Poster abstracts

Poster number 73 submitted by Keith Van Nostrand

Molecular mechanics analysis of minimal energy RNA conformational change pathways

Keith P. Van Nostrand (Biochemistry and Biophysics at University of Rochester), David H. Mathews (Biochemistry and Biophysics at University of Rochester), Scott D. Kennedy (Biochemistry and Biophysics at University of Rochester)

Abstract:
Conformational changes are important in RNA for both binding and catalysis. We are developing computational methods for exploring and understanding pathways for defined conformational changes.
One system of study is the conformational change of a non-canonical pair. In an NMR structure of an AA mismatch in the sequence:

5’ GGUGAAGGCU3’
3’PCCGAAGCCG 5’

(P = purine), the AA non-canonical pair is in conformational exchange between a minor and major conformations. The conversion of the major trans Hoogsteen-sugar to the minor trans sugar-Hoogsteen non-canonical pair occurs on the NMR timescale.
We used the AMBER molecular mechanics software package to model conformational change pathways. Nudged Elastic Band (NEB) was used to predict minimal potential energy paths using a series of all atom images of the system along the path. Both TMD and NEB provided insight into conformational change pathway. NEB provided a time-independent and discrete low potential energy pathway.
Predicted pathways from NEB were analyzed and a reaction coordinate determined for the conformational change. This reaction coordinate involved an improper dihedral angle defined by C8, C4, and N1 on one adenine and C5 on the second adenine in the non-canonical pair. The minor state had an improper dihedral value of about 0 degrees, while the major state had a value of about 180 degrees. Umbrella sampling was then used to predict the free energy profile along the 360 degree reaction coordinate. Umbrella sampling was done using 36 windows of 10 degrees each with 12 ns of sampling per window for 6 different random number seeds. Total sampling involved about 2.6 microseconds of MD spanning about 7 total years of CPU time. The free energy profile suggested errors in the AMBER force field because there was a reversal in the relative free energies of the major and minor structures. Investigation of a putative stacked state identified in the free energy profiles indicated the force field overestimated stacking stability. Revaluation of the free energy profile via QM/MM calculations with PM3-PDDG improved the free energy profile.

References:
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Keywords: Molecular Mechanics, RNA Conformational Dynamics, Conformational Change Pathways