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Perturbation of the dimer interface residue Trp109 resonance provides additional support for binding at the dimer interface hot spot.
Selective [C-δ1- methyl]isoleucine labeling provided a set of NMR probes for monitoring binding at the dimer interface near the aromatic hot spot.
Together with the kinetics results, these structural and dynamics data suggest an inhibitory mechanism in which binding at the dimer interface impacts loop movements that are required for product release.
Addition of a >5-fold molar excess of compound 2 or 3 to KSHV Pr Δ196 yielded resonance perturbations in both the C H and N H HSQC spectra indicative of binding at the dimer interface in the same pocket bound by DD2.
In fact, a significant number of transporters function as dimers and/or show 2-fold symmetry with substrate binding at the dimer or domain interface in the crystal structures, suggesting a common mechanism for substrate transport that could also apply to TSPO.
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However, a significant subset of the binding molecules was found to bind elsewhere on the protein, and we identified this novel ligand binding site at the dimer interface using X-ray crystallography.
Table 3 Comparison between computed binding affinities at the dimer interface in Pf TrxR and experimental IC 50 values Molecule Computed binding affinity (kcal/mol) Exptl.
Table 4 Comparison between computed binding affinities at the dimer interface and experimental IC 50 values in Pf TrxR and h TrxR Molecule PfTrxR hTrxR 2,4-DNPS Exptl.
Loop 312−320, which undergoes a shift upon putrescine binding, is at the dimer interface.
NMR and crystallographic studies reveal that it engages a previously unknown binding site at the dimer interface.
Indeed recent studies on the CDF transporter EcFieF (YiiP) from Escherichia coli localised a substrate binding site at the dimer interface created by the TMDs II and V [ 31].
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