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21.
Daldrop P Reyes FE Robinson DA Hammond CM Lilley DM Batey RT Brenk R 《Chemistry & biology》2011,18(3):324-335
The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design. 相似文献
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Zhao ZY McLeod A Harusawa S Araki L Yamaguchi M Kurihara T Lilley DM 《Journal of the American Chemical Society》2005,127(14):5026-5027
We constructed a modified form of the VS ribozyme containing an imidazole ring in place of adenine at position 756. The novel ribozyme is active in both cleavage and ligation reactions. The reaction is efficient, although relatively slow. The results are consistent with a role for nucleobase catalysis in the catalytic mechanism of this ribozyme. 相似文献
25.
Shadforth I Dunkley T Lilley K Crowther D Bessant C 《Rapid communications in mass spectrometry : RCM》2005,19(22):3363-3368
Perhaps the greatest difficulty in interpreting large sets of protein identifications derived from mass spectrometric methods is whether or not to trust the results. For such experiments, the level of confidence in each protein identification made needs to be far greater than the often used 95% significance threshold to avoid the identification of many false-positives. To provide higher confidence results, we have developed an innovative scoring strategy coupling the recently published Average Peptide Score (APS) method with pre-filtering of peptide identifications, using a simple peptide quality filter. Iterative generation of these filters in conjunction with reversed database searching is used to determine the correct levels at which the APS and peptide quality thresholds should be set to return virtually zero false-positive reports. This proceeds without the need to reference a known dataset. 相似文献
26.
The growth of smooth thick (80 μm) films of highly-ordered ZnS on GaAs substrates [oriented near the (100)] by open tube vapour transport in H2:HCl gas flow has been investigated. We have found the surface features of the layers to be similar to those associated with GaAs epitaxy, particularly the “sand-dune” type of hillock. To obtain smooth layers, the substrates must be off the (100) plane, and precleaned in HCl acid. The most critical factor during growth was the HCl transport gas concentration (1.2-1.4%). We have investigated the influence of growth parameters on surface quality and Si contamination. The Si concentration in the films was found to be approximately directly proportional to the growth rate of the layers. 相似文献
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Laura M. Lilley Sarah Kamper Michael Caldwell Zer Keen Chia David Ballweg Luke Vistain Jeffrey Krimmel Teresa Anne Mills Keith MacRenaris Paul Lee Emily Alexandria Waters Thomas J. Meade 《Angewandte Chemie (International ed. in English)》2020,59(1):388-394
Our lab has developed a new series of self‐immolative MR agents for the rapid detection of enzyme activity in mouse models expressing β‐galactosidase (β‐gal). We investigated two molecular architectures to create agents that detect β‐gal activity by modulating the coordination of water to GdIII. The first is an intermolecular approach, wherein we designed several structural isomers to maximize coordination of endogenous carbonate ions. The second involves an intramolecular mechanism for q modulation. We incorporated a pendant coordinating carboxylate ligand with a 2, 4, 6, or 8 carbon linker to saturate ligand coordination to the GdIII ion. This renders the agent ineffective. We show that one agent in particular (6‐C pendant carboxylate) is an extremely effective MR reporter for the detection of enzyme activity in a mouse model expressing β‐gal. 相似文献
29.
Walker SH Lilley LM Enamorado MF Comins DL Muddiman DC 《Journal of the American Society for Mass Spectrometry》2011,22(8):1309-1317
A library of neutral, hydrophobic reagents was synthesized for use as derivatizing agents in order to increase the ion abundance
of N-linked glycans in electrospray ionization mass spectrometry (ESI MS). The glycans are derivatized via hydrazone formation
and are shown to increase the ion abundance of a glycan standard more than 4-fold. Additionally, the data show that the systematic
addition of hydrophobic surface area to the reagent increases the glycan ion abundance, a property that can be further exploited
in the analysis of glycans. The results of this study will direct the future synthesis of hydrophobic reagents for glycan
analysis using the correlation between hydrophobicity and theoretical non-polar surface area calculation to facilitate the
development of an optimum tag for glycan derivatization. The compatibility and advantages of this method are demonstrated
by cleaving and derivatizing N-linked glycans from human plasma proteins. The ESI-MS signal for the tagged glycans are shown to be significantly more abundant,
and the detection of negatively charged sialylated glycans is enhanced. 相似文献
30.
Joseph R. Wheatley Annabel R. Beacham Paul M. de Q. Lilley David J. Watkin George W. J. Fleet 《Tetrahedron: Asymmetry》1994,5(12)
Isopropylidene and cyclohexylidene ketals of γ- and δ-heptonolactones derived from Kiliani ascensions of protected L-rhamnose may constitute suitable intermediates for the preparation of mimics of L-rhamnose. The X-ray crystal structure of 7-deoxy-3,4-O-isopropylidene-L-glycero-L-galacto-heptono-1,5-lactone provides an example of a δ-lactone in a boat conformation with a substituent in a flagpole position. The size of ring in the lactones is completely consistent with Hudson's classical lactone rotation rule of 1910. 相似文献