Figure 10.

Multiple in-solution conformations for TPP riboswitch in the absence of TPP ligand. (A) Spectral clustering analysis. There are two clusters in the no-ligand state. The major cluster (red) reflects an unstructured state with few internucleotide interactions. The minor cluster (blue) is more highly structured than the major cluster specifically in the region of the thiamine binding pocket (blue closed circles). (B, C) Nucleotides that are more structured in the minor cluster – which flank the thiamine-binding pocket – are emphasized in blue on RNA secondary and tertiary structure models. The thiamine moiety is gray in panel C.