So I found a really interesting group of proteins on the molecule of the month website, called the circadian clock proteins. These proteins create our 24-hour internal cycle that involves when we get hungry, tired, etc. Thanks to the circadian clock proteins, our internal clock knows when the days get shorter and longer, when the seasons change and what time of day it is. One of these depictions even looks kind of like a clock. I think these would lend themselves well to a protein toy as well!
Another version of the bacterial clock protein, using computer graphics similar to Goodsell’s: http://www.sciencephoto.com/media/151096/view