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Transfection experiments suggest that TCF binding sites can function in combination to enhance transcriptional activity.
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The possible functions of the σ binding sites are quite varied and many are dependent on whether the binding site can function as a promoter.
We assume that mutations that result in loss of function can occur at any binding site, and that non-functional binding sites can also undergo gain of function mutations.
There are examples of highly conserved regulatory sequences with a conserved function but binding sites can also appear, disappear, or alter their sequence even between relatively closely related species; see, e.g., refs. [ 18- 22].
Variants in mature miRNAs or miRNA binding sites can generate gain and loss of function, leading to alterations of the genetic pathways in which those miRNAs are involved [ 17].
The most important component they lack is the three dimensional structure for each transcription factor, because the visualization of the transcription factor, especially binding sites, can help further understanding the mechanism and functions of transcription factors, which is indispensible to structural genomics [ 29, 30].
The presence and location of these binding sites can therefore give useful clues for deducing the biochemical function of an uncharacterized protein.
Perturbation of several binding sites can individually lead to a dramatic and nonlinear reduction in the ADAMTS5 enhancer function (Figure 3).
Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known.
These binding sites can be considered as prerequisite or allosteric binding sites.
In addition, the electrostatic potential binding energy and similarity between the binding sites can be calculated based on the binding pose of the ligand.
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