Jennifer C. J. Barna

Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments

Abstract A new method for sampling in two-dimensional nuclear magnetic resonance experiments is proposed and tested using one-dimensional spectra as models. The free induction decays are sampled exponentially, using many points where the signal-to-noise ratio (S/N) is high and a few where it is low. Using the maximum entropy method to reconstruct spectra, much higher resolution can be obtained than by using conventional sampling (for a given number of data points). The method is shown to work for FIDs having even very poor S/N. It should prove valuable in the future for 2D NMR experiments where at present valuable high-resolution information is lost as a result of the necessity for truncation of data sets in t1 in order to optimize sensitivity.

Structural studies on cyanoginosins-LR, -YR, -YA, and -YM, peptide toxins from Microcystis aeruginosa

The structures of the hepatotoxins of general name cyanoginosins-XY are proposed to be cyclo-D-Ala-L-X-erythro-β-methyl-D-isoAsp-L-Y-Adda-D-isoGlu-N-methyldehydroAla (1) where X and Y represent variable amino acids and Adda is 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid (2). The structural studies on four variant toxins utilised n.m.r. and mass spectral methods analogous to those recently used to determine the structure of cyanoginosin-LA. [graphic omitted] (1)

A leucine-rich repeat peptide derived from the Drosophila Toll receptor forms extended filaments with a β-sheet structure

Leucine‐rich repeats (LRRs) are 22–28 amino acid‐long sequence motifs found in a family of cytoplasmic, membrane and extracellular proteins. There is evidence that LRRs function in signal transduction, cellular adhesion and protein‐protein interactions. Here we report unusual properties of a synthetic LRR peptide derived from the sequence of the Drosophila membrane receptor Toll. In neutral solution the peptide forms a gel revealed by electron microscopy to consist of extended filaments approximately 8 nm in thickness. As the gel forms, the circular dichroism spectrum of the peptide solution changes from one characteristic of random coil to one associated with β‐sheet structures. Molecular modelling suggests that the peptides form an amphipathic structure with a predominantly apolar and charged surface. Based on these results, models for the gross structure of the peptide filaments and a possible molecular mechanism for cellular adhesion are proposed.

Conventional and exponential sampling for 2D NMR experiments with application to a 2D NMR spectrum of a protein

In two-dimensional NMR experiments on biological macromolecules, one is frequently compelled to acquire fewer points in t, than ideally required. This truncation of the signal in t, optimizes sensitivity at the expense of resolution (I) and may lead to a great loss of information through merging of cross peaks, cancellation between antiphase peaks, and “truncation artifacts.” We (2) and others (

Structural studies on the peptide moroidin from Laportea moroides

4) have shown how the maximum entropy method (MEM), when used to process conventionally acquired 2D NMR data, avoids many of the artifacts and alleviates the loss of resolution. Recently, however, we have attempted to optimize resolution and sensitivity in 2D NMR experiments by considering alternative methods of data acquisition. We have proposed (5, 6) a novel form of selective data sampling which we call exponential sampling. In this method many tl points would be acquired near the beginning of the experiment where the signal-to-noise ratio is high but some points, acquired with an exponentially decreasing frequency, would be acquired later in the experiment to aid the determination of high-resolution information. Such sampling would be used in conjunction with a data-processing method such as MEM; the conventional Fourier transform of data sampled in this way is unsatisfactory as it contains artifacts due to the many unmeasured points. In this paper we extend our previous work where we demonstrated the use of exponential sampling in conjunction with MEM (5, 6) and show that exponential sampling should allow us to increase the available resolution in 2D NMR experiments. Further, as a practical demonstration we show that it can produce a large improvement in resolution in a 2D NMR spectrum of a protein. As in previous work (5, 6) the data were acquired conventionally and the exponential sampling was generated subsequently. In deciding how to carry out a 2D NMR experiment the choice before one is often as follows: one may acquire (1) N tl points with 2m scans per point or, for example, (2) 2N points with m scans per point. Where signal-to-noise is poor one is normally forced to adopt course (l), that is, to truncate the data in order to optimize sensitivity. Once the possibility is available of (3) exponentially sampling, for example, N out of 2N points with 2m scans per point, the choice is wider. We have already shown, using one-dimensional models (5, 6), that exponential sampling of N points out of 2N is successful even when the signal-to-noise is very poor. Here (7) we show that course (3) is the best option compared to options (1) and (2). When acquiring a 2D NMR

Use of CLEAN in conjunction with selective data sampling for 2D NMR experiments

Abstract By a combination of chemical, 1H and 13C NMR, and mass spectrometric studies, two alternative structures for Moroidin, from Laportea moroides , have been elucidated. Moroidin, which may be responsible at least in part for the toxicity of Laportea moroides , is a tricyclic octapeptide containing an unusual C-N linkage between tryptophan and histidine residues.

Structural features that affect the binding of teicoplanin, ristocetin A, and their derivatives to the bacterial cell-wall model N-acetyl-D-alanyl-D-alanine

We have recently shown(I, 2) that using one form of nonuniform selective data sampling during acquisition, which we call exponential sampling, one should be able to obtain increased resolution in two-dimensional NMR spectra. The use of exponential sampling was demonstrated using one-dimensional spectra acting as models for the second dimension in 2D NMR spectra. The data were acquired normally and the appropriate data sampling was produced before maximum entropy method (MEM) data processing on a separate computer. We have also demonstrated the first application of exponential sampling to a 2D NMR spectrum of a protein (3, 4). It is for such spectra of biological macromolecules that the method is intended, exponential sampling in t, followed by suitable data processing gives an improvement on conventional sampling of the same number of t, points even when the latter is also followed by MEM data processing. Exponential sampling is ideally suited to experiments where the signals of interest are in-phase; i.e., the free induction decay is cosine modulated in tl . This includes, for example, the NOESY experiment. Where the signal does not simply decay exponentially in tl (e.g., COSY) modified sampling schemes are neces=-u-Y (2). When processing very noisy data sets using MEM the relative intensities of peaks are distorted. This is a problem, particularly when processing 2D NOESY spectra where the relative intensities are used to determine ‘H-‘H distance constraints. We have, therefore, explored the possibility of using other data processing methods in conjunction with our methods of selective data sampling. In this note we show that exponential sampling can also be used in conjunction with the CLEAN method (3). CLEAN was introduced in the field of astronomy by Hogbom (5) and later applied by others to NMR data (6-8). A discussion of its application to radioastronomical data has recently been given (9) and we have recently made a comparison of the results obtainable after conventional sampling using CLEAN, MEM, and linear predictive singular value decomposition (3). When CLEAN is used to process conventionally sampled truncated data, a “mask” or “beam” is constructed by Fourier transforming a step function corresponding to the length of acquisition of the truncated signal followed by zeros (7). The mask has characteristic broadness and “sine wiggles.” This corrupted frequency-domain mask is then subtracted from the corrupted spectrum, produced by a Fourier transform of

Structure elucidation of two triterpenoid tetrasaccharides from Androsace saxifragifolia

Studies with the title antibiotics have confirmed that the N-terminal amino groups of such glycopeptides play a major role in binding to N-acetylD-alanyl-D-alanine; one sugar is found to affect free energy of binding but the other sugars and fatty acid groups attached to the aglycones have more uncertain roles.

The stereochemical dependence of one-bond carbon-carbon coupling constants

Saxifragifolins A and B, two new triterpenoid tetrasaccharides isolated from the aerial part of Androsace saxifragifolia, were respectively shown to be androsacenol-3-O-{β-D-xylopyranosyl-(1 → 2)-β-D-glucopyranosyl-(1 → 4)-[β-D-glucopyranosyl-(1 → 2)]-α-L-arabinopyranoside}(1) and cyclamiretin A 3-O-{β-D-xylopyranosyl-(1 → 2)-β-D-glucopyranosyl-(1 → 4)-[β-D-glucopyranosyl-(1 → 2)]-α-L-arabinopyranoside}(2). The structural details were elucidated by a combination of fast-atom-bombardment mass spectrometry, chemical degradation, and one- and two-dimensional n.m.r. spectroscopy.

Carbon-13 N.M.R. evidence for an unsymmetrical hydrogen bond in the CLS-enols of β-diketones

Abstract Spin-spin coupling constants for carbon-carbon single bonds vary with the orientation of lone pairs on adjacent nitrogen atoms and of adjacent carbonyl groups.