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A more detailed look at region 1 reveals the greatest disparity between Rep2 and Rep5 occurs at the RBE binding interface in the major groove of the ITR (Fig. 6F).
The extensive disruption of the ASV binding interface in the R155K-ASV complex is in agreement with inhibitor potency drop from 2.7 to 142.7 nM.
In addition, it was possible to carry out a full backbone relaxation analysis of AR1−AR4 of IκBα, and the results reveal multiple time scales of motion centered around the binding interface in the complex with NF-κB.
Both the convex and concave surfaces of AR domains are used to mediate protein−protein interactions, with the concave surface of the β-hairpins forming the binding interface in the majority of complexes studied so far.
Compared with the Dpo4 polymerase that shows nearly no changes in the emission spectra at the binding interface in the complexed states, the pol β complex shows spectral changes and suggests tighter recognition.
These dramatic changes in the binding sites and at the active site were not clearly observed in Dpo4 and reflect the nature of the binding interface in the pol β DNA complex.
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Earlier studies mapped the HBGA binding interfaces in the P domain (Tan et al., 2004, 2008) that formed P dimers (Tan et al., 2004) and/or P particles (Tan et al., 2008, 2011; Tan and Jiang, 2005), when the P domain is expressed in E. coli.
The CCP4 program [25] was then employed to determine the contact areas of two different ATP binding interfaces in the 2ZUB, 2ZUC or 2ZUC left-handed filaments.
Functional convergence of strains with the same HBGA targets subsequently resulted in acquisition of analogous HBGA binding interfaces in the two genogroups that share an overall structural similarity, despite their distinct locations and amino acid compositions.
Moreover, it is possible to incorporate existing knowledge about protein interactions and protein binding interfaces in the point matching procedure, providing an ideal framework for comprehensive data integration.
We confirmed this by introducing several mutations at the putative NL-binding interface in the context of NX1α III).
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