In reference to System Proteomics:
On Carl Zimmer's blog, The Loom, I found Your Yeasty Network. His post references this open access paper:Protein Complex Evolution Does Not Involve Extensive Network Rewiring, by van Dam and Snel in the Netherlands. They are trying to determine relationships within something they term an "interactome." Zimmer loves the illustration (see his link).
Although the paper doesn't refer to protein complexes at synapses specifically, I should think anything that has to do with evolution of protein complexes will have to do with protein complexes at synapses.
Inside his post Zimmer refers to another of his posts, Carrying ancient history in the gut - here, he examines the differences between the protein complexes of yeast (more complex) and giardia (simpler).