Investigating Trajectories of Molecular Dynamics with a Tripeptide using YASARA[1]
Andrew Michaelson
Northeastern University
February 23rd, 2010
Instructor: Professor Mary Jo Ondrechen
Course: Molecular Modeling CHEM 5638
Using a modern software package such as YASARA[1] a simple tripeptide may be constructed to
investigate trajectories using molecular dynamics. Molecular dynamics uses numerical methods to
approximate what is happening to a molecule for a given time period. This allows a virtual experiment
of what is happening in silico to transpire. Using the tripeptide Proline-Serine-Lysine (PSK) this paper
examines the trajectories of the heavy atoms of this tripeptide via its molecular dynamics.
Graph 1 depicts the how the tripeptide Proline-Serine-Lysine behaves in water at 310 Kelvin in a 6.0
angstrom box at a pH of 7.0 and a NaCl concentration of 0.9% with a water density of 1.0 from 0
picoseconds to 850 picoseconds. A forcefield using Yamber3 was used, with a simulation speed of
normal, and the solvent molecules also maintained a fixed density. Trajectory analysis should begin at
85 picoseconds (circled in green) which is the highest point on the plot before equilibrium was reached.
If a linear regression line was drawn through the plot from this point until 850 picoseconds (circled in
blue) it would appear to be almost completely horizontal which would mean that equilibrium had been
reached.
Figure 1 depicts the beginning phase of the equilibrium of the tripeptide Proline-Serine-Lysine in a cis
conformation at 85 picoseconds with the counterion chloride (Cl-) which has been used to balance this
solution.
Figure 2 is a representative picture of what happens to the tripeptide Proline-Serine-Lysine at
equilibrium time-point 585 picoseconds where the molecule has nearly reached its final equilibrium
conformation.
The final time point of 850 picoseconds (circled in blue) is not shown since at this time point the
tripeptide appeared to split since the 6.0 angstrom box size was used to expedite the time it took to run
this experiment in silico.
Throughout this simulation the tripeptide appeared to undergo a variety of conformational changes.
Initially at 0 picoseconds the tripeptide followed a Proline at the top attached to Serine underneath
attached to Lysine at the left of that conformation. At about 90 picoseconds not long after equilibrium
started to take place at the choloride ion was near the Proline residue a bend appeared that put the
molecule in a cis conformation. At 175 picoseconds a 90 degree conformation appeared where the
Proline followed by the Serine at the hinge of the bend occurred with Lysine facing down from that
point. At around 190 picoseconds a trans conformation appeared. From the 600 picosecond time-point
the chloride ion switches to a closer position to the Lysine residue; this happens since at the end of the
Lysine group is amine group (NH3+) which is positively charged which attracts the negative chloride
ion in the equilibrium state. At around 710 picoseconds the Lysine appears to be both on the top and
bottom of the 6.0 angstrom box this occurred since the box size was smaller than normal to help
expedite the molecular dynamics simulation of the calculation. The final conformation was Proline
attached to Serine in a 120 degree like bend attached to Lysine just below that. The cis and trans
conformations of this tripeptide was due to Proline since it is a cyclic molecule and can easily switch
from one conformation to the other.
This shows how a tripeptide can be simulated to show a trajectory using molecular dynamics to depict
its motion. In this experiment an equilibrium position was achieved which showed how the heavy atom
RMSD values for the tripeptide Proline-Lysine-Serine varied with time over the course of this
molecular dynamics simulation.
References:
1. YASARA Biosciences (2007) YASARA: Yet another scientific artificial reality application.
Available: http://www.yasara.org/. Accessed 02 February 2010.
2. Krieger E, Darden T, Nabuurs S, Finkelstein A, Vriend G. Making optimal use of empirical energy
functions: force field parameterization in crystal space. Proteins (2004) 57:678–683.