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The expression vector pcDNA 3.1 (Invitrogen, Carlsbad, CA, USA) was mutated to remove the CMV promoter by sequential digestion with MluI and NheI followed by blunt-end ligation.
For expression in plants, the pUBQ10 promoter (AT4G05310; Norris et al., 1993; Krebs et al., 2012), inserted between Hind III/Spe I sites of a modified pUC19 plasmid (kindly provided by Jörg Kudla, University of Münster), was mutated to remove a Sac I site within the pUBQ10.
The 454 amino acid C-terminus region (Cter) of PfEMP1 (PFD1235w) containing the transmembrane and cytosolic domains of PfEMP1 was amplified from P. falciparum cDNA (TMATSF/TMATSR1), mutated to remove the internal Kpn I site without changing the amino acid sequence, tailed with A-overhangs, cloned into pGEM-T, and sequenced.
The H2A gene was HA-tagged and mutated to remove R3 (ΔR3), to replace R11 with alanine (R11A) or lysine (R11K), or to combine two mutations (ΔR3R11A).
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Based on the hypothesis that the reduced toxicity of LF-HMA was due to the two additional residues (HM), we mutated pSJ115 to remove the two codons specifying HM, producing LF-A, with the native N-terminal sequence matching LF-A/St (Fig. 1).
In light of the assigned FAPP2 function, the Thr 11 Leu 12 wedge extremity in the conserved PH domain of full-length FAPP2 was mutated to GG and EE sequences to remove penetrant hydrophobic bulk and introduce repulsive force, respectively.
The initial model used for building was that of the WT MauG preMADH complex [Protein Data Bank (PDB) entry 3L4M] with solvent and ligands removed, and Gln103 mutated to Asn.
The AS mutant, C6A/C111S, is a "pseudo-WT" SOD1 in which both free cysteines have been removed by mutation, with the buried cys6 mutated to alanine and the surface cys111 changed to serine.
C15 was mutated to alanine and also to the more conservative serine to remove the thiol but minimally alter the polarity and size of the side chain.
In every case, the native amino acid was mutated to a smaller side chain (usually alanine), thereby removing the potential stabilizing contact without introducing steric clash.
The PLP and α-ketoglutarate ligands and water molecules were removed from the search model and residue K188 was mutated to alanine before calculations.
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Justyna Jupowicz-Kozak
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