Data from: Binding position dependent modulation of smoothened activity by Cyclopamine

Cyclopamine is a natural alkaloid that is known to act as an agonist when
it binds to the Cysteine Rich Domain (CRD) of the Smoothened receptor and
as an antagonist when it binds to the Transmembrane Domain (TMD). To study
the effect of cyclopamine binding to each binding site experimentally,
mutations in the other site are required. Hence, simulations are critical
for understanding the WT activity due to binding at different sites.
Additionally, there is a possibility that cyclopamine could bind to both
sites simultaneously especially at high concentration, the implications of
which remain unknown. We performed three independent sets of simulations
to observe the receptor activation with cyclopamine bound to each site
independently (CRD, TMD) and bound to both sites simultaneously. Using
multi-milliseconds long aggregate MD simulations combined with Markov
state models and machine learning, we explored the dynamic behavior of
cyclopamine's interactions with different domains of WT SMO. A higher
population of the active state at equilibrium, a lower activation free
energy barrier of ~ 2 kcal/mol, and expansion of the hydrophobic tunnel to
facilitate cholesterol transport agrees with the cyclopamine's
agonistic behavior when bound to the CRD of SMO. A higher population of
the inactive state at equilibrium, a higher free energy barrier of ~ 4
kcal/mol and restricted the hydrophobic tunnel to impede cholesterol
transport showed cyclopamine's antagonistic behavior when bound to
TMD. With cyclopamine bound to both sites, there was a slightly larger
inactive population at equilibrium and an increased free energy barrier (~
3.5 kcal/mol). The tunnel was slightly larger than when solely bound to
TMD, and showed a balance between agonism and antagonism with respect to
residue movements exhibiting an overall weak antagonistic effect.