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We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein.
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Background: Protein plasticity in response to ligand binding abrogates the notion of a rigid receptor site.
Comparison with a known pharmacophore model and the binding affinity of a new rigid H3 antagonist (compound 1, pKi = 8.02) allowed the characterization of a binding scheme which could also account for the different affinities observed in a recently reported series of potent H3 antagonists, characterized by a 2-aminobenzimidazole moiety.
The specificity of binding does not arise out of a rigid lock and key type of interaction, but rather requires both the paratope and the epitope to undergo slight conformational changes in each other's presence.
The addition of a rigid aromatic ring into the cyclic hexapeptide structure (Fig. 3: DMP728 and DMP757) enhances the binding affinity of αIIBβ3 (Liu et al. 2010; Jacobson et al. 2011; Danhier et al. 2012).
The utility of a rigid crust?
This robot is composed of a rigid platform suspended by six rigid struts of fixed length.
These results show that, in all three cases, the absence of a rigid 3-D organization may have contributed to the antigenicity of these sequences by increasing their exposure and availability to antibody binding.
Hydrolysis of these three ATP molecules to give ADP, together with binding of a further three ATP molecules to the remaining three nucleotide-free subunits results in a perfect hexameric rigid form.
Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion.
There is no evidence of significant conformational changes occurring in either the Ley carbohydrate antigen or the hu3S193 binding site, which suggests a rigid fit binding mechanism.
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