Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

119-POS Board 39 Sigma-r Plots - A Fast and Intuitive Way to Visualize the Global Properties of Molecular Dynamics Trajectories Hao Zhou 1 , Shangyang Li 1 , Lee Makowski 2 . 1 Northeastern University, Boston, MA, USA, 2 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.

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