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The large (300-fold) difference in potency between analogs containing (4R)- and (4S -4-fluoroproline was rationalized by analyzing inhibitor–enzyme interactions in crystal structures of related compounds and by molecular modeling which indicated that the more potent (4S -4-fluoroproline isomer stabilizes a proline ring conformation that is preferred for binding to the enzyme.
There is typically one particular nucleotide preferred for binding; the sequence is called the target sequence.
Pull-down assays with single amino acid mutants of hRio2NES-R reveal that smaller hydrophobic residues such as leucine in the Φ3 position and isoleucine, leucine, and valine in the Φ4 position are preferred for binding to CRM1.
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Additionally, His39 in CBX2 chromodomain interrupted the structured aromatic cage, partly explaining the reason for UNC3866 preferring for binding to CBX7.
Furthermore, in vitro optimization studies demonstrated that the sequence 5′ -GTAAACA-3′ is preferred for FOXP3 binding to DNA [ 8].
It has been suggested that the faces preferred for the binding of enzymes have hydrophobic character [ 8, 25, 26].
Secondly, the sssRNAs do not exhibit the marked bias to 5' terminal uridine (miRNAs) or adenosine nucleotides (siRNAs) that is preferred for ARGONAUTE binding (Additional file 8).
The more palindromic nature of the high-affinity cre sites (in comparison low-affinity cre sites) might create a more symmetric DNA conformation, preferred for CcpA binding.
If there is a stoichiometric imbalance, the monomer in excess may have time to transit for a preferred-for-binding to a nonpreferred conformation (inactive for binding).
This native ChIP method is generally considered superior for assessing histone modifications [ 32] while cross-linked ChIP is preferred for studying chromatin binding proteins.
Especially when multiple targeting ligands are introduced into a protein subunit, which is preferred for high avidity binding, aberrant folding of chimeric proteins can occur.
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