2.6 | RNA Folding intermediate, R1138
Ewan McRae and Ebbe Andersen supplied two designed (‘origami’) RNA
structures as CASP targets (15). One of these, R1138, was found to have
two conformations (now PDB 7PTK and 7PTL, Figure 4): these represent the
mature form, and an intermediate form present in solution for
approximately the first 8 to 10 hours after transcription. Participants
were asked to predict both conformations within the set of five models
allowed for a target. This is a large molecule (720 bases). There are
quite accurate models of the mature form (TM ~0.8), but
not of the intermediate. However, inspection of the structure suggests
the free energy of the intermediate is likely substantially higher than
the mature form compared to the free energy spread in the other ensemble
targets and to situations explored in benchmarking studies (17-20), so
it is unclear whether the enhanced sampling methods used there and on
the other targets could be effective.