I prefer to use Illustrator, which has great features, like the pen tool and direct select options, that are easy to use and make objects highly manipulatable. Many researchers typically create graphics using Microsoft PowerPoint or Adobe Illustrator. I also rely on other resources, such as graphical abstracts from journal articles, that can give me inspiration for designing my own graphics. I try to depict the overall shape of the molecule by drawing the structures as simple shapes. When I generate protein schematics for figures, I emphasize the main points of protein structures without getting bogged down in the details. Is the goal to show how a conformational change in a protein allows it to interact with a substrate? Or is it to show that a specific region of the protein interacts with a substrate? Or is the goal to show that the protein changes the structure of the interacting partner upon binding? All of these determine the level of detail that must be included. To find the right balance between these two, it is important to first identify what readers should be focusing on. However, if over-simplified cartoons are used, such as ‘blobs’ or other stylized shapes, there is too much of a disconnect between the figure and what is really happening at the mechanistic level, in particular as it pertains to interaction between components. If the figure contains too much detailed information, such as secondary structure, then the figure becomes too complicated for the general audience.
When making a figure that summarizes the mechanism of a protein, it is important to maintain as much of the key structural components while also making the figure simple to understand.
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