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We postulate that this bifunctional binding mode is important for ensuring the glycolipid adopts an appropriate bound conformation for its recognition by iNKT cell TCRs.
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The thermodynamic parameters, enthalpy change (Δ H), and entropy change (Δ S) of reaction are important for confirming what binding mode is active.
The dileucine peptide in the unlatched structure (Kelly et al., 2008) used for comparison is derived from CD4, but it is important to emphasize that this binding mode is dependent on phosphorylation and is unrelated to Nef-dependent downregulation.
This binding mode is rather specific to the complexation of copper with peptides containing a histidyl residue which is known to be an important metal-binding site in proteins.
This means that the RNA binding mode is preserved.
This is especially important in drug discovery and development projects where no receptor structure is available or more frequently no verified binding mode is known and mostly ligand based approaches can be applied to generate hit compounds.
The first binding mode is adopted by the H3 peptides, whereas the other mode is adopted by the H4 peptides.
However, their binding mode is entirely different.
This binding mode is consistent with the observed experimental SAR (vide infra) and is significantly different from the two closely related binding modes previously postulated in the literature.
By contrast, binding mode 4 was clearly disfavored in chain A, indicating that this binding mode is incompatible with the partially constrained (active) conformation.
The QM/MM simulation using this alternative substrate binding mode was, in contrast, quite stable and underscored several important binding interactions with the enzyme.
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