RNA Folding Energy Landscapes in mRNA splicing

Wednesday, October 17, 2007 - 11:15am - 12:15pm
Lind 409
Shi-Jie Chen (University of Missouri)
We develop a statistical mechanical model for RNA/RNA complexes with both intramolecular and intermolecular interactions. As an application of the model, we compute the free energy landscapes, which give the full distribution for all the possible conformations for spliceosomal snRNA complexes. Different snRNA experiments found contrasting structures, our free energy landscape theory shows why these structures emerge and how they compete with each other. In addition, the energy landscapes suggest possible mechanisms for the conformational switches in splicing. The change of the energy landscape shape gives information about the conformational changes. We find multiple (native-like and misfolded) intermediates formed through base-pairing rearrangements in snRNA complexes. Furthermore, the energy landscape gives the stabilities of all the possible (functional) intermediates and such information is directly related to splicing efficiency.