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Thus, a single lysine residue could have five different modification states (i.e., acetyl, unmodified, me1, me2, and me3), and specific binding proteins can recognize these specific modifications.
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The ring-carboxylate moiety is evidently not absolutely required for binding since these TyrAa proteins can recognize TYR (alanyl sidechain) as a competitive inhibitor.
SET-domain proteins can recognize their target genes through direct or indirect interaction with site-specific chromatin-binding factors, including factors recognizing specific histone modifications.
In summary, these results confirm that Sp1 protein can recognize and bind to its binding element in the HIV-1 promoter folded into a G-quadruplex configuration.
We show that the three Sp1 binding motifs can adopt different forms of G-quadruplex structure and that the Sp1 protein can recognize and bind to its site folded into a G-quadruplex.
The DNA sequence motif that is recognized by the binding protein can be computed; the precise regulatory sites in the genome for any transcription factor can be identified; the direct downstream targets of any transcription factor can be determined; and the clustering of transcription-regulatory proteins at specific DNA sites can be assessed.
Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment.
It is now recognized that, in addition to direct integrin activators, both α- and β-tail-binding proteins can suppress integrin activation.
Also, at least two groups of proteins, methyl-binding domain proteins (14) and CxxC proteins (15), can recognize the unmethylated or methylated state of DNA and transmit signals to other regulatory proteins.
HNF1α and HNF1β are highly homologous protein that can recognize the same binding site and form heterodimers [ 32].
ETV1, ETV4 and ETV5 have highly conserved COP1-binding motifs, which can recognize COP1 [ 17, 22].
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