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Solvent exposure of the bulky charged side chains of these lysines and arginines facilitates binding of an anionic lipid head group via attractive electrostatic forces (Figure 7B), although these interactions are not explicitly taken into account in the applied docking algorithm (GOLD software [29]).
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In summary, spontaneous binding of the anionic substrate occurred during the 20 ns simulations of the ferric NdCld, and anions bind tightly to the cavity, regardless of their character or the presence of Arg173.
The initial reaction includes binding of the anionic substrate chlorite to the ferric resting state of NdClds forming the corresponding complex.
The conserved and (as the X-ray structures suggest) mobile distal arginine supports binding of the anionic chlorite to the ferric resting state of Cld.
By comparison, binding of the anionic phenolic ligand protocatechuate to PcaV involves direct contacts to His and Arg from helix one (corresponding to HucR helix α2).
Initially it was thought that the lysine contributed to the positive surface charge near the active site and thus was responsible for the high, diffusion-limited rate constant for binding of the anionic substrate.
Ligands relevant to this project, which have been employed because they fulfil the criteria put forward by the isolobal analogy, consist of an anionic heteroatom binding to the metal centre in a κ1-mode.
This effect may result from the binding of anionic heparins to a wide range of proteins and molecules, thus affecting their biological activities.
In the presence of mixtures of cationic and anionic surfactants, the preferential binding of anionic surfactants to calcium carbonate particles has been found (Cui et al. 2010; Cui et al. 2012).
For instance, Payne et al. showed that incubation of NPs with serum proteins could result in either increased or decreased cellular binding of cationic or anionic NPs as a result of the protein corona formed on the NP surface [43].
In the field of molecular recognition, the guanidinium group has been established as a highly effective functional group in the binding of anionic guests.
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