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19F NMR has recently emerged as an efficient, sensitive tool for analyzing protein binding to small molecules, and surface plasmon resonance (SPR) is also a popular tool for this purpose.
A few cases of nucleic acids binding to small molecules in solution have been demonstrated by capturing aptamer onto a streptavidin sensor surface directly or via hybridization.
Motif M3 was found to be a part of aptamer structure (the region binding to small molecules) of FMN riboswitches [ 38, 39].
Rice Hbs could potentially function within cells through O 2-transport and -signaling, binding to small molecules (most notably NO) and other as yet undetermined mechanisms.
To address this limitation, we developed and validated a high-throughput and scalable SPR-based strategy for characterizing aptamer binding to small molecules.
The ability of a protein to bind small, drug-like molecules with a high affinity is referred to as "druggability" (ligandability often refers to the more general ability of binding to small molecules).
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Residues lining the inhibitor binding pocket are strictly conserved between ALK1 and ALK2 explaining their common binding to small molecule BMP inhibitors, including K02288 (Fig. 1c) [ 16].
Furthermore, these methods consider many aspects of protein molecular function including binding to small organic molecules, inorganic groups, for example, iron-sulfur clusters and metal ions, and interactions with nucleic acids and other proteins [ 17].
Hfq is a small abundant RNA-binding protein that functions as a global posttranscriptional regulator of gene expression by binding to small regulatory RNA molecules (sRNAs) and facilitating their interaction with mRNA molecules [45].
Here we report an improved platform for characterizing binding properties of aptamers to small molecules.
We report the development of a surface plasmon resonance-based platform for rapid characterization of kinetic and equilibrium binding properties of aptamers to small molecules.
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