Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data

and Computer Simulations

Poster Abstracts

156

119-POS

Board 39

Sigma-r Plots - A Fast and Intuitive Way to Visualize the Global Properties of Molecular

Dynamics Trajectories

Hao Zhou

, Shangyang Li

, Lee Makowski

Northeastern University, Boston, MA, USA,

Northeastern University, Boston, MA, USA.

The increasing availability of computational MD simulation software and high performance

computing platforms makes possible generation of nano- to micro- second trajectories which

contain substantial information about the internal motions of proteins, but pose challenges of

storage, sharing and analysis of the data. In order to take advantage of these huge data sets,

condensing this information into a form that is intuitive becomes an essential task. Here we

discuss the merits of the sigma-r plot, a plot of the averaged standard deviation of intermolecular

distances of each atom pair in an MD trajectory as a function of intermolecular distance. This

representation reduces the four dimensional data (3D space + simulation time) to a single, one

dimensional plot that exhibits the average range of motion at different length scales within a

macromolecule. A sigma-r plot can be generated for all atoms or for C-alpha atoms only; it can

be used for the entire molecule or individual domains. Here we demonstrate that a sigma-r plot

can distinguish differences in the global dynamic behavior of the four major SCOP fold classes.

We also show that differences in domain structure and molecular weight produce recognizable

features in sigma-r plots. Plots generated from trajectories with longer simulation time reflect

more complete sampling of the structural ensemble. Sigma-r plots generated from all atom

positions make possible fascile comparison to experimental measures such as the x-ray solution

scattering.