1. Analyzing Properties of RNA Coarse Grained Structures
Danny Vo, David Bell, and Pengyu Ren*
*University of Texas at Austin
Background
 Molecular Dynamics (MD) is a simulation
technique significantly faster than
Crystallographic studies, which uses extremely
complex calculations, often too intensive for
even the strongest supercomputers to perform
in a timely manner
 Forces on each atom are calculated, then their
positions are moved using Newton’s laws of
motions
 This project focuses on the Coarse Grain model
which represents nucleotides with five atoms (as
opposed to twenty), reducing computational
expenses while optimizing accuracy and speed
 Being able to simulate macromolecules will aid
drug development, as properties such as binding
sites can be discovered without the need of wet
samples
Methodology
 Python: General purpose, high level
programming language with simple syntax
used for most of our software. Additional
scripts are utilized for ease of user accesses to
Tinker
 Tinker: Software used to computationally
calculate various parameters such as Potential
Energy, Force Field Interactions, and Root
Mean Square Distance
 PyMOL: Open source imaging system used to
visualize high quality 3D protein structures
and other molecules/macromolecules
Sample Result
Energy Analysis via Tinker (Analyze.x):
• Total Potential Energy : 2397.46083275 Kcal/mole
• Total Electric Charge : -11.00000 Electrons
• Effective Total Charge : -1.25357 Electrons
1ZIH RNA Structure 1ZIH Minimized RNA Structure
Energy Analysis via Tinker (Analyze.x):
• Total Potential Energy : 7349.12832442 Kcal/mole
• Total Electric Charge : -11.00000 Electrons
• Effective Total Charge : -1.25357 Electrons
RMSD Calculated between both structures via Tinker
(Superpose.x):
• Root Mean Square Distance : 2.291733 Angstroms
Program Flow Example (Analyze)1ZIH and 1ZIH Min combined
Conclusions
 Coarse grained model allows
quicker computations without
sacrificing accuracy
 Creating scripts to aid the
user in accessing Tinker makes
the process less cumbersome
 Using MD with the Coarse
Grained model is much more
efficient than Crystallographic
studies when theorizing, but
Crystallographic is still the
gold standard
References
 Z. Xia, D. P. Gardner, R. R. Gutell, and P.
Ren, “Coarse-Grained Model for
Simulation of RNA Three-Dimensional
Structures,” The Journal of Physical
Chemistry B, vol. 114, no. 42, pp. 13497–
13506, Oct. 2010.
 J. D. Durrant and J. A. McCammon,
“Molecular dynamics simulations and drug
discovery,” BMC biology, vol. 9, no. 1, p.
71, 2011.
 “RCSB Protein Data Bank - RCSB PDB.”
[Online]. Available:
http://www.rcsb.org/pdb/home/home.do
. [Accessed: 25-Nov-2015].