It's more that a certain number of postive centres at a certain distance line up with a number of negative centers at the same distance but, there is definatly the fitting part too proteins fold certain ways and are generally stable unless denatured.There is also the fact that a particle can be Sterically hindred so that there are directions it cannot bond from because of other groups blocking.They don't fit at puzzle pieces but as semisolid clouds of matter where one part of one molecule needs to be the right size and align properly with the right groups on the other molecule.