For the most part, it should be more a matter of replacing occurrences of $() and $$() with slightly different occurrences of $() and possibly _. That last thing is the Underscore.js library, which I'm quite fond of. Prototype.js sort-of is an earlier version of jQuery and Underscore combined, so it does both DOM and collections manipulation while jQuery does mostly DOM and Underscore only collections. (OK, jQuery can also do collections but somehow that feels clumsy or wrong to me.)
Unfortunately, there's not directly a way to do the conversion gradually, but you could start with doing an inventory of the Prototype.js functionality/syntax that's actually used.