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Comparison of protein in two different orientations with linkers binding to the opposite sides of the protein demonstrates the possibility of utilizing the constructed surfaces as photoelectronic devices.
ATP hydrolysis in the cis ring changes the potentials within the system such that ATP binding to the opposite (trans) ring triggers the release of all ligands from the cis ring of GroEL through a complex network of allosteric communication between the rings.
ATP hydrolysis is not required for protein folding; rather, ATP hydrolysis in the GroES-bound ring is a prerequisite for ATP binding to the opposite ring.
Could this be binding to the opposite, convex surface of the AP-1 mu1 subunit, similar to the Phe-based APP signal binding to AP-4 mu4?
Hydrolysis in the GroES-bound ring is a prerequisite for ATP binding to the opposite ring, which in turn triggers the allosteric discharge of GroES, ADP, and substrate, whether folded or not, from the folding chamber.
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When in its Fe3+ state, the SOR [Fe(His)4Cys] center can adopt an octahedral geometry, with an extra glutamate ligand binding to the Fe in the position opposite to the axial cysteine [Fe(His)4CysGlu].
The latter may include the competition of PDE4D with other proteins for binding to the receptor or, in an opposite fashion, PDE4D may act as a scaffold by tethering additional proteins to the receptor complex such as the exchange protein activated by cAMP or PKA-anchoring proteins (Dodge-Kafka et al, 2005).
Electrostatic force played an important role in the binding due to the opposite charges on porphyrin and the protein.
Because only one face of the FMN is accessible within the protein environment, moving the substrate binding site to the opposite side of the cofactor appeared impractical.
Once bound, the transporter can undergo a conformational change exposing the substrate binding site to the opposite side of the plasma membrane, thereby permitting translocation.
In contrast, most of the positively selected residues in subclade A are surface exposed, including regions on the putative substrate-binding surface and along the interior of the protein traversing from the substrate-binding surface to the opposite surface of the protein.
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