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The aza-peptide component of APE binds in the substrate-binding regions of Mpro in a substrate-like manner, with excellent structural and chemical complementarity.
It was revealed that auxin binds in the substrate-binding pocket of TIR1 and promotes the further recruitment of Aux/IAA.
This CagA peptide was named MKI (for MARK2 kinase inhibitor) in analogy to PKI, a well-described peptide inhibitor of protein kinase A. Interestingly, the manner in which the MKI sequence of CagA binds in the substrate-binding cleft of Par1b/MARK2 is reminiscent of the manner by which PKI binds to and inhibits PKA.
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The complex of CYP3A4 with one substrate molecule bound in the substrate-binding pocket may be taken as a reasonable model of the catalytically competent complex.
The other, protein kinase inhibitor, binds to the substrate-binding site.
Characteristically, steroidal inhibitors bind to the substrate-binding site in an irreversible manner [ 45], leading to degradation of the protein drug complex.
In the substrate-binding domain, all three enzymes bind uridyl nucleotides.
In contrast, it is reported that XIAP can further bind to the substrate-binding cleft of active caspase-3, via its N-terminal linker, hence, providing a steric blockade mechanism for substrate binding.
In fact, while nonsteroidal compounds bind to the p450 site of the aromatase complex, the steroidal compounds bind to the substrate-binding pocket.
On the other hand, the substrate-binding groove has evolved to bind kinase-specific substrates and our analysis demonstrates that this is accompanied by large variability in the substrate-binding groove.
The former mimic the substrate and are supposed to bind in the substrate binding site (SUB), a narrow hydrophobic tunnel [19].
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