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Here, we present high-resolution crystal structures of CtpB in a resting and multiple active conformations.
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The crystal structures provide evidence of multiple active site conformations in the substrate-free form of the enzyme, which is consistent with a conformational selection mechanism of substrate binding.
If some states E′ are not completely inactive, then total reactivity is averaged over multiple (partially) active conformations (not shown).
We propose that Smo adopts multiple inactive and active conformations, which influence its localization and trafficking on the primary cilium.
To address this problem, we have developed a computationally efficient ActiveGEnSeMBLE method that systematically predicts multiple conformations that are likely in the GPCR activation landscape, including multiple active- and inactive-state conformations.
On the contrary, Hawkins et al.[15] reported that the ROCS-based virtual screening using a single conformation for a query molecule outperforms a pharmacophore modeling using the pharmacophores developed from multiple active compounds (up to 20).
The structures of partially active conformations were not considered as suitable templates as they present features of active conformations in the extracellular parts of the receptors and features of inactive conformations in the cytoplasmic parts.
In one study, a model of the TSHR TMD was produced based on 15 GPCRs in their inactive conformations, 3 GPCRs in partially active conformations and 1 in fully active conformation [14].
TMD_Ac is based on the same three GPCRs as TMD_In, but in their active conformations.
Some structures have crystallized in catalytically active conformations, whereas others appear to be in inactive or native conformations.
In contrast, when comparing inactive with fully active conformations, the situation reverses.
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