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With the binding of transcription factors, the dsDNA probes are protected from cleavage by Fok I.
However, cohesin around the centromeres is protected from cleavage until anaphase II by the Sgo1/PP2A complex.
Upon addition of Mrs1, extensive regions in the RNA became protected from cleavage.
In the free bI3 RNA, only ∼20% of nucleotides are protected from cleavage prior to binding by the Mrs1 protein (top panel, Figure 1A).
Mass spectrometry analyses of trypsin-digested, thrombin-resistant polypeptides indicated that the first sulfatide-binding site of N-PTB is located upstream of a putative thrombin cleavage site (Lys30, Gly31) and protected from cleavage when bound to sulfatide liposomes (Fig. 1A, 3B, and C).
In L-Snord115 containing the C67 to G67 substitution, the D-box1 region appeared completely protected from cleavage.
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Instead, the sulfatide-bound pool remains protected from thrombin cleavage and modulates the clotting response by sequestering Dab2 away from binding to the αIIbβ3 integrin receptor.
In addition, liposome-binding assays combined with mass spectroscopy studies revealed that thrombin, a strong platelet agonist, cleaved N-PTB at a site located between the basic motifs, a region that becomes protected from thrombin cleavage when bound to sulfatides.
In the context of this structure, individual ribonucleotides and secondary structural elements that are protected from chemical cleavage or undergo structural transitions upon Rev binding were identified using detailed RNA footprinting experiments.
First, the polypeptide exposed within the β-lactamase could have a restricted conformational freedom and be somehow protected from proteolytic cleavage [ 3].
KL3 DNA would be protected from this cleavage by EcoRII methylation at the second position in the EcoRII-C recognition sequence (forming CCmWGG where Cm = 5-methylcytosine) [ 83].
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