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This finding suggests that the influence of nucleotide composition at individual sites in a HSE on binding affinity may be non-additive.
In any event, LILRA1 follows this rule: if it displays self-interaction of Lys42 with Glu68, the binding affinity may be reduced relative to LILRB1 or B2.
This pH-dependent binding affinity may be explained by the formation of a C-terminal α-helix, which competes with the ligand for the binding cavity at low pH [7], [8], [37].
In other words, the overall agreement between the PWM score and the binding affinity may be relatively weak.
A lower binding affinity may be caused by a lower association rate constant (kon[rNTP]; Figure 1a), a faster dissociation rate (koff; Figure 1a), or both.
The differential response observed here correlates with the higher affinity of the TLR9 receptor for the hybrid (Fig 7), therefore binding affinity may be important in determining cytokine response.
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Our results suggest that estimating the protein protein and the protein genome binding affinities may be sufficient to predict which pathway occurs.
On the other hand, Wang et al. [25] have reported from a comprehensive evaluation of ten docking programs that the correlation between the scores of some programs (Gold, Glide and Surflex, among others) and the binding affinities may be high for certain protein families (up to 0.7).
It is noteworthy that as Fc-dimerized Fz4CRD may mimic Fz4 receptor dimerization at the cellular surface, these tighter binding affinities may be more indicative of Norrin binding in the physiologically relevant environment.
Although very high binding affinities may be achieved for unfolded structures such as designed peptides IGA and GGG and natural ZFs, catalytic zinc sites will likely require further structural contributions from a larger protein matrix for the stabilization of unsaturated coordination spheres and substrate binding.
A low signal/background ratio in the danyslated-peptide assays and low binding-peptide affinity may be responsible for high peptide concentration required in the interaction studies.
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