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Alternatively, the insertion in Hes7BAP prevents binding of an accessory factor that is only required in the authentic, in vivo environment.
Based on the considerations presented above, it can be suggested that rearrangements would occur on binding of an accessory Ca2+, leading to formation of a groove structure.
The base 5′ to the HBS (5′-ACGTG-3′) could be involved in the binding of an accessory protein, alter the conformation and activity of HIF-1 bound to the site, or selectively bind different post-translationally modified forms of HIF-1.
Binding of an accessory protein to an mRNA does not implicate the protein as an ITAF.
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Nonetheless, it is tempting to speculate that reorganization of the helical insertion, either by binding to an accessory protein or posttranslational modification, could trigger formation of FAN1 dimers.
Moreover, these mechanisms are well suited to hinder or promote binding of further accessory proteins, thus providing a powerful link between competitive binding and structure feedback.
Hence, no binding of the accessory helix of Cpx(26-83) to SCΔ60 is detocted in theSCΔ60perisents.
Similarly, transcription termination involves the binding of multiple accessory proteins which may affect the pattern of mutations and repair at the 3'-end.
It is theoretically possible that binding of the central complexin helix to the SNARE complex is required in order to enable binding of the accessory helix of the second complexin molecule.
To test for binding of the accessory helix under conditions where the central helix binding site was more saturated, we performed experiments with SCΔ60 prebound to 3.0 equivalents of CpxI(47-134) (93% binding based on the Kd described above).
In these assays, 1.5 equivalents of CpxI lacking the accessory helix [CpxI(47-134)] were used to block the central helix binding site of SCΔ60, and the heat observed on addition of CpxI(26-83) was attributed to binding of the accessory helix of CpxI(26-83) to SCΔ60.
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