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While SH3-induced dimerization of the DH domain would obscure the Cdc42 binding interface, it is unlikely that this is the mechanism by which intersectin-1L GEF activity is autoinhibited.
In the context of protein interaction networks and the nature of the binding interface, it is possible to predict when subfunctionalization might be possible.
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Because the single intrinsic W325 is located on the finger subdomain and is far from the binding interface, it was used as a control site.
However, a protein with many transient interaction partners may transiently interact with its different partners through the same binding interface (though it is possible that the protein may form a transient complex with its partners through multiple distinct binding interfaces), thus the PPID of the protein may not well reflect the proportion of its interface residues [ 22].
Relatedly, how easily does orthologous neofunctionalization occur and how dependent upon protein fold and binding interface size is it?
Interestingly, 2 residues shown through crystallography to be contacts in the binding interface were also identified as being under diversifying selection (D48 and I115 in CPXV-BR, E48 and L115 in ECTV).
Identification of binding interface region is especially useful for cellular pathways analysis and drug design.
Moreover, it was suggested that ANTXR2 residue H121 might be a key component of this triggering mechanism since this residue is located at the PA domain 2 binding interface and is conserved in ANTXR1 [18], [18].
However, the binding interface was more likely to be weakened by the mutation, and the heteromer might be prone to dissociate under extreme conditions as evidenced by a significant decrease in the stability (Fig. 3).
This secondary binding interface is only specific for Nef, and has never been reported with other natural AP-2 cargo proteins [ 29].
However, the AlkA DNA binding interface is not positively charged, and few electrostatic DNA contacts are observed in crystal structures of AlkA·DNA complexes.
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