Predicting Coaxial Stacking by Free Energy Minimization. David Mathews Department of Biochemistry & Biophysics University of Rochester Medical Center. Predicting Coaxial Stacking:. Rahul Tyagi. Multibranch Loops (MBL). http://www.stanford.edu/~esorin.
Department of Biochemistry & Biophysics
University of Rochester Medical Center
1 stacked on 2 mediated by mismatch
Secondary structure representation
2 flush stacked on 3
“The stacking configuration with lowest free energy as predicted by
Nearest Neighbour Parameters exists in naturally occurring RNAs.”
Model based on work by Walter, Kim and others in Turner lab.
Basepair center and basepair plane definition
from Biochemistry 2nd Ed. by Garrett & Grisham
Criteria for stacking
a. Basepair plane tilt
< 26º for Flush / 32º for MM
b. Distance between basepair “centers”
< 5 Å for Flush / 12 Å for MM
(based on Gabb et al., J. Mol. Graph., 14, 6-11
Burkard et al., JMB, 290, 967-982
and Gendron at al., JMB, 308, 919-936
c. Basepair shear
angle between inter-center vector
and baseplane normal vectors
relaxed tilt and distance criteria:
distance of basepair centers from normal to the other basepair < 10 Å
Base Stack Cascade
The ribosome RNA structures provide maximum data.
Just 4 out of 51 possible configurations!
K3/2 < K1, K2 < K3
A stack is more probable if it is part of many different configurations of low free energy.
Both plots show a sharp drop at 0.70
So 70% was chosen to be the cut-off value for prediction