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The POU domain of Oct-4 is a conserved DNA-binding domain that binds as a monomer to the octamer sequence motif, 5′-ATGCAAAT-3′ (Botquin et al, 1998).
SRs are a class of ligand-activated TFs; they include a ligand-binding domain which activates gene expression in the presence of specific sex or adrenal steroid hormones and a DNA-binding domain, which binds as a dimer to palindromic REs consisting of two half-sites each six bases long (Bentley, 1998; Bain et al., 2007).
Mnt binds as a tetramer to a palindromic binding site.
It binds as a tetramer to a symmetric binding site and, in earlier work, all single base changes to the consensus site were synthesized and their change in binding affinity measured.
NFI binds as a dimer, and its preferred binding sequence is a palindrome composed of two half sites TTGGCANNNTGCCAA.
The HD of Pax6 preferentially binds as a dimer to the palindromic DNA binding site: TAATYNRATTA (Y is C or T; R is A or G; N is any nucleotide), which is known as the P3 site.
In both of the two crystal forms presented the inhibitor binds as a sandwich of two molecules at the nucleoside binding site.
TRAIL binds as a homotrimer to DR4 and DR5, which upon binding will trimerise and form a death-inducing signalling complex.
Upon hormone binding, the activated ligand-bound receptor translocates into the nucleus and binds as a homodimer to glucocorticoid response elements within the promoter region of target genes.
Cilastatin binds as a normal substrate and is orientated in a perfect near-attack conformer for formation of a tetrahedral intermediate with the zinc-bound water/hydroxide.
NF-κB binds as a homo- or heterodimer of Rel homology domain-containing proteins to κBREs by specifically recognizing two binding footprints surrounding a central spacer in which the AATTY site is found.
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