13)C-(1)H moieties at the 1', 2', 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY.
Lipophilicity determination of diazine analogues of ridogrel. Part 2: Application of 3D QSAR for prediction of log k'w and log P
Pharmazie, 1996
A Practical Approach to Isolate 48S Complexes: Affinity Purification and Analyses
The HCV IRES is a highly structured RNA which mediates cap-independent translation initiation in ... more The HCV IRES is a highly structured RNA which mediates cap-independent translation initiation in higher eukaryotes. This function is encoded in conserved structural motifs in the two major domains of HCV and HCV-like IRESs, which play crucial and distinct roles along the initiation pathway. In this review, I discuss structural features of IRES domains and how these RNA motifs function as RNA-based initiation factors to form 48S initiation complexes and 80S ribosomes with only a subset of canonical, protein-based eukaryotic initiation factors.
Biophysical studies of RNA require concentrated samples that are chemically and structurally homo... more Biophysical studies of RNA require concentrated samples that are chemically and structurally homogeneous. Historically, the most widely used methods for preparing these samples involve in vitro transcription, denaturation of the RNA, purification based on size, and subsequent refolding. These methods are useful but are inherently slow and do not guarantee that the RNA is properly folded. Possible mis-folding is of particular concern with large, complexly folded RNAs. To address these problems, we have developed methods for purifying in vitro transcribed RNAs in their native, folded states. These methods also have the advantage of being rapid and readily scaled to virtually any size RNA or transcription amount. Two methods are presented: the first is an affinity chromatography approach and the second is a weak ion-exchange chromatography approach. Both use equipment and materials readily available to almost any lab and hence should provide flexibility for those seeking alternate appr...
Novel Diazinyl 3-PYRIDYL Ketones : Efficient Synthesis and Complete Assigment of 1H and 13C NMR Spectra
† The notation of the NMR structures is as follows: <SArdc-> and <SArdc+> are the final 20 simula... more † The notation of the NMR structures is as follows: <SArdc-> and <SArdc+> are the final 20 simulated annealing structures; SA* is the mean structure obtained by averaging the coordinates of the individual SA structures best-fitted to each other. The number or terms for the various restraints is given in parentheses; for final force values see methods section. Heavy-atom r.m.s. deviations are defined as the average difference between <SA> versus SA*. ‡ None of the final structures exhibited distance violations larger than 0.5 Å and dihedral violations larger than 10°. Only structurally useful intraresidue distance restraints, involving protons separated by more than three bonds, are included. § The axial (Da) and rhombic (R) components of the final alignment tensors are listed in TableS1. * Chemical shifts are referenced according to ref. . Sample conditions: 10mM sodium phosphate buffer, pH 6.40, 25º. † Numbering according to ref.
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Papers by Peter Lukavsky