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Previously, we suggested a structural model based on the self-assembly of motifs taken from Escherichia coli galactoside acetyltransferase (Protein Data Bank 1krr, chain A, residues 131 165, denoted krr1), which produced a very stable nanotube in molecular dynamics simulations.
This program identifies sequence elements that are at least 15 nucleotides long with at least 75% of the sequence containing "A" residues.
Significantly increased targeting of the A residues was observed in AGA, CAA and CGA, whereas significantly decreased targeting of A was noticed in CTA (Table S1).
The MolProbity results confirm that the phosphoprotein, chain A, residues ∼214 219 and ∼253 262 are in contact with the nucleoprotein, chain K, at residues 356 369.
Instead, we used a 79 bp Actin2 intron flanked by two "A" residues on either side and had it synthesized by GenScript (Piscataway, NJ).
Here, we show that the two A residues in the internal loop are unpaired but stacked on each other and that their sugars are inverted.
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The DNA-binding helix-turn-helix motif (α3 and α4 helices), the QRDR-A (residues 74 113) and the catalytic residues involved in DNA cleavage, namely R128 and Y129, are localised in the DNA-gate.
To improve mapping quality, in the subsequent analyses we focused on non-encoded tails with a maximum of 20% non-A residues.
To test the function of the putative NES, site-directed mutations that cause substitutions of conserved NES-A residues were first selected to identify hypermorphic alleles.
The per-nucleotide frequencies of non-A residues in non-encoded tails in Nab3, Nrd1 and Trf4 experiments, were 2.5, 3.1 and 5.1%, respectively.
In the CENP-A specific region of the chimeric nucleosome, CENP-C residue Y725 binds in a hydrophobic pocket created by CENP-A residues I133 and L137.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com