Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function
Figure 2
Proposed folding pathway for the TPP riboswitches tenA (a) and thiM (b).
Structures formed in the sensing windows are represented in red boxes; downhill folding window structures are found in blue boxes; and functional window structures are represented inside the green boxes. Double-head arrows represent structures that can interchange. Broken-line structural elements in downhill folding window (blue box) represent structural elements that would be coerced to form in the presence of ligand. Colored circles adjacent to structures are marked by their points on the respective energy landscape to the right. Yellow arrows represent the series of structures accessed in the presence of ligand. For all sequence lengths inside of a window, the energy landscape repeatedly displays similar patterns (see Materials and Methods). The specific sequence length corresponding to the window shown is given following the length range. For full description of energy landscape characteristics see Figure S5.