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Trajectory analysis: titin domain extension

To use Timeline to identify events in a trajectory, we must choose which parameters to examine, perform the required analyses, and explore the resulting 2D data sets. We use as an example the titin I91 extension trajectory introduced above, and start with examining secondary structure, to get an overall sense of the architectural changes that take place during forced extension. Then we will look at geometric fluctuations during the trajectory, which will both illustrate how to use some of the Timeline tools and provide some hints as to when and where important events are taking place in the I91 extension. Then we will look at the hydrogen bond breaking between the $\beta$-strands of the domain's $\beta$-sheets, to get more insight into how the protein architecture handles applied force.

Secondary structure during titin domain extension

We examine how the secondary structure of the domain changes as the force extension takes place. We can see visually by animating the 3D trajectory that the domain begins as a $\beta$-sandwich then unravels as the force extension takes place, but there is more to the story; we can make a 2D data plot to examine the fate of each $\beta$-strand.

Thresholding and changing appearance: examining RMSF

There are two related ways to help examine how the values of a data set are distributed: first, by using the Threshold Count tool; second, by changing the color scaling range of the 2D plot. The Threshold Count tool adds up, for each frame, the number of residues or selections that fall within a given range, then plots these numbers for all frames. The plot is dynamically updated as the Threshold Min and Max values are changed. Here we review how to do this for the Root Mean Square Fluctuation data set examined in Figure 4, then use the results from this to set the color scaling range, in order to identify which structures are involved in the fluctuation events.

More on changing appearance.

Perform other changes to the Timeline plot, to see features that may be helpful when working with different data sets or different structures:

Examine backbone hydrogen bonds during titin extension

Figure 10: Exploring hydrogen bonds during titin I91 extension. The top panel shows hydrogen bond for all residues of I91 for all frames of the loaded trajectory. In the middle and bottom rows, structure corresponding to the red highlight rectangle in the zoomed-in Timeline 2D data plot (left panel) is shown in the 3D view (right panel). Hydrogen bonds are plotted as white when formed, and black when broken. The middle row shows highlighted a single, unbroken backbone hydrogen bond. The bottom row shows highlighted the same backbone hydrogen bond, now broken, at a later time frame.

Now we will look at the hydrogen bond breaking pattern during the I91 extension trajectory. Since we are looking at the protein architecture, we will examine the bonds between the partner $\beta$-strands that make up the two $\beta$-sheets which form the I91 domain $\beta$-sandwich.

Using Data Files and Data Collections

These features help with saving and loading completed calculations (so you won't have to spend time calculating them again), and with creating and browsing sets of pre-computed calculations.

next up previous contents
Next: Analysis Scripts Up: Timeline Tutorial Previous: Interface and controls   Contents