Complex Protein Structures

Slide3My graduate thesis focussed on HP urease, an enzyme with approximately 148,000 atoms. This massive system is difficult for a sighted person to analyze, let alone a blind individual. One of the techniques I used was detailing motion in terms of distance, deviations, and radial distributions between set residue pairs, as shown below in Figure 3. Mapping movement mathematically allowed me to ask the readers very concrete questions. It became a matter of accessing data mathematically, rather than in a complex visualization with lots of extraneous, distracting visual factors.

I would ask the readers to describe any general trends: for example, the green line has a steep upward climb from 100 to 200 ns. This is a mathematical approach to understanding molecular motion that avoided visual dependence and instead utilized a reader’s detailing of minima, maxima, plateaus and other features on a Cartesian plot.  Mathematical approaches like this are often a good alternative for visually-impaired researchers, and can, as in the case of my project, lead to unique discoveries that sighted students pass over.

Figure 3

 

See Alternative Visualizations for more information on performing research on complex protein structures.

 

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